From c60ace9a8668a5792595782344852aa62a293b55 Mon Sep 17 00:00:00 2001 From: joboog Date: Fri, 3 May 2024 22:21:27 +0200 Subject: [PATCH] [doc] update webpage --- docs/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/OGS6_h5.html | 2 +- docs/search.json | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/index.html b/docs/index.html index 5b608fb..5a71e60 100644 --- a/docs/index.html +++ b/docs/index.html @@ -62,7 +62,7 @@

r2ogs6

Pipeline Status Test Coverage DOI JOSS Submission

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r2ogs6 is an R-API to the multiphysics simulator OpenGeoSys 6. r2ogs6 allows pre-processing (preparing input files), executing simulation runs, retrieving, post-processing and visualizing output data in R. Furthermore, the package comes with functionality to define ensemble runs.

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r2ogs6 is an R-API to the multiphysics simulator OpenGeoSys 6. r2ogs6 allows pre-processing (preparing input files), executing simulation runs, retrieving, post-processing and visualizing output data in R. Furthermore, the package comes with functionality to define ensemble runs.

Setup

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4ef2c68..8f5d5cf 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,7 +5,7 @@ articles: dev_workflow_vignette: dev_workflow_vignette.html ensemble_workflow_vignette: ensemble_workflow_vignette.html user_workflow_vignette: user_workflow_vignette.html -last_built: 2024-05-03T20:11Z +last_built: 2024-05-03T20:20Z urls: reference: https://joboog.github.io/r2ogs6/reference article: https://joboog.github.io/r2ogs6/articles diff --git a/docs/reference/OGS6_h5.html b/docs/reference/OGS6_h5.html index 9a3ed42..6e812fc 100644 --- a/docs/reference/OGS6_h5.html +++ b/docs/reference/OGS6_h5.html @@ -231,7 +231,7 @@

Examplesogs6_h5 #> OGS6_h5 #> h5 path: -#> /tmp/RtmpBchsQP/temp_libpathaca25e6824bd/r2ogs6//extdata/benchmarks/EllipticPETSc/cube_1e3_np3.h5 +#> /tmp/RtmpBchsQP/temp_libpathaca2226b66ea/r2ogs6//extdata/benchmarks/EllipticPETSc/cube_1e3_np3.h5 #> #> # h5 file structure ------------------------------------------------------------ #> group name otype dclass dim diff --git a/docs/search.json b/docs/search.json index ae5b797..3cfa010 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"https://joboog.github.io/r2ogs6/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"How to Contribute to r2ogs6","title":"How to Contribute to r2ogs6","text":"happy contributions!","code":""},{"path":"https://joboog.github.io/r2ogs6/CONTRIBUTING.html","id":"bug-reports","dir":"","previous_headings":"","what":"Bug reports?","title":"How to Contribute to r2ogs6","text":"Please open issue bug , set bugfix label, add clear problem description, , possible add minimal working example.","code":""},{"path":"https://joboog.github.io/r2ogs6/CONTRIBUTING.html","id":"new-features","dir":"","previous_headings":"","what":"New features?","title":"How to Contribute to r2ogs6","text":"Open new issue idea.","code":""},{"path":"https://joboog.github.io/r2ogs6/CONTRIBUTING.html","id":"contribute-code","dir":"","previous_headings":"","what":"Contribute code?","title":"How to Contribute to r2ogs6","text":"Clone repo. Add author contributor DESCRIPTION. Add code. Push repo submit merge request.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":"`r2ogs6` is an R-API to the open-source multiphysics simulator [OpenGeoSys 6](https://www.opengeosys.org). Copyright (C) 2021 Helmholtz Centre for Environmental Research - UFZ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . r2ogs6 Copyright (C) 2021 Helmholtz Centre for Environmental Research - UFZ This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"hi-there","dir":"Articles","previous_headings":"","what":"Hi there!","title":"r2ogs6 Developer Guide","text":"Welcome dev guide r2ogs6. collection tips, useful info (admittedly warnings) hopefully make life bit easier developing package.","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"the-basics","dir":"Articles","previous_headings":"","what":"The basics","title":"r2ogs6 Developer Guide","text":"dive implementation details, take look exactly package structured first. r2ogs6 developed using workflow described . strongly recommend keeping way save time headaches. … main folder R/ find lot scripts, can grouped following categories: export_*.R export functions generate_*.R code generation read_in_*.R import functions ogs6_*.R simulation class definitions prj_*.R class definitions XML tags found .prj file *_utils.R utility functions used multiple scripts","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"the-classes","dir":"Articles","previous_headings":"","what":"The classes","title":"r2ogs6 Developer Guide","text":"r2ogs6 largely built top S3 classes moment. reasons elaborate later, viable switch R6 classes. let’s look first. ….","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"generating-new-classes","dir":"Articles","previous_headings":"","what":"Generating new classes","title":"r2ogs6 Developer Guide","text":"’ve familiarized OpenGeoSys 6, know lot, lot mean LOT parameters special cases regarding .prj XML tags. nice new class based tag, consider . save () bit typing, ’ve written useful functions .","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"analyse_xml","dir":"Articles","previous_headings":"Generating new classes","what":"analyse_xml()","title":"r2ogs6 Developer Guide","text":"first arguably important one analyse_xml(). matches files folder, reads XML searches XML elements given name. analyses elements returns useful information , namely names attributes child elements. prints summary findings also returns list look moment. used function two things: Analysing … . Secondly, soon decided tags represented class, used function output class generation.","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"generate_","dir":"Articles","previous_headings":"Generating new classes","what":"generate_*()","title":"r2ogs6 Developer Guide","text":"say .prj files stored folder. show workflow small dataset (, folder two .prj files) , path usually passed analyse_xml() directory containing benchmark files OpenGeoSys 6 can downloaded . Now say decided going make class based element tag name nonlinear_solver. readability reasons, store results analyse_xml() variable pass generator function. want, can skip step call analyse_xml() generator function directly. First, define path specify files ending .prj parsed. ’m looking elements named nonlinear_solver, ’m looking whole document. often isn’t best option since sometimes nodes may name contain different things depending exact position document, also case . narrow , change xpath accordingly. Now can sure future class generated correct parameters. analyse_xml() returns named list invisibly, let’s short look . can see list contains xpath parameter passed analyse_xml(), along three named logical vectors called children, attributes both_sorted respectively. can read like : attribute child element specified xpath always occurred, required parameter new class. Else, optional parameter. logical vectors sorted occurrency, rarest children attributes go end logical vector. Now, let’s generate code! S3 classes, generate constructor like : S3 classes, generate helper like : R6 classes, generate constructor like : Ta-daa, now nice stubs. Copy script R folder package, add documentation validation ’re almost done.","code":"test_folder <- system.file(\"extdata/vignettes_data/analyse_xml_demo\", package = \"r2ogs6\") analysis_results <- analyse_xml(path = test_folder, pattern = \"\\\\.prj$\", xpath = \"//nonlinear_solver\", print_findings = TRUE) #> #> I parsed 2 valid XML files matching your pattern. #> #> I found at least one element named nonlinear_solver in the following file(s): #> beam.prj #> beam3d.prj #> #> In total, I found 5 element(s) named nonlinear_solver. #> #> These are the child elements I found: #> name ex_occ p_occ total total_mean #> 1 name 2 0.4 2 0.4 #> 2 type 2 0.4 2 0.4 #> 3 max_iter 2 0.4 2 0.4 #> 4 linear_solver 2 0.4 2 0.4 #> 5 maximum_iterations 1 0.2 1 0.2 #> 6 error_tolerance 1 0.2 1 0.2 #> 7 damping 1 0.2 1 0.2 analysis_results <- analyse_xml(path = test_folder, pattern = \"\\\\.prj$\", xpath = \"/OpenGeoSysProject/nonlinear_solvers/nonlinear_solver\", print_findings = TRUE) #> #> I parsed 2 valid XML files matching your pattern. #> #> I found at least one element named nonlinear_solver in the following file(s): #> beam.prj #> beam3d.prj #> #> In total, I found 2 element(s) named nonlinear_solver. #> #> These are the child elements I found: #> name ex_occ p_occ total total_mean #> 1 name 2 1.0 2 1.0 #> 2 type 2 1.0 2 1.0 #> 3 max_iter 2 1.0 2 1.0 #> 4 linear_solver 2 1.0 2 1.0 #> 5 damping 1 0.5 1 0.5 analysis_results #> $xpath #> [1] \"/OpenGeoSysProject/nonlinear_solvers/nonlinear_solver\" #> #> $children #> name type max_iter linear_solver damping #> TRUE TRUE TRUE TRUE FALSE #> #> $attributes #> logical(0) #> #> $both_sorted #> name type max_iter linear_solver damping #> TRUE TRUE TRUE TRUE FALSE generate_constructor(params = analysis_results, print_result = TRUE) #> new_prj_nonlinear_solver <- function(name, #> type, #> max_iter, #> linear_solver, #> damping = NULL) { #> structure(list(name = name, #> type = type, #> max_iter = max_iter, #> linear_solver = linear_solver, #> damping = damping, #> xpath = \"nonlinear_solvers/nonlinear_solver\", #> attr_names = c(), #> flatten_on_exp = character() #> ), #> class = \"prj_nonlinear_solver\" #> ) #> } #> generate_helper(params = analysis_results, print_result = TRUE) #> #'prj_nonlinear_solver #> #'@description tag: nonlinear_solver #> #'@param name #> #'@param type #> #'@param max_iter #> #'@param linear_solver #> #'@param damping Optional: #> #'@export #> prj_nonlinear_solver <- function(name, #> type, #> max_iter, #> linear_solver, #> damping = NULL) { #> #> # Add coercing utility here #> #> new_prj_nonlinear_solver(name, #> type, #> max_iter, #> linear_solver, #> damping) #> } #> generate_R6(params = analysis_results, print_result = TRUE) #> OGS6_nonlinear_solver <- R6::R6Class(\"OGS6_nonlinear_solver\", #> public = list( #> #'@description #> #'Creates new OGS6_nonlinear_solverobject #> #'@param name #> #'@param type #> #'@param max_iter #> #'@param linear_solver #> #'@param damping Optional: initialize = function(name, #> type, #> max_iter, #> linear_solver, #> damping = NULL){ #> self$name <- name #> self$type <- type #> self$max_iter <- max_iter #> self$linear_solver <- linear_solver #> self$damping <- damping #> } #> ), #> #> active = list( #> #'@field name #> #'Access to private parameter '.name' #> name = function(value) { #> if(missing(value)) { #> private$.name #> }else{ #> private$.name <- value #> } #> }, #> #> #'@field type #> #'Access to private parameter '.type' #> type = function(value) { #> if(missing(value)) { #> private$.type #> }else{ #> private$.type <- value #> } #> }, #> #> #'@field max_iter #> #'Access to private parameter '.max_iter' #> max_iter = function(value) { #> if(missing(value)) { #> private$.max_iter #> }else{ #> private$.max_iter <- value #> } #> }, #> #> #'@field linear_solver #> #'Access to private parameter '.linear_solver' #> linear_solver = function(value) { #> if(missing(value)) { #> private$.linear_solver #> }else{ #> private$.linear_solver <- value #> } #> }, #> #> #'@field damping #> #'Access to private parameter '.damping' #> damping = function(value) { #> if(missing(value)) { #> private$.damping #> }else{ #> private$.damping <- value #> } #> }, #> #> #'@field is_subclass #> #'Access to private parameter '.is_subclass' #> is_subclass = function() { #> private$.is_subclass #> }, #> #> #'@field subclasses_names #> #'Access to private parameter '.subclasses_names' #> subclasses_names = function() { #> private$.subclasses_names #> }, #> #> #'@field attr_names #> #'Access to private parameter '.attr_names' #> attr_names = function() { #> private$.attr_names #> } #> ), #> #> private = list( #> .name = NULL, #> .type = NULL, #> .max_iter = NULL, #> .linear_solver = NULL, #> .damping = NULL, #> .is_subclass = TRUE, #> .subclasses_names = character(), #> .attr_names = c(), #> ) #> )"},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"integrating-new-classes","dir":"Articles","previous_headings":"","what":"Integrating new classes","title":"r2ogs6 Developer Guide","text":"Now class, need tell package exists. ’re reading exporting .prj file, knows automatically turn content nonlinear_solver tag object new class way around. achieve , execute code data_raw/xpaths_for_classes.R. update xpaths_for_classes parameter, adding entry class. Afterwards, run xpaths_for_classes[[\"your_class_name\"]]. return xpath parameter class like : class ’ve created .prj top level class child top level wrapper node like processes, add corresponding OGS6 private parameter active field. example, processes node represented list, added private parameter .processes = list() active field processes. lot things r2ogs6 package work way bit “meta”. Often times, functions called via eval(parse(text = call_string)) call_string example concatenated info parameter names certain class. saves lot code regarding import, export script generation requires ’ve made respective info available shown . ’ve analysed files, generated code, created new class registered package… now? ’s actually, ’s workflow. Well, least ’s supposed .","code":"xpaths_for_classes[[\"prj_process\"]] # A class can have multiple xpaths if the represented node occurs at different positions. xpaths_for_classes[[\"prj_convergence_criterion\"]]"},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"recursive-function-guide","dir":"Articles","previous_headings":"","what":"Recursive function guide","title":"r2ogs6 Developer Guide","text":"wasn’t , ’m afraid might take look functions handling import, export benchmark script generation. bit tricky use recursion far proven efficient structure-wise exactly fun think .","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"conclusion","dir":"Articles","previous_headings":"","what":"Conclusion","title":"r2ogs6 Developer Guide","text":"hope ’ve taken away helpful information short guide. make changes improve workflow, please update vignette next dev!","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"r2ogs6 Ensemble Guide","text":"Hi ! practical guide OGS6_Ensemble class r2ogs6 package. show can use class set ensemble runs OpenGeoSys 6, extract results plot . want follow tutorial, ’ll need r2ogs6 installed loaded. prerequisites r2ogs6 described detail r2ogs6 User Guide vignette. Additionally, ’ll need following benchmark files: Theis’ Problem described Theis solution well pumping described General instructions download OpenGeoSys 6 benchmark files can found .","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"theis-problem","dir":"Articles","previous_headings":"","what":"Theis’ problem","title":"r2ogs6 Ensemble Guide","text":"consider following parameters sensitivity analysis: permeability porosity storage","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"setup","dir":"Articles","previous_headings":"Theis’ problem","what":"Setup","title":"r2ogs6 Ensemble Guide","text":"First, create simulation object base ensemble read .prj file.","code":"# Change this to fit your system testdir_path <- tempdir() sim_path <- paste0(testdir_path, \"/axisym_theis_sim\") ogs6_obj <- OGS6$new(sim_name = \"axisym_theis\", sim_path = sim_path) # Change this to fit your system prj_path <- system.file(\"extdata/benchmarks/AxiSymTheis/\", \"axisym_theis.prj\", package = \"r2ogs6\") read_in_prj(ogs6_obj, prj_path, read_in_gml = T)"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"single-parameter-sequential-run","dir":"Articles","previous_headings":"Theis’ problem","what":"Single-parameter sequential run","title":"r2ogs6 Ensemble Guide","text":"Let’s create small ensemble alter value storage. Say don’t want hardcode values, instead examine effects changing storage 1%, 10% 50%. can use percentages_mode parameter OGS6_Ensemble . already defaults TRUE, ’m merely explicit demonstration purposes. Now can start simulation.","code":"# Assign percentages percentages <- c(-50, -10, -1, 0, 1, 10, 50) # Define an ensemble object ogs6_ens <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list(list(ogs6_obj$media[[1]]$properties[[4]]$value, percentages)), percentages_mode = TRUE) ogs6_ens$run_simulation() lapply(ogs6_ens$ensemble, ogs6_read_output_files)"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"plot-results-for-single-simulation","dir":"Articles","previous_headings":"Theis’ problem > Single-parameter sequential run","what":"Plot results for single simulation","title":"r2ogs6 Ensemble Guide","text":"simulations (hopefully) ran successfully - great! Now ’d nice see results. Say ’re interested pressure data. may leave point_ids parameter. defaults points dataset - specify ’s 500 slow building vignette. can see ’s one row per timestep point ID. Say want plot average pressure timestep, , mean pressure values rows timestep. ’ll consider first simulation now. plot chunk p-t-first-plot","code":"# This will get a combined dataframe storage_tbl <- ogs6_ens$get_point_data(point_ids = c(0, 1, 2), keys = c(\"pressure\")) # Let's look at the first 10 rows of the dataset head(storage_tbl, 10) #> # A tibble: 10 × 8 #> id x y z pressure timestep sim_id perc #> #> 1 0 0.305 0 0 0 0 1 -50 #> 2 0 0.305 0 0 6.99 8.64 1 -50 #> 3 0 0.305 0 0 9.77 86.4 1 -50 #> 4 0 0.305 0 0 13.3 1728 1 -50 #> 5 0 0.305 0 0 16.2 24192 1 -50 #> 6 0 0.305 0 0 16.6 172800 1 -50 #> 7 0 0.305 0 0 16.6 604800 1 -50 #> 8 0 0.305 0 0 16.6 864000 1 -50 #> 9 1 305. 0 0 0 0 1 -50 #> 10 1 305. 0 0 0 8.64 1 -50 # Get average pressure from first simulation avg_pr_first_sim <- storage_tbl[storage_tbl$sim_id == 1,] %>% group_by(timestep) %>% summarize(avg_pressure = mean(pressure)) # Plot pressure over time for first simulation ggplot(data = avg_pr_first_sim) + geom_point(mapping = aes(x = as.numeric(row.names(avg_pr_first_sim)), y = avg_pressure)) + xlab(\"Timestep\")"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"plot-results-for-multiple-simulations","dir":"Articles","previous_headings":"Theis’ problem > Single-parameter sequential run","what":"Plot results for multiple simulations","title":"r2ogs6 Ensemble Guide","text":"plot chunk p-t--plot Now average pressure time simulations (rows). Since ’re pretty similar, let’s put plot better comparison. plot chunk p-t--combined-plot","code":"# Get average pressure for all simulations avg_pr_df <- storage_tbl %>% group_by(sim_id, timestep) %>% summarise(avg_pressure = mean(pressure)) # Plot pressure over time for all simulations ggplot(avg_pr_df, aes(x = as.numeric(as.factor(timestep)), y = avg_pressure)) + geom_point(aes(color = as.factor(sim_id))) + geom_line(aes(color = as.factor(sim_id))) + xlab(\"Timestep\") + labs(color = \"sim id\") + facet_grid(rows = vars(sim_id)) ggplot(avg_pr_df, aes(x = as.numeric(as.factor(timestep)), y = avg_pressure, group = sim_id)) + geom_point(aes(color = as.factor(sim_id))) + geom_line(aes(color = as.factor(sim_id))) + labs(color = \"sim id\") + xlab(\"Timestep\")"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"multi-parameter-sequential-run","dir":"Articles","previous_headings":"Theis’ problem","what":"Multi-parameter sequential run","title":"r2ogs6 Ensemble Guide","text":"far ’ve considered storage parameter. Now want look two parameters influence simulation, let’s put ensemble together. permeability can reuse percentages already . porosity, doesn’t work - original value 1 values can range 0 1, ’ll supply shorter vector. time ’s important set OGS6_Ensemble parameter sequential_mode TRUE change supplied parameters sequentially means end 18 (7 + 7 + 4) simulations equal sum elements value vectors supply (’ve named values clarity, naming optional though). default FALSE give error message value vectors length even , wouldn’t want - number simulations equal length one value vector (thus requiring length). Generally, set sequential_mode TRUE want examine influence parameters simulation independently. want examine parameters influence wanting test parameter combinations, default mode way go. Now can start simulation. take short time. soon simulations done, can extract point data much like . time want plot point x coodinates x axis ’re leaving point_ids get points. Also just want data last timestep. Plotting time! Since set sequential_mode TRUE, dataframe just created contains name column allows us group parameters. ’ve also set percentages_mode TRUE, also column perc allows us group percentages. Now can simply use facet grid plot. plot chunk p-t-group-plot Ta-Daa! can see permeability influence pressure. Though may seem suspicious, porosity storage plotted correctly - points just placed right top . Since porosity can’t go value 1 original value, value vector went -50% 0% line colors porosity storage differ. Maybe want try use logarithmic approach storage. won’t work built-functionality OGS6_Ensemble ’ll set Ensemble little differently. , can run simulation right away. Let’s check can observe influence storage pressure now. plot chunk p-t-log-plot","code":"# Change this to fit your system sim_path <- paste0(testdir_path, \"/axisym_theis_sim_big\") ogs6_obj$sim_path <- sim_path ogs6_ens_big <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list(per = list(ogs6_obj$media[[1]]$properties[[1]]$value, values = percentages), por = list(ogs6_obj$media[[1]]$properties[[3]]$value, c(-50, -10, -1, 0)), sto = list(ogs6_obj$media[[1]]$properties[[4]]$value, values = percentages)), sequential_mode = TRUE) ogs6_ens_big$run_simulation() lapply(ogs6_ens_big$ensemble, ogs6_read_output_files) # Get combined dataframe per_por_sto_df <- ogs6_ens_big$get_point_data( keys = c(\"pressure\"), start_at_timestep = ogs6_ens_big$ensemble[[1]]$pvds[[1]]$last_timestep) # Make plot ggplot(per_por_sto_df, aes(x = x, y = -pressure, # Flip pressure because source term was positive group = perc)) + geom_point(aes(color = as.factor(perc))) + xlab(\"Radius (m)\") + ylab(\"Head (m)\") + labs(color = \"%\") + facet_grid(cols = vars(name), labeller = as_labeller(c(per = \"permeability\", por = \"porosity\", sto = \"storage\"))) # Calculate log value log_val <- log(as.numeric( ogs6_obj$media[[1]]$properties[[4]]$value), base = 10) # Apply changes to log value log_vals <- vapply(percentages, function(x){ log_val + (log_val * (x / 100)) }, FUN.VALUE = numeric(1)) # Transfer back to non-logarithmic scale back_transf_vals <- 10^log_vals # Change sim_path to fit your system ogs6_obj$sim_path <- paste0(testdir_path, \"/axisym_theis_sim_log_storage\") # Set up new ensemble ogs6_ens_sto <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list( sto = list( ogs6_obj$media[[1]]$properties[[4]]$value, values = back_transf_vals) ), percentages_mode = FALSE, sequential_mode = TRUE ) ogs6_ens_sto$run_simulation() lapply(ogs6_ens_sto$ensemble, ogs6_read_output_files) # Get combined dataframe sto_df <- ogs6_ens_sto$get_point_data( keys = c(\"pressure\"), start_at_timestep = ogs6_ens_sto$ensemble[[1]]$pvds[[1]]$last_timestep) # Supply percentages manually since we couldn't use `percentages_mode` percs <- vapply(sto_df$sim_id, function(x){percentages[[x]]}, FUN.VALUE = numeric(1)) ggplot(sto_df, aes(x = x, y = -pressure)) + geom_point(aes(color = as.factor(percs))) + xlab(\"Radius (m)\") + ylab(\"Head (m)\") + labs(color = \"%\")"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"theis-solution-for-well-pumping","dir":"Articles","previous_headings":"","what":"Theis solution for well pumping","title":"r2ogs6 Ensemble Guide","text":"consider following parameters sensitivity analysis: permeability porosity slope","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"setup-1","dir":"Articles","previous_headings":"Theis solution for well pumping","what":"Setup","title":"r2ogs6 Ensemble Guide","text":"First, create simulation object base ensemble read .prj file. time want specify output file gets written last timestep.","code":"# Change this to fit your system sim_path <- paste0(testdir_path, \"/theis_sim\") ogs6_obj <- OGS6$new(sim_name = \"theis\", sim_path = sim_path) # Change this to fit your system prj_path <- system.file(\"extdata/benchmarks/theis_well_pumping/\", \"theis.prj\", package = \"r2ogs6\") read_in_prj(ogs6_obj, prj_path, read_in_gml = T) # Increase each_steps ogs6_obj$time_loop$output$timesteps$pair$each_steps <- 200"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"multi-parameter-sequential-run-1","dir":"Articles","previous_headings":"Theis solution for well pumping","what":"Multi-parameter sequential run","title":"r2ogs6 Ensemble Guide","text":"Now can start simulation. simulations run, can extract plot results like . avoid cluttering plot, extract pressure values single line. , get IDs points x axis. plot chunk p-x-plot Let’s take closer look permeability. plot chunk p-x-subset-plot Maybe want try use logarithmic approach slope. won’t work built-functionality OGS6_Ensemble ’ll set Ensemble little differently. , can run simulation right away. Let’s check can observe influence slope pressure now. plot chunk p-x-log-plot","code":"# Assign percentages percentages <- c(-50, -10, -1, 0, 1, 10, 50) ogs6_ens_theis_2 <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list( per = list(ogs6_obj$parameters[[3]]$values, values = percentages), por = list(ogs6_obj$parameters[[2]]$value, values = percentages), slo = list( ogs6_obj$media[[1]]$phases[[1]]$properties[[1]]$independent_variable[[2]]$slope, values = percentages) ), sequential_mode = TRUE ) ogs6_ens_theis_2$run_simulation() lapply(ogs6_ens_theis_2$ensemble, ogs6_read_output_files) # Extract point ids get_point_ids_x <- function(points){ x_axis_ids <- numeric() for(i in seq_len(dim(points)[[1]])) { if (points[i, ][[2]] == 0 && points[i, ][[3]] == 0) { x_axis_ids <- c(x_axis_ids, (i - 1)) } } return(x_axis_ids) } point_ids_x <- get_point_ids_x( ogs6_ens_theis_2$ensemble[[1]]$pvds[[1]]$OGS6_vtus[[1]]$points) # Get combined dataframe per_por_slo_df <- ogs6_ens_theis_2$get_point_data( point_ids = point_ids_x, keys = c(\"pressure\"), start_at_timestep = ogs6_ens_theis_2$ensemble[[1]]$pvds[[1]]$last_timestep) # Make plot ggplot(per_por_slo_df, aes(x = x, y = pressure / 9806.65, # 1mH2O = 9806.65 kPa group = perc)) + geom_point(aes(color = as.factor(perc))) + xlab(\"Radius (m)\") + ylab(\"Absenkung (m)\") + labs(color = \"%\") + facet_grid(cols = vars(name), labeller = as_labeller(c(per = \"permeability\", por = \"porosity\", slo = \"slope\" ))) per_df <- subset(per_por_slo_df, name == \"per\") # Make plot ggplot(per_df, aes(x = x, y = pressure)) + geom_point(aes(color = as.factor(perc))) + xlab(\"Radius (m)\") + ylab(\"Head (m)\") + labs(color = \"%\") # Calculate log value log_val <- log(as.numeric( ogs6_obj$media[[1]]$phases[[1]]$properties[[1]]$independent_variable[[2]]$slope), base = 10) # Apply changes to log value log_vals <- vapply(percentages, function(x){ log_val + (log_val * (x / 100)) }, FUN.VALUE = numeric(1)) # Transfer back to non-logarithmic scale back_transf_vals <- 10^log_vals # Change sim_path to fit your system ogs6_obj$sim_path <- paste0(testdir_path, \"/theis_sim_log_slope\") # Set up new ensemble ogs6_ens_slo <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list( slo = list( ogs6_obj$media[[1]]$phases[[1]]$properties[[1]]$independent_variable[[2]]$slope, values = back_transf_vals) ), percentages_mode = FALSE, sequential_mode = TRUE ) ogs6_ens_slo$run_simulation() lapply(ogs6_ens_slo$ensemble, ogs6_read_output_files) # Filter point ids point_ids_x <- get_point_ids_x( ogs6_ens_slo$ensemble[[1]]$pvds[[1]]$OGS6_vtus[[1]]$points) # Get combined dataframe slo_df <- ogs6_ens_slo$get_point_data( point_ids = point_ids_x, keys = c(\"pressure\"), start_at_timestep = ogs6_ens_slo$ensemble[[1]]$pvds[[1]]$last_timestep) # Supply percentages manually since we couldn't use `percentages_mode` percs <- vapply(slo_df$sim_id, function(x){percentages[[x]]}, FUN.VALUE = numeric(1)) ggplot(slo_df, aes(x = x, y = pressure / 9806.65)) + # 1mH2O = 9806.65 kPa geom_point(aes(color = as.factor(percs))) + xlab(\"Radius (m)\") + ylab(\"Head (m)\") + labs(color = \"%\")"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"r2ogs6 Ensemble Guide","text":"OGS6_Ensemble class useful tool set ensemble runs sensitivity analyses. vignette, learned create OGS6_Ensemble objects. looked parameters sequential_mode percentages_mode influence ensemble object initialised. started simulations via OGS6_Ensemble$run_simulation() extracted information output files plot .","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"prerequisites","dir":"Articles","previous_headings":"","what":"Prerequisites","title":"User Guide","text":"guide assumes r2ogs6 dependencies installed. ’s case, please take look installation instructions provided README.md file repository. loading r2ogs6, first need set package options knows look OpenGeoSys 6.","code":"# Set path for OpenGeoSys 6 options(\"r2ogs6.default_ogs6_bin_path\" = \"your_ogs6_bin_path\")"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"creating-your-simulation-object","dir":"Articles","previous_headings":"","what":"Creating your simulation object","title":"User Guide","text":"represent simulation object, r2ogs6 uses R6 class called OGS6. ’re new R6 objects, don’t worry. Creating simulation object easy. call class constructor provide parameters: sim_name name simulation sim_path relevant files simulation ’s , now simulation object.","code":"# Change this to fit your system # sim_path <- system.file(\"extdata/benchmarks/flow_no_strain\", # package = \"r2ogs6\") sim_path <- tempdir() ogs6_obj <- OGS6$new(sim_name = \"my_simulation\", sim_path = sim_path)"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"defining-the-simulation-parameters","dir":"Articles","previous_headings":"","what":"Defining the simulation parameters","title":"User Guide","text":"’s two ways can define simulation parameters. Either load benchmark file define simulation manually.","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"loading-a-benchmark-file","dir":"Articles","previous_headings":"Defining the simulation parameters","what":"Loading a benchmark file","title":"User Guide","text":"quickest easiest way define simulation using already existing benchmark. take look OpenGeoSys documentation, ’ll find plenty benchmarks choose along link project file GitLab top respective page. demonstration purposes, use project HydroMechanics benchmarks, can found . NOTE: r2ogs6 tested every existing benchmark. Due large number input parameters, might encounter cases import fails.","code":"# Change this to fit your system #prj_path <- paste0(sim_path, \"/flow_no_strain.prj\") prj_path <- system.file(\"extdata/benchmarks/flow_no_strain/flow_no_strain.prj\", package = \"r2ogs6\") read_in_prj(ogs6_obj, prj_path = prj_path, read_in_gml = T)"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"setting-up-your-own-opengeosys-6-simulation","dir":"Articles","previous_headings":"Defining the simulation parameters","what":"Setting up your own OpenGeoSys 6 simulation","title":"User Guide","text":"Setting simulation possible . Since ’s plenty required optional input parameters, might want call get_status() occasionally get brief overview simulation. tells input parameters missing can run simulation. Since haven’t defined anything far, ’ll see lot red . results gave us hint can add. ’ll go try find possible input data. Say want find process objects. rule thumb, classes named prefix prj_ followed XML tag name .prj file. exceptions rule subclasses lead duplicate class names. class prj_time_loop example contains subclass representing process child element confused process children first level processes node directly root node .prj file. , subclass named prj_tl_process. Let’s try adding something now. add data simulation object, use OGS6$add(). can use method top level .prj element, means ’re limited prj_parameter objects. Since already read .prj file earlier, won’t run snippet. ’d like complete example manually defining simulation parameters, ’s script flow_free_expansion.R examples/workflow_demos folder.","code":"# Call on the OGS6 object (note the R6 style) ogs6_obj$get_status() #> ✓ 'processes' has at least one element #> ✓ 'time_loop' is defined #> ✓ 'nonlinear_solvers' has at least one element #> ✓ 'linear_solvers' has at least one element #> ✓ 'parameters' has at least one element #> ✓ 'process_variables' has at least one element #> ✗ 'mesh' is defined #> ✗ 'geometry' is defined #> ✓ 'media' has at least one element #> ✗ 'test_definition' has at least one element #> ✗ 'curves' has at least one element #> ✓ 'meshes' has at least one element #> ✗ 'local_coordinate_system' is defined #> ✗ 'search_length_algorithm' is defined #> ✗ 'chemical_system' is defined #> ✗ 'python_script' is defined #> ✗ 'insitu' is definedYour OGS6 object has all necessary components. #> You can try calling ogs6_run_simulation().Note that this calls more validation functions, so you may not be done just yet. # To take a look at the documentation, use ? followed by the name of a class ?prj_process # Add a parameter ogs6_obj$add(prj_parameter(name = \"E\", type = \"Constant\", value = 1e+10)) # Add a process variable ogs6_obj$add( prj_process_variable( name = \"pressure\", components = 1, order = 1, initial_condition = \"pressure0\", boundary_conditions = list( boundary_condition = prj_boundary_condition( type = \"Neumann\", parameter = \"flux_in\", geometrical_set = \"cube_1x1x1_geometry\", geometry = \"left\", component = 0 ) ) ) )"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"running-the-simulation","dir":"Articles","previous_headings":"","what":"Running the simulation","title":"User Guide","text":"soon ’ve added necessary parameters, can try starting simulation. run additional checks start OpenGeoSys 6. write_logfile set FALSE, output OpenGeoSys 6 shown console.","code":"ogs6_run_simulation(ogs6_obj)"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"retrieve-the-results","dir":"Articles","previous_headings":"","what":"Retrieve the results","title":"User Guide","text":"simulation finished, might want plot results. retrieve ? went expected, don’t need call extra function ogs6_run_simulation() already calls ogs6_read_output_files() internally. need decide information want extract. Say ’re interested pressure Parameter last timestep. easy example, one .pvd file produced. plot chunk user-guide-plot Similar idea .pvd output, hdf5 files automatically referenced $h5s returned simulation. , added file artificially benchmark library demonstration. can seen, hdf5 files particular structure. work data, simple method get_h5() allows access different data elements raw starting point post processing data. functions HDF5 handles dataset processing can used directly rhdf5 package, course. path hd5 file available active field h5_path can accessed changed OGS6 object. file reasonably “clean” structure, convenient way importing data using method get_df returns tibble table.","code":"ogs6_read_output_files(ogs6_obj) # Extract relevant info into dataframe result_df <- ogs6_obj$pvds[[1]]$get_point_data(keys = c(\"pressure\")) result_df <- result_df[(result_df$timestep!=0),] # Plot results ggplot(result_df, aes(x = x, y = y, color = pressure)) + geom_point() + #geom_raster(interpolate = T)+ #geom_contour_filled()+ xlab(\"x coordinate\") + ylab(\"y coordinate\") + theme_bw() ogs6_obj$h5s #> [[1]] #> OGS6_h5 #> h5 path: #> /work/ufz/r2ogs6/inst/extdata/benchmarks/EllipticPETSc/cube_1e3_np3.h5 #> #> # h5 file structure ------------------------------------------------------ #> group name otype dclass dim #> 0 / t_0 H5I_GROUP #> 1 /t_0 D1_left_front_N1_right H5I_DATASET FLOAT 1895 #> 2 /t_0 Linear_1_to_minus1 H5I_DATASET FLOAT 1895 #> 3 /t_0 MaterialIDs H5I_DATASET INTEGER 1233 #> 4 /t_0 geometry H5I_DATASET FLOAT 3 x 1895 #> 5 /t_0 pressure H5I_DATASET FLOAT 1895 #> 6 /t_0 topology H5I_DATASET INTEGER 11097 #> 7 /t_0 v H5I_DATASET FLOAT 3 x 1895 #> 8 / t_1 H5I_GROUP #> 9 /t_1 pressure H5I_DATASET FLOAT 1895 #> 10 /t_1 v H5I_DATASET FLOAT 3 x 1895 h5_list <- ogs6_obj$h5s[[1]]$get_h5(\"/\") example_h5 <- rhdf5::H5Fopen(ogs6_obj$h5s[[1]]$h5_path) example_h5 #> HDF5 FILE #> name / #> filename #> #> name otype dclass dim #> 0 t_0 H5I_GROUP #> 1 t_1 H5I_GROUP str(example_h5$t_0) #> List of 7 #> $ D1_left_front_N1_right: num [1:1895(1d)] 1 1 1 1 1.01 ... #> $ Linear_1_to_minus1 : num [1:1895(1d)] 1 0.8 0.6 1 0.8 0.6 1 0.8 0.6 1 ... #> $ MaterialIDs : int [1:1233(1d)] 0 0 0 0 0 0 0 0 0 0 ... #> $ geometry : num [1:3, 1:1895] 0 0 0 0.1 0 0 0.2 0 0 0 ... #> $ pressure : num [1:1895(1d)] 0 0 0 0 0 0 0 0 0 0 ... #> $ topology : int [1:11097(1d)] 9 0 1 4 3 49 50 53 52 9 ... #> $ v : num [1:3, 1:1895] 0 0 0 0 0 0 0 0 0 0 ... rhdf5::h5closeAll() df <- ogs6_obj$h5s[[1]]$get_df(group = \"/t_0\", names = \"pressure\") df #> # A tibble: 1,895 × 5 #> x y z time pressure #> #> 1 0 0 0 0 0 #> 2 0.1 0 0 0 0 #> 3 0.2 0 0 0 0 #> 4 0 0.1 0 0 0 #> 5 0.1 0.1 0 0 0 #> 6 0.2 0.1 0 0 0 #> 7 0 0.2 0 0 0 #> 8 0.1 0.2 0 0 0 #> 9 0.2 0.2 0 0 0 #> 10 0 0.3 0 0 0 #> # … with 1,885 more rows"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"running-multiple-simulations","dir":"Articles","previous_headings":"","what":"Running multiple simulations","title":"User Guide","text":"want run one multiple simulations, can use simulation object just created blueprint ensemble run. workflow described detail .","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"benchmark-script-generation","dir":"Articles","previous_headings":"","what":"Benchmark script generation","title":"User Guide","text":"Another feature r2ogs6 benchmark script generation. , two functions. ogs6_generate_benchmark_script() creates R script .prj file ogs6_generate_benchmark_scripts() wrapper former. Instead single .prj file path, takes directory path argument. Let’s look parameters ogs6_generate_benchmark_script() first. Say project file sim_file.prj want generate script . Please, make sure directories referencing exist. Now defined parameters, can generate benchmark script. hand, want generate R scripts multiple () benchmarks, can use wrapper function ogs6_generate_benchmark_scripts(). parameters basically , time supply directory path instead .prj path start . can download benchmarks (subfolder need) set path location system. ’re set! Note ogs6_generate_benchmark_scripts() reconstruct structure folder benchmarks stored , e. g. ’s file path//file.prj, find corresponding R script sim_path//file.R. , can generate scripts benchmarks single call. course can modify path liking ’re interested generating scripts certain subfolders. Furthermore, can restrict script generation benchmarks used test OGS 6. NOTE: New benchmarks .prj parameters constantly added OGS6. benchmark contains parameters added r2ogs6 yet, script generation functions work. case, skipped original error message displayed console.","code":"# The path to the project file you want to generate a script from prj_path <- \"your_path/sim_file.prj\" # The path you want to save the simulation files to sim_path <- \"your_sim_directory/\" # The path to your `ogs.exe` (if not already specified in `r2ogs6` options) ogs6_bin_path <- \"your_ogs6_bin_path/\" # The path you want your benchmark script to be saved to script_path <- \"your_script_directory/\" ogs6_generate_benchmark_script(prj_path = prj_path, sim_path = sim_path, ogs6_bin_path = ogs6_bin_path, script_path = script_path) # The path to the directory you want to generate R scripts from path <- \"path/to/ogs/Tests/Data/Elliptic/\" # The path you want to save the simulation files to sim_path <- \"your_sim_directory/\" # The path you want your benchmark scripts to be saved to script_path <- sim_path # Optional: Use if you want to start from a specific `.prj` file starting_from_prj_path <- \"\" # Optional: Use if you want to skip specific `.prj` files skip_prj_paths <- character() # Optional: Use if you want to skip specific `.prj` files skip_prj_paths <- character() # Optional: Use if you want to restrict scripting to specific `.prj` files only_prj_files <- character() ogs6_generate_benchmark_scripts(path = path, sim_path = sim_path, script_path = script_path, starting_from_prj_path = starting_from_prj_path, skip_prj_paths = skip_prj_paths, only_prj_files = only_prj_files) # extract *.prj files that are used as tests rel_testbm_paths <- get_benchmark_paths(\"path/to/ogs-source-code/ProcessLib/\") rel_testbm_paths <- sapply(rel_testbm_paths, basename) ogs6_generate_benchmark_scripts(path = path, sim_path = sim_path, script_path = script_path, only_prj_files = rel_testbm_paths)"},{"path":"https://joboog.github.io/r2ogs6/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Ruben Heinrich. Author. Johannes Boog. Author, maintainer. Philipp Schad. Author. Helmholtz Centre Environmental Research - UFZ. Copyright holder, funder.","code":""},{"path":"https://joboog.github.io/r2ogs6/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Heinrich R, Boog J, Schad P (2024). r2ogs6: API multi-physics simulator OpenGeoSys-v6. R package version 0.4.644.","code":"@Manual{, title = {r2ogs6: An API to the multi-physics simulator OpenGeoSys-v6}, author = {Ruben Heinrich and Johannes Boog and Philipp Schad}, year = {2024}, note = {R package version 0.4.644}, }"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"r2ogs6","dir":"","previous_headings":"","what":"An API to the multi-physics simulator OpenGeoSys-v6","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"r2ogs6 R-API multiphysics simulator OpenGeoSys 6. r2ogs6 allows pre-processing (preparing input files), executing simulation runs, retrieving, post-processing visualizing output data R. Furthermore, package comes functionality define ensemble runs.","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"setup","dir":"","previous_headings":"","what":"Setup","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"r2ogs6 requires installation OpenGeoSys 6. Furthermore, Python including libraries numpy vtk required read .vtu .pvd files produced OpenGeoSys 6. can install installed r2ogs6. r2ogs6 tested following environment: python==3.10.12, vtk==9.3.0, numpy==1.26.4","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"r2ogs6-installation","dir":"","previous_headings":"Setup","what":"r2ogs6 Installation","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"First, open terminal clone r2ogs6 repository local machine. install r2ogs6, first need R-packages remotes BiocManager. remotes used installing r2ogs6 BiocManager set URLs search dependencies CRAN bioconductor.org. instance, dependency rhdf5 available bioconductor.org. Open R console specific project: remotes, can now install r2ogs6 preferred library.","code":"git clone https://gitlab.opengeosys.org/ogs/tools/r2ogs6.git cd r2ogs6 # Now checkout the latest stable release git checkout tags/v0.4.643 install.packages(c(\"remotes\", \"BiocManager\")) # Install r2ogs6. Change the path to that of the cloned repository! remotes::install_local( path=\"path/to/r2ogs6\", dependencies=\"Imports\", repos=BiocManager::repositories() )"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"set-up-python","dir":"","previous_headings":"Setup > r2ogs6 Installation","what":"Set-up Python","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"OpenGeoSys 6 requires Python installation version 3.8–3.11.","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"linux-systems","dir":"","previous_headings":"Setup > r2ogs6 Installation > Set-up Python","what":"Linux systems","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"Python installed yet can reticulate library R console. Otherwise can use package manager linux distribution.","code":"reticulate::install_python(version = \"3.10:latest\")"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"windows","dir":"","previous_headings":"Setup > r2ogs6 Installation > Set-up Python","what":"Windows","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"Ideally, install Python Python Windows installer. course also try:","code":"reticulate::install_python(version = \"3.10:latest\")"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"install-python-dependencies-and-opengeosys-6","dir":"","previous_headings":"Setup > r2ogs6 Installation","what":"Install Python dependencies and OpenGeoSys 6","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"Create Python virtual environment specific name (e.g. \"r2ogs6) path Python executable just installed. Make sure reticulate::py_config()$python points python executable newly installed Python virtual environment. can try force reticulate use executable environment : work, quit R session create .Renviron file project folder: file read start-R forces reticulate use specific Python executable. Double check: can install OpenGeoSys 6 (Python dependencies numpy vtk installed alongside) Python module. aware, install OpenGeoSys 6 version compatible r2ogs6 version, see releases. Check OpenGeoSys 6 installed correctly. OpenGeoSys 6 binary located /path///python_env/bin/ogs (Linux) /path///python_env/Scripts/ogs (Windows). active R session can temporarily set path default using r2ogs6 (sets options(\"r2ogs6.default_ogs6_bin_path\").) setting permanently, create config.yml file project directory.","code":"reticulate::virtualenv_create(envname=\"r2ogs6\", python=\"/path/to/python\") reticulate::use_virtualenv(envname=\"r2ogs6\") # .Renviron linux RETICULATE_PYTHON=/path/to/your/virtualenv/bin/python reticulate::py_config() library(r2ogs6) install_ogs(ogs_version = \"6.4.4\", envname = \"r2ogs6\") reticulate::py_module_available(\"ogs\") set_ogs6_bin_path() # config.yml for linux default: r2ogs6.default_ogs6_bin_path: /path/to/python_env/bin/ogs"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"alternative-manual-setup-of-python-environment","dir":"","previous_headings":"Setup > r2ogs6 Installation","what":"Alternative manual setup of Python environment","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"Alternatively, can set python environment including OpenGeoSys 6 without reticulate; look . aware, download install OpenGeoSys 6 version compatible r2ogs6 version, see releases. Nevertheless r2ogs6 uses reticulate hood. make sure reticulate::py_config() shows correct Python environment configured.","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"tutorials use r2ogs6 package, look vignettes: User Guide Ensemble Guide Developer Guide","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"links","dir":"","previous_headings":"","what":"Links","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"OpenGeoSys Project OpenGeoSys source code OpenGeoSys documentation","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6 — OGS6","title":"OGS6 — OGS6","text":"Constructor OGS6 base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6 — OGS6","text":"sim_name Simulation name. value must string sim_path Simulation path. value must string logfile Logfile path. value must string gml .gml. read-geometry .prj geometry tag. value must string meshes .prj meshes tag. value must list strings vtus .vtus. value must list OGS6_vtu objects python_script .prj python_script tag. value must string search_length_algorithm .prj search_length_algorithm tag. value must prj_search_length_algorithm object processes .prj processes tag. value must list prj_process objects time_loop .prj time_loop tag. value must prj_time_loop object local_coordinate_system .prj local_coordinate_system tag. value must prj_local_coordinate_system object media .prj media tag. value must list prj_medium objects parameters .prj parameters tag. value must list prj_parameter objects chemical_system .prj chemical_system tag. value must prj_chemical_system object curves .prj curves tag. value must list prj_curve objects process_variables .prj process_variables tag. value must list prj_process_variable objects nonlinear_solvers .prj nonlinear_solvers tag. value must list prj_nonlinear_solver objects linear_solvers .prj linear_solvers tag. value must list prj_linear_solver objects test_definition .prj test_definition tag. value must list prj_vtkdiff objects insitu .prj insitu tag. value must prj_insitu object pvds .pvds. value must list OGS6_pvd objects h5s h5s value must class H5IdComponent returned rhdf5::h5read(). mshs mshs value must object class OGS6_msh. include include value must string.","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6 — OGS6","text":"OGS6$new() OGS6$add() OGS6$add_gml() OGS6$add_mesh() OGS6$update_component() OGS6$get_status() OGS6$print() OGS6$print_log() OGS6$clear() OGS6$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6 — OGS6","text":"Creates new OGS6 object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$new(sim_name, sim_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"sim_name string: Simulation name sim_path string: Path files simulation saved","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\")"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-add-","dir":"Reference","previous_headings":"","what":"Method add()","title":"OGS6 — OGS6","text":"Adds .prj simulation component","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$add(x)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"x object .prj `prj` class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-1","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add(prj_parameter(name = \"foo\", type = \"bar\"))"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-add-gml-","dir":"Reference","previous_headings":"","what":"Method add_gml()","title":"OGS6 — OGS6","text":"Adds reference file ending .gml optionally, OGS6_gml object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$add_gml(gml)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"gml string | OGS6_gml: Either path file extension .gml OGS6_gml object.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-2","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add_gml(\"this_works.gml\") \\dontrun{ogs6_obj$add_gml(\"this_doesnt.oops\")}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-add-mesh-","dir":"Reference","previous_headings":"","what":"Method add_mesh()","title":"OGS6 — OGS6","text":"Adds reference .vtu file optionally, OGS6_vtu object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$add_mesh(path, axisym = FALSE, read_in_vtu = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"path string: path axisym flag: mesh axially symmetrical? read_in_vtu flag: Optional: .vtu file just copied read ?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-3","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add_mesh(\"this_works.vtu\") \\dontrun{ogs6_obj$add_mesh(\"this_doesnt.oops\")}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-update-component-","dir":"Reference","previous_headings":"","what":"Method update_component()","title":"OGS6 — OGS6","text":"Update component OGS6 object.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$update_component(cmpts)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"cmpts list(sublist, length(sublist) == 2): first element sublist character calls OGS6 component, second one corresponding value.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-4","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"\\dontrun{ogs6_obj$update_component(list( list(\"ogs6_obj$parameters[[1]]$value\", 2.3), list(\"ogs6_obj$media[[1]]$properties[[2]]$value\", 1.0e-3)))}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-get-status-","dir":"Reference","previous_headings":"","what":"Method get_status()","title":"OGS6 — OGS6","text":"Checks OGS6 object necessary parameters starting simulation","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$get_status(print_status = TRUE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"print_status flag: status printed console?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-5","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$get_status()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6 — OGS6","text":"Overrides default printing behaviour print_log","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-print-log-","dir":"Reference","previous_headings":"","what":"Method print_log()","title":"OGS6 — OGS6","text":"Prints logfile console (exists)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$print_log()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-clear-","dir":"Reference","previous_headings":"","what":"Method clear()","title":"OGS6 — OGS6","text":"Clears components OGS6 object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$clear(which)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"character: names components (default). want delete components, run names(ogs6_prj_top_level_classes()) available options.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6 — OGS6","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"## ------------------------------------------------ ## Method `OGS6$new` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ## ------------------------------------------------ ## Method `OGS6$add` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add(prj_parameter(name = \"foo\", type = \"bar\")) ## ------------------------------------------------ ## Method `OGS6$add_gml` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add_gml(\"this_works.gml\") if (FALSE) ogs6_obj$add_gml(\"this_doesnt.oops\") ## ------------------------------------------------ ## Method `OGS6$add_mesh` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add_mesh(\"this_works.vtu\") if (FALSE) ogs6_obj$add_mesh(\"this_doesnt.oops\") ## ------------------------------------------------ ## Method `OGS6$update_component` ## ------------------------------------------------ if (FALSE) ogs6_obj$update_component(list( list(\"ogs6_obj$parameters[[1]]$value\", 2.3), list(\"ogs6_obj$media[[1]]$properties[[2]]$value\", 1.0e-3))) ## ------------------------------------------------ ## Method `OGS6$get_status` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$get_status() #> ✗ 'processes' has at least one element #> ✗ 'time_loop' is defined #> ✗ 'nonlinear_solvers' has at least one element #> ✗ 'linear_solvers' has at least one element #> ✗ 'parameters' has at least one element #> ✗ 'process_variables' has at least one element #> ✗ 'mesh' is defined #> ✗ 'geometry' is defined #> ✗ 'media' has at least one element #> ✗ 'test_definition' has at least one element #> ✗ 'curves' has at least one element #> ✗ 'meshes' has at least one element #> ✗ 'local_coordinate_system' is defined #> ✗ 'search_length_algorithm' is defined #> ✗ 'chemical_system' is defined #> ✗ 'python_script' is defined #> ✗ 'insitu' is defined"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_Chain — OGS6_Chain","title":"OGS6_Chain — OGS6_Chain","text":"Constructor OGS6_Chain base class","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_Chain — OGS6_Chain","text":"OGS6_Chain$new() OGS6_Chain$ogs6_run_simulation() OGS6_Chain$print_log() OGS6_Chain$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_Chain — OGS6_Chain","text":"Creates new OGS6_Chain object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Chain — OGS6_Chain","text":"","code":"OGS6_Chain$new(ogs6_obj, iter_n)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Chain — OGS6_Chain","text":"ogs6_obj OGS6: simulation object. iter_n number: Number iterations (length chain)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"method-ogs-run-simulation-","dir":"Reference","previous_headings":"","what":"Method ogs6_run_simulation()","title":"OGS6_Chain — OGS6_Chain","text":"Runs simulation. calls r2ogs6::ogs6_run_simulation() internally. chains, output written logfiles.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Chain — OGS6_Chain","text":"","code":"OGS6_Chain$ogs6_run_simulation()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"method-print-log-","dir":"Reference","previous_headings":"","what":"Method print_log()","title":"OGS6_Chain — OGS6_Chain","text":"Reads logfile simulation prints console. calls print_log internally. index specified, print logfile last object chain.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Chain — OGS6_Chain","text":"","code":"OGS6_Chain$print_log(index)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Chain — OGS6_Chain","text":"index number: chain index OGS6 object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_Chain — OGS6_Chain","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Chain — OGS6_Chain","text":"","code":"OGS6_Chain$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Chain — OGS6_Chain","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_Ensemble — OGS6_Ensemble","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Constructor OGS6_Ensemble base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_Ensemble — OGS6_Ensemble","text":"dp_parameters Getter private parameter '.dp_parameters' parameter_percs Getter private parameter '.parameter_percs' parameter_values Getter private parameter '.parameter_values' ens_path Getter private parameter '.ens_path' ensemble Getter private parameter '.ensemble'","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_Ensemble — OGS6_Ensemble","text":"OGS6_Ensemble$new() OGS6_Ensemble$print() OGS6_Ensemble$run_simulation() OGS6_Ensemble$get_point_data() OGS6_Ensemble$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Creates new OGS6_Ensemble object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$new( ogs6_obj, parameters, sequential_mode = FALSE, percentages_mode = TRUE )"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Ensemble — OGS6_Ensemble","text":"ogs6_obj OGS6: simulation object. parameters list(sublist, length(sublist) == 2): first element sublist references OGS6 parameter, second one list vector values. Note second elements sublists must length. sequential_mode flag: Defaults `FALSE` percentages_mode flag: Defaults `TRUE`","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Overrides default printing behaviour","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-run-simulation-","dir":"Reference","previous_headings":"","what":"Method run_simulation()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Runs simulation. calls r2ogs6::ogs6_run_simulation() internally. ensembles, output always written logfiles.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$run_simulation(parallel = FALSE, overwrite = T, verbose = F)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Ensemble — OGS6_Ensemble","text":"parallel flag: function run parallel? implementented via 'parallel' package. overwrite flag: existing files overwritten? verbose flag","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-get-point-data-","dir":"Reference","previous_headings":"","what":"Method get_point_data()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Wrapper `OGS6_pvd$get_point_data()` Returns combined dataframe extra `name` / `perc` column depending `sequential_mode` / `percentages_mode` used.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$get_point_data( pvd_id = 1, point_ids, keys, start_at_timestep, end_at_timestep )"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Ensemble — OGS6_Ensemble","text":"pvd_id number: Optional: .pvd consider OGS6$pvds. Defaults 1. point_ids numeric: Optional: Point IDs. Defaults . keys character: Optional: `Name` attributes `DataArray` elements. Defaults . start_at_timestep number: Optional: Timestep start . Defaults first timestep. end_at_timestep number: Optional: Timestep end . Defaults last timestep.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Ensemble — OGS6_Ensemble","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_gml — OGS6_gml","title":"OGS6_gml — OGS6_gml","text":"Constructor OGS6_gml base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_gml — OGS6_gml","text":"gml_path Getter private parameter '.gml_path' name Access private parameter '.name' points Access private parameter '.points' polylines Access private parameter '.polylines' surfaces Access private parameter '.surfaces' attr_names Getter private parameter '.attr_names' flatten_on_exp Getter private parameter '.flatten_on_exp'","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_gml — OGS6_gml","text":"OGS6_gml$new() OGS6_gml$print() OGS6_gml$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_gml — OGS6_gml","text":"Creates new OGS6_gml object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_gml — OGS6_gml","text":"","code":"OGS6_gml$new( gml_path = NULL, name = NULL, points = NULL, polylines = NULL, surfaces = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_gml — OGS6_gml","text":"gml_path string: Optional: Path .gml file name string: Geometry name points tibble: Must 3 vectors named 'x', 'y' 'z', may optional 'name' vector polylines list(list(\"foo\", c(1, 2))): surfaces list(list(\"foo\", c(1, 2, 3), c(2, 3, 4)))","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_gml — OGS6_gml","text":"Overrides default printing behaviour","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_gml — OGS6_gml","text":"","code":"OGS6_gml$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_gml — OGS6_gml","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_gml — OGS6_gml","text":"","code":"OGS6_gml$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_gml — OGS6_gml","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6_gml — OGS6_gml","text":"","code":"OGS6_gml$new( name = \"cube_1x1x1_geometry\", points = tibble::tibble( x = c(0, 0, 0, 0), y = c(0, 0, 1, 1), z = c(0, 1, 1, 0), name = c(\"origin\", \"\", \"\", \"\") ), polylines = list(polyline = list(\"front_left\", c( pnt = 0, pnt = 1 ))), surfaces = list(surface = list( name = \"left\", element = c(p1 = 0, p2 = 1, p3 = 2), element = c(p1 = 0, p2 = 3, p3 = 2) )) ) #> OGS6_gml #> path: #> name: cube_1x1x1_geometry #> #> points #> # A tibble: 4 × 4 #> x y z name #> #> 1 0 0 0 \"origin\" #> 2 0 0 1 \"\" #> 3 0 1 1 \"\" #> 4 0 1 0 \"\" #> #> polylines #> $polyline #> $polyline$name #> [1] \"front_left\" #> #> $polyline$ #> pnt pnt #> 0 1 #> #> #> #> surfaces #> $surface #> $surface$name #> [1] \"left\" #> #> $surface$element #> p1 p2 p3 #> 0 1 2 #> #> $surface$element #> p1 p2 p3 #> 0 3 2 #> #>"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":null,"dir":"Reference","previous_headings":"","what":"wrapper for rhdf5::h5read() — OGS6_h5","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"Small class wrap h5 data r2ogs6 workflow.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"OGS6_h5 NOTE: beta-version guaranteed work current three existing [benchmarks](https://doxygen.opengeosys.org/d9/d28/ogs_file_param__prj__time_loop__output__hdf.html) contain *.h5 files. complicated files can always handled method $get_h5 may refer package rhdf5.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"h5_path Getter/setter private parameter `.h5_path`","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"OGS6_h5$new() OGS6_h5$print() OGS6_h5$get_h5() OGS6_h5$get_df() OGS6_h5$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"function called automatically simulation run give overview h5 output data.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$new(h5_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"h5_path path *.h5 file.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"Overrides default print method","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"examples-1","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) ogs6_h5 \\dontrun{ogs6_obj$h5s}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-get-h-","dir":"Reference","previous_headings":"","what":"Method get_h5()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"return h5 object processing rhdf5 package.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$get_h5(name = \"/\", ...)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"name Optional: *character* indicates element h5 file access. Default *\"/\"* return entire file list. ... Optional: arguments passed function h5read.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"list data elements element accessed name","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"examples-2","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"\\dontrun{h5_list <- ogs6_obj$h5s[[1]]$get_h5(\"/times\")}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-get-df-","dir":"Reference","previous_headings":"","what":"Method get_df()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"Method retrieve HDF5 output tibble assuming standardized structure OGS6 HDF5 output. times geometry added default.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$get_df(group, names = \"geometry\")"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"group *character* names *character* names hdf5 element displayed printing OGS5_h5 object, without leading \"/\".","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"examples-3","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) df <- ogs6_h5$get_df(\"/t_0\", \"pressure\") \\dontrun{df <- ogs6_obj$h5s[[1]]$get_df(\"/t_0\", \"pressure\")}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"## ------------------------------------------------ ## Method `OGS6_h5$new` ## ------------------------------------------------ h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) ## ------------------------------------------------ ## Method `OGS6_h5$print` ## ------------------------------------------------ h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) ogs6_h5 #> OGS6_h5 #> h5 path: #> /tmp/RtmpBchsQP/temp_libpathaca25e6824bd/r2ogs6//extdata/benchmarks/EllipticPETSc/cube_1e3_np3.h5 #> #> # h5 file structure ------------------------------------------------------------ #> group name otype dclass dim #> 0 / t_0 H5I_GROUP #> 1 /t_0 D1_left_front_N1_right H5I_DATASET FLOAT 1895 #> 2 /t_0 Linear_1_to_minus1 H5I_DATASET FLOAT 1895 #> 3 /t_0 MaterialIDs H5I_DATASET INTEGER 1233 #> 4 /t_0 geometry H5I_DATASET FLOAT 3 x 1895 #> 5 /t_0 pressure H5I_DATASET FLOAT 1895 #> 6 /t_0 topology H5I_DATASET INTEGER 11097 #> 7 /t_0 v H5I_DATASET FLOAT 3 x 1895 #> 8 / t_1 H5I_GROUP #> 9 /t_1 pressure H5I_DATASET FLOAT 1895 #> 10 /t_1 v H5I_DATASET FLOAT 3 x 1895 if (FALSE) ogs6_obj$h5s ## ------------------------------------------------ ## Method `OGS6_h5$get_h5` ## ------------------------------------------------ if (FALSE) h5_list <- ogs6_obj$h5s[[1]]$get_h5(\"/times\") ## ------------------------------------------------ ## Method `OGS6_h5$get_df` ## ------------------------------------------------ h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) df <- ogs6_h5$get_df(\"/t_0\", \"pressure\") if (FALSE) df <- ogs6_obj$h5s[[1]]$get_df(\"/t_0\", \"pressure\")"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_msh — OGS6_msh","title":"OGS6_msh — OGS6_msh","text":"Small class support MSH mesh files. Note MSH files legacy format OGS5. recommended switch VTU files.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_msh — OGS6_msh","text":"msh_path Getter/setter private parameter `.msh_path`","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_msh — OGS6_msh","text":"OGS6_msh$new() OGS6_msh$print() OGS6_msh$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_msh — OGS6_msh","text":"reates new OGS6_vtu object..","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_msh — OGS6_msh","text":"","code":"OGS6_msh$new(msh_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_msh — OGS6_msh","text":"msh_path path *.msh file.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_msh — OGS6_msh","text":"Overrides default print method","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_msh — OGS6_msh","text":"","code":"OGS6_msh$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_msh — OGS6_msh","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_msh — OGS6_msh","text":"","code":"OGS6_msh$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_msh — OGS6_msh","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_pvd — OGS6_pvd","title":"OGS6_pvd — OGS6_pvd","text":"Constructor OGS6_pvd base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_pvd — OGS6_pvd","text":"pvd_path Getter private parameter '.pvd_path' datasets Getter private parameter '.datasets' vtu_paths Getter `datasets` `file` abs_vtu_paths Gets absolute .vtu paths, e.g. `dirname(pvd_path)` + `datasets` `file` last_timestep Gets last timestep timesteps Gets timesteps private parameter `datasets` OGS6_vtus Getter private parameter `.OGS6_vtus`","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_pvd — OGS6_pvd","text":"OGS6_pvd$new() OGS6_pvd$print() OGS6_pvd$vtu_by_timestep() OGS6_pvd$timestep_by_vtu() OGS6_pvd$get_point_data_at() OGS6_pvd$get_point_data() OGS6_pvd$get_cell_data() OGS6_pvd$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_pvd — OGS6_pvd","text":"Creates new OGS6_pvd object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$new(pvd_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"pvd_path string: Path .pvd file","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_pvd — OGS6_pvd","text":"Overrides default printing behaviour","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-vtu-by-timestep-","dir":"Reference","previous_headings":"","what":"Method vtu_by_timestep()","title":"OGS6_pvd — OGS6_pvd","text":"Returns .vtu path specified timestep","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$vtu_by_timestep(timestep)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"timestep string: Timestep","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-timestep-by-vtu-","dir":"Reference","previous_headings":"","what":"Method timestep_by_vtu()","title":"OGS6_pvd — OGS6_pvd","text":"Returns timestep specified .vtu path","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$timestep_by_vtu(vtu_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"vtu_path string: .vtu path","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-get-point-data-at-","dir":"Reference","previous_headings":"","what":"Method get_point_data_at()","title":"OGS6_pvd — OGS6_pvd","text":"Returns tibble containing point data","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$get_point_data_at( coordinates, keys, start_at_timestep, end_at_timestep )"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"coordinates list(numeric): List coordinates (coordinate numeric vector length 3) keys character: Optional: `Name` attributes `DataArray` elements. Defaults . start_at_timestep number: Optional: Timestep start . Defaults first timestep. end_at_timestep number: Optional: Timestep end . Defaults last timestep.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-get-point-data-","dir":"Reference","previous_headings":"","what":"Method get_point_data()","title":"OGS6_pvd — OGS6_pvd","text":"Returns tibble containing point data","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$get_point_data(point_ids, keys, start_at_timestep, end_at_timestep)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"point_ids numeric: Optional: Point IDs. Defaults . keys character: Optional: `Name` attributes `DataArray` elements. Defaults . start_at_timestep number: Optional: Timestep start . Defaults first timestep. end_at_timestep number: Optional: Timestep end . Defaults last timestep.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-get-cell-data-","dir":"Reference","previous_headings":"","what":"Method get_cell_data()","title":"OGS6_pvd — OGS6_pvd","text":"Returns tibble containing cell data","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$get_cell_data(cell_ids, keys, start_at_timestep, end_at_timestep)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"cell_ids numeric: Optional: Cell IDs. Defaults . keys character: Optional: `Name` attributes `DataArray` elements. Defaults . start_at_timestep number: Optional: Timestep start . Defaults first timestep. end_at_timestep number: Optional: Timestep end . Defaults last timestep.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_pvd — OGS6_pvd","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_vtu — OGS6_vtu","title":"OGS6_vtu — OGS6_vtu","text":"Constructor `OGS6_vtu` base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_vtu — OGS6_vtu","text":"vtu_path Getter private parameter `.vtu_path` number_of_points Getter NumberOfPoints parameter `.vtkUnstructuredGrid` number_of_cells Getter NumberOfCells parameter `.vtkUnstructuredGrid` points Getter Points parameter `.dsa_vtkUnstructuredGrid` cells Getter Cells parameter `.dsa_vtkUnstructuredGrid` field_data Getter FieldData parameter `.dsa_vtkUnstructuredGrid` point_data Getter PointData parameter `.dsa_vtkUnstructuredGrid` cell_data Getter CellData parameter `.dsa_vtkUnstructuredGrid` vtkPointLocator Getter private parameter `.vtkPointLocator` vtkUnstructuredGrid Access private parameter `.vtkUnstructuredGrid` dsa_vtkUnstructuredGrid Getter private parameter `.dsa_vtkUnstructuredGrid`","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_vtu — OGS6_vtu","text":"OGS6_vtu$new() OGS6_vtu$print() OGS6_vtu$get_field_data() OGS6_vtu$get_point_coords() OGS6_vtu$get_point_data_at() OGS6_vtu$get_point_data() OGS6_vtu$get_cell_data() OGS6_vtu$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_vtu — OGS6_vtu","text":"Creates new OGS6_vtu object.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$new(vtu_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"vtu_path string: Path .vtu file","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_vtu — OGS6_vtu","text":"Overrides default printing behaviour.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-field-data-","dir":"Reference","previous_headings":"","what":"Method get_field_data()","title":"OGS6_vtu — OGS6_vtu","text":"Gets FieldData.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_field_data(keys)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"keys character: Optional: `Name` attributes `DataArray` elements, defaults `FieldData`.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"OGS6_vtu — OGS6_vtu","text":"list format list(value_a = 1, value_b = 2), names reference `Name` attributes `DataArray` elements.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-point-coords-","dir":"Reference","previous_headings":"","what":"Method get_point_coords()","title":"OGS6_vtu — OGS6_vtu","text":"Gets coordinates specific points IDs.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_point_coords(point_ids)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"point_ids numeric: Point IDs","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"OGS6_vtu — OGS6_vtu","text":"`point_ids` number, coordinate array. point_ids` numeric vector length > 1, list coordinate arrays.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-point-data-at-","dir":"Reference","previous_headings":"","what":"Method get_point_data_at()","title":"OGS6_vtu — OGS6_vtu","text":"Gets PointData specified coordinates.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_point_data_at(coordinates, keys)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"coordinates list(numeric): List coordinates (coordinate numeric vector length 3) keys character: Optional: `Name` attributes `DataArray` elements, defaults `PointData`","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-point-data-","dir":"Reference","previous_headings":"","what":"Method get_point_data()","title":"OGS6_vtu — OGS6_vtu","text":"Gets PointData points IDs `point_ids`.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_point_data(point_ids, keys)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"point_ids numeric: Optional: Point IDs, defaults keys character: Optional: `Name` attributes `DataArray` elements, defaults `PointData`","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"OGS6_vtu — OGS6_vtu","text":"tibble::tibble row represents point.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-cell-data-","dir":"Reference","previous_headings":"","what":"Method get_cell_data()","title":"OGS6_vtu — OGS6_vtu","text":"Gets CellData cells IDs `cell_ids`.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_cell_data(cell_ids, keys)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"cell_ids numeric: Optional: Cell IDs, defaults keys character: Optional: `Name` attributes `DataArray` elements, defaults `CellData`","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"OGS6_vtu — OGS6_vtu","text":"tibble::tibble row represents cell.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_vtu — OGS6_vtu","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/construct_ogs_command.html","id":null,"dir":"Reference","previous_headings":"","what":"construct_ogs_command — construct_ogs_command","title":"construct_ogs_command — construct_ogs_command","text":"Constructs call string 'system2()'.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/construct_ogs_command.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"construct_ogs_command — construct_ogs_command","text":"","code":"construct_ogs_command(ogs6_bin_path, singularity_opts)"},{"path":"https://joboog.github.io/r2ogs6/reference/construct_ogs_command.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"construct_ogs_command — construct_ogs_command","text":"ogs6_bin_path string: Optional: Path OpenGeoSys 6 executable OpenGeoSys container (singularity image) file. Defaults options(\"r2ogs6.default_ogs6_bin_path\") singularity_opts string: Optional: Options singularity exec command. Defaults options(\"r2ogs6.singularity_opts\")","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/construct_ogs_command.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"construct_ogs_command — construct_ogs_command","text":"string: Call object.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/install_ogs.html","id":null,"dir":"Reference","previous_headings":"","what":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","title":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","text":"Install specific version OpenGeoSys 6 (OGS) along necessary Python packages `vtk` `numpy` specified Python virtual environment. Note, work `conda` environments.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/install_ogs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","text":"","code":"install_ogs(..., ogs_version = \"6.4.4\", envname = \"r2ogs6\")"},{"path":"https://joboog.github.io/r2ogs6/reference/install_ogs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","text":"... Rest arguments passed \"py_install()\" ogs_version version OGS install (default: 6.4.4). envname name Python virtual environment (default: r2ogs6).","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/install_ogs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","text":"None.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_call_ogs6.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_call_ogs6 — ogs6_call_ogs6","title":"ogs6_call_ogs6 — ogs6_call_ogs6","text":"Makes system call OpenGeoSys 6 retrieves exit code.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_call_ogs6.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_call_ogs6 — ogs6_call_ogs6","text":"","code":"ogs6_call_ogs6( ogs6_obj, write_logfile = TRUE, ogs6_bin_path, verbose = F, singularity_opts )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_call_ogs6.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_call_ogs6 — ogs6_call_ogs6","text":"ogs6_obj OGS6: Simulation object write_logfile flag: output written logfile? FALSE, output written console. TRUE, logfile directory created ogs6$sim_path directory ogs6_bin_path string: Optional: Path OpenGeoSys 6 executable OpenGeoSys container (singularity image) file. Defaults options(\"r2ogs6.default_ogs6_bin_path\") verbose flag singularity_opts string: Optional: Options singularity exec command. Defaults options(\"r2ogs6.singularity_opts\")","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_export_sim_files.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_export_sim_files — ogs6_export_sim_files","title":"ogs6_export_sim_files — ogs6_export_sim_files","text":"Creates ogs6$sim_path directory exist yet exports / copies simulation files .","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_export_sim_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_export_sim_files — ogs6_export_sim_files","text":"","code":"ogs6_export_sim_files( ogs6_obj, overwrite = T, copy_ext_files = F, test_mode = F )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_export_sim_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_export_sim_files — ogs6_export_sim_files","text":"ogs6_obj OGS6: Simulation object overwrite flag: existing files overwritten? copy_ext_files flag: external files references ogs6_obj copied ogs6_obj$sim_path? test_mode flag: TRUE, check status ogs6_obj exporting files. Defaults FALSE","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_script.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate benchmark script — ogs6_generate_benchmark_script","title":"Generate benchmark script — ogs6_generate_benchmark_script","text":"Generates R script existing `.prj` benchmark file.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_script.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate benchmark script — ogs6_generate_benchmark_script","text":"","code":"ogs6_generate_benchmark_script( prj_path, sim_path, ogs6_bin_path, script_path, read_in_gml = FALSE, read_in_vtu = FALSE )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_script.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate benchmark script — ogs6_generate_benchmark_script","text":"prj_path string: `.prj` file script based sim_path string: Path simulation files saved ogs6_bin_path string: Path OpenGeoSys executable. Defaults options(\"r2ogs6.default_ogs6_bin_path\"). script_path string: Path benchmark script saved read_in_gml flag: Optional: `.gml` file just copied read ? read_in_vtu flag: Optional: `.vtu` file(s) just copied read ?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_scripts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate benchmark scripts — ogs6_generate_benchmark_scripts","title":"Generate benchmark scripts — ogs6_generate_benchmark_scripts","text":"wrapper function `ogs6_generate_benchmark_script()`.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_scripts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate benchmark scripts — ogs6_generate_benchmark_scripts","text":"","code":"ogs6_generate_benchmark_scripts( path, sim_path, script_path, read_in_gml, read_in_vtu = FALSE, starting_from_prj_path = \"\", skip_prj_paths = character(), only_prj_files = character() )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_scripts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate benchmark scripts — ogs6_generate_benchmark_scripts","text":"path string: Path benchmark directory generate scripts sim_path string: Path simulation files saved script_path string: Path benchmark script saved read_in_gml flag: Optional: `.gml` file just copied read ? read_in_vtu flag: Optional: `.vtu` file(s) just copied read ? starting_from_prj_path string: Optional: `.prj` path start skip_prj_paths character: Optional: `.prj` paths skip only_prj_files character: Optional: `.prj` files limit .","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_structured_mesh.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","title":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","text":"Wrapper function call generateStructuredMesh.exe (VTK mesh generator). full documentation see https://www.opengeosys.org/docs/tools/meshing/structured-mesh-generation/","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_structured_mesh.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","text":"","code":"ogs6_generate_structured_mesh(args_str, ogs6_utils_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_structured_mesh.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","text":"args_str string: arguments script called ogs6_utils_path string: Optional: Path OpenGeoSys6 utils folder. Defaults options(\"r2ogs6.default_ogs6_utils_path\")","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_structured_mesh.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","text":"string: .vtu file path","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_combinations.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_get_combinations — ogs6_get_combinations","title":"ogs6_get_combinations — ogs6_get_combinations","text":"Gets possible combinations supplied vectors","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_combinations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_get_combinations — ogs6_get_combinations","text":"","code":"ogs6_get_combinations(...)"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_combinations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_get_combinations — ogs6_get_combinations","text":"... vector:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_medium_property.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_get_medium_property — ogs6_get_medium_property","title":"ogs6_get_medium_property — ogs6_get_medium_property","text":"Returns medium property based property name","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_medium_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_get_medium_property — ogs6_get_medium_property","text":"","code":"ogs6_get_medium_property(medium, name)"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_medium_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_get_medium_property — ogs6_get_medium_property","text":"medium prj_medium name string: property name","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_medium_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ogs6_get_medium_property — ogs6_get_medium_property","text":"prj_pr_property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_prj_top_level_classes.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_prj_top_level_classes — ogs6_prj_top_level_classes","title":"ogs6_prj_top_level_classes — ogs6_prj_top_level_classes","text":"Returns named character vector OGS6 top level .prj tags (names) represented r2ogs6 classes along class names (values).","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_prj_top_level_classes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_prj_top_level_classes — ogs6_prj_top_level_classes","text":"","code":"ogs6_prj_top_level_classes()"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_prj_top_level_classes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ogs6_prj_top_level_classes — ogs6_prj_top_level_classes","text":"character","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_read_output_files.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_read_output_files — ogs6_read_output_files","title":"ogs6_read_output_files — ogs6_read_output_files","text":"Read generated .pvd files add ogs6_obj","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_read_output_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_read_output_files — ogs6_read_output_files","text":"","code":"ogs6_read_output_files(ogs6_obj)"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_read_output_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_read_output_files — ogs6_read_output_files","text":"ogs6_obj OGS6: Simulation object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_run_simulation.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_run_simulation — ogs6_run_simulation","title":"ogs6_run_simulation — ogs6_run_simulation","text":"Wrapper function calls ogs6_export_sim_files(), ogs6_call_ogs6() ogs6_read_output_files().","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_run_simulation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_run_simulation — ogs6_run_simulation","text":"","code":"ogs6_run_simulation( ogs6_obj, write_logfile = TRUE, ogs6_bin_path, overwrite = T, copy_ext_files = F, verbose = F, singularity_opts )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_run_simulation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_run_simulation — ogs6_run_simulation","text":"ogs6_obj OGS6: Simulation object write_logfile flag: output written logfile? FALSE, output written console. TRUE, logfile directory created ogs6$sim_path directory ogs6_bin_path string: Optional: OpenGeoSys 6 executable path. Defaults options(\"r2ogs6.default_ogs6_bin_path\") overwrite flag: existing files overwritten? copy_ext_files flag: external files references ogs6_obj copied ogs6_obj$sim_path? verbose flag singularity_opts string: Optional: Options singularity exec command. Defaults options(\"r2ogs6.singularity_opts\")","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_borehole_heat_exchanger.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","title":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","text":"tag: borehole_heat_exchanger","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_borehole_heat_exchanger.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","text":"","code":"prj_borehole_heat_exchanger( type, flow_and_temperature_control, borehole, grout, pipes, refrigerant, use_bhe_pipe_network = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_borehole_heat_exchanger.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","text":"type string: flow_and_temperature_control prj_flow_and_temperature_control: borehole list: grout list: pipes prj_pipes: refrigerant list: use_bhe_pipe_network Optional: string (\"true\" | \"false\"):","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_borehole_heat_exchanger.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","text":"","code":"prj_borehole_heat_exchanger( type = \"1U\", flow_and_temperature_control = prj_flow_and_temperature_control( type = \"TemperatureCurveConstantFlow\", flow_rate = 2e-04, temperature_curve = \"inflow_temperature\" ), borehole = list(length = \"18.0\", diameter = \"0.13\"), grout = list( density = \"2190.0\", porosity = \"0.0\", heat_capacity = \"1735.160\", thermal_conductivity = \"0.806\" ), pipes = prj_pipes( longitudinal_dispersion_length = 0.001, inlet = list( diameter = \" 0.013665\", wall_thickness = \"0.003035\", wall_thermal_conductivity = \"0.39\" ), outlet = list( diameter = \"0.013665\", wall_thickness = \"0.003035\", wall_thermal_conductivity = \"0.39\" ), distance_between_pipes = 0.053 ), refrigerant = list( density = \"992.92\", viscosity = \"0.00067418\", specific_heat_capacity = \"4068\", thermal_conductivity = \"0.62863\", reference_temperature = \"298.15\" ) ) #> Renaming elements of vector to fit their default names: 'density', 'porosity', 'specific_heat_capacity', 'thermal_conductivity' #> $type #> [1] \"1U\" #> #> $flow_and_temperature_control #> $type #> [1] \"TemperatureCurveConstantFlow\" #> #> $flow_rate #> [1] 2e-04 #> #> $temperature_curve #> [1] \"inflow_temperature\" #> #> $power #> NULL #> #> $power_curve #> NULL #> #> $flow_rate_curve #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger/flow_and_temperature_control\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_flow_and_temperature_control\" #> #> $borehole #> $borehole$length #> [1] \"18.0\" #> #> $borehole$diameter #> [1] \"0.13\" #> #> #> $grout #> $grout$density #> [1] \"2190.0\" #> #> $grout$porosity #> [1] \"0.0\" #> #> $grout$specific_heat_capacity #> [1] \"1735.160\" #> #> $grout$thermal_conductivity #> [1] \"0.806\" #> #> #> $pipes #> $longitudinal_dispersion_length #> [1] 0.001 #> #> $inlet #> $inlet$diameter #> [1] \" 0.013665\" #> #> $inlet$wall_thickness #> [1] \"0.003035\" #> #> $inlet$wall_thermal_conductivity #> [1] \"0.39\" #> #> #> $outlet #> $outlet$diameter #> [1] \"0.013665\" #> #> $outlet$wall_thickness #> [1] \"0.003035\" #> #> $outlet$wall_thermal_conductivity #> [1] \"0.39\" #> #> #> $distance_between_pipes #> [1] 0.053 #> #> $outer #> NULL #> #> $inner #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger/pipes\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_pipes\" #> #> $refrigerant #> $refrigerant$density #> [1] \"992.92\" #> #> $refrigerant$viscosity #> [1] \"0.00067418\" #> #> $refrigerant$specific_heat_capacity #> [1] \"4068\" #> #> $refrigerant$thermal_conductivity #> [1] \"0.62863\" #> #> $refrigerant$reference_temperature #> [1] \"298.15\" #> #> #> $use_bhe_pipe_network #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_borehole_heat_exchanger\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_boundary_condition.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_boundary_condition — prj_boundary_condition","title":"prj_boundary_condition — prj_boundary_condition","text":"tag: boundary_condition","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_boundary_condition.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_boundary_condition — prj_boundary_condition","text":"","code":"prj_boundary_condition( type, parameter = NULL, geometrical_set = NULL, geometry = NULL, component = NULL, mesh = NULL, alpha = NULL, u_0 = NULL, constraint_type = NULL, constraining_process_variable = NULL, constraint_threshold = NULL, constraint_direction = NULL, area_parameter = NULL, bc_object = NULL, flush_stdout = NULL, property_name = NULL, initial_value_parameter = NULL, constant_name = NULL, coefficient_current_variable_name = NULL, coefficient_other_variable_name = NULL, coefficient_mixed_variables_name = NULL, threshold_parameter = NULL, comparison_operator = NULL, time_interval = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_boundary_condition.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_boundary_condition — prj_boundary_condition","text":"type string: parameter string: geometrical_set Optional: string: geometry Optional: string: component Optional: string | double: mesh Optional: string: alpha Optional: string: u_0 Optional: string: constraint_type Optional: string: constraining_process_variable Optional: string: constraint_threshold Optional: string | double: constraint_direction Optional: string: area_parameter Optional: string: bc_object Optional: string: flush_stdout Optional: string: property_name Optional: string: initial_value_parameter Optional: string: constant_name Optional: string: coefficient_current_variable_name Optional: string: coefficient_other_variable_name Optional: string: coefficient_mixed_variables_name Optional: string: threshold_parameter Optional: string: comparison_operator Optional: string: time_interval Optional: list 2, character:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_boundary_condition.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_boundary_condition — prj_boundary_condition","text":"","code":"prj_boundary_condition( type = \"Neumann\", parameter = \"flux_in\", geometrical_set = \"cube_1x1x1_geometry\", geometry = \"left\", component = 0 ) #> $type #> [1] \"Neumann\" #> #> $parameter #> [1] \"flux_in\" #> #> $geometrical_set #> [1] \"cube_1x1x1_geometry\" #> #> $geometry #> [1] \"left\" #> #> $component #> [1] 0 #> #> $mesh #> NULL #> #> $alpha #> NULL #> #> $u_0 #> NULL #> #> $constraint_type #> NULL #> #> $constraining_process_variable #> NULL #> #> $constraint_threshold #> NULL #> #> $constraint_direction #> NULL #> #> $area_parameter #> NULL #> #> $bc_object #> NULL #> #> $flush_stdout #> NULL #> #> $property_name #> NULL #> #> $initial_value_parameter #> NULL #> #> $constant_name #> NULL #> #> $coefficient_current_variable_name #> NULL #> #> $coefficient_other_variable_name #> NULL #> #> $coefficient_mixed_variables_name #> NULL #> #> $threshold_parameter #> NULL #> #> $comparison_operator #> NULL #> #> $time_interval #> NULL #> #> $xpath #> [1] \"process_variables/process_variable/boundary_conditions/boundary_condition\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_boundary_condition\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_capillary_pressure.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_capillary_pressure — prj_capillary_pressure","title":"prj_capillary_pressure — prj_capillary_pressure","text":"tag: capillary_pressure","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_capillary_pressure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_capillary_pressure — prj_capillary_pressure","text":"","code":"prj_capillary_pressure( type, pd = NULL, sr = NULL, smax = NULL, m = NULL, pc_max = NULL, has_regularized = NULL, curve = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_capillary_pressure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_capillary_pressure — prj_capillary_pressure","text":"type string: pd Optional: string | double: sr Optional: string | double: smax Optional: string | double: m Optional: string | double: pc_max Optional: string | double: has_regularized Optional: string, \"true\" | \"false\": curve Optional: list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_capillary_pressure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_capillary_pressure — prj_capillary_pressure","text":"","code":"prj_capillary_pressure( type = \"vanGenuchten\", pd = 2e+06, sr = 0.4, smax = 1, m = 0.3288590604, pc_max = 2e+07, has_regularized = \"true\" ) #> $type #> [1] \"vanGenuchten\" #> #> $pd #> [1] 2e+06 #> #> $sr #> [1] 0.4 #> #> $smax #> [1] 1 #> #> $m #> [1] 0.3288591 #> #> $pc_max #> [1] 2e+07 #> #> $has_regularized #> [1] \"true\" #> #> $curve #> NULL #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/capillary_pressure\" #> [2] \"processes/process/porous_medium/porous_medium/capillary_pressure\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_capillary_pressure\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_reaction.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_chemical_reaction — prj_chemical_reaction","title":"prj_chemical_reaction — prj_chemical_reaction","text":"tag: chemical_reaction","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_reaction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_chemical_reaction — prj_chemical_reaction","text":"","code":"prj_chemical_reaction( stoichiometric_coefficients, reaction_type, first_order_rate_constant )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_reaction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_chemical_reaction — prj_chemical_reaction","text":"stoichiometric_coefficients numeric: reaction_type string: first_order_rate_constant double:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_system.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_chemical_system — prj_chemical_system","title":"prj_chemical_system — prj_chemical_system","text":"tag: chemical_system","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_system.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_chemical_system — prj_chemical_system","text":"","code":"prj_chemical_system( chemical_solver, mesh, linear_solver = NULL, database = NULL, solution = NULL, knobs = NULL, kinetic_reactants = NULL, rates = NULL, equilibrium_reactants = NULL, surface = NULL, user_punch = NULL, use_high_precision = NULL, exchangers = NULL, chemical_reactions = NULL, number_of_components = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_system.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_chemical_system — prj_chemical_system","text":"chemical_solver string: Either \"Phreeqc\" \"SelfContained\". mesh string: linear_solver Optional: string: database string: Required chemical_solver == \"Phreeqc\" . solution prj_solution: Required chemical_solver == \"Phreeqc\". knobs Optional: list: kinetic_reactants Optional: list, prj_kinetic_reactant: rates Optional: list, prj_rate: equilibrium_reactants Optional: list, prj_phase_component: surface Optional: user_punch Optional: use_high_precision Optional: exchangers Optional: prj_exchangers chemical_reactions list: Required chemical_solver == \"SelfContained\". number_of_components integer: Required chemical_solver == \"SelfContained\".","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_system.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_chemical_system — prj_chemical_system","text":"","code":"prj_chemical_system( chemical_solver = \"Phreeqc\", database = \"PSINA_12_07_110615_DAV_s.dat\", solution = prj_solution( temperature = 25, pressure = 1, pe = 4, components = list( component = \"C(4)\", component = \"Ca\" ), charge_balance = \"pH\" ), mesh = \"calcite_ReactiveDomain\", knobs = list( max_iter = \"100\", relative_convergence_tolerance = \"1e-12\", tolerance = \"1e-15\", step_size = \"100\", scaling = \"0\" ), equilibrium_reactants = list( phase_component = prj_phase_component( name = \"Calcite\", saturation_index = 0, initial_amount = 0.000207 ) ) ) #> $chemical_solver #> [1] \"Phreeqc\" #> #> $mesh #> [1] \"calcite_ReactiveDomain\" #> #> $linear_solver #> NULL #> #> $database #> [1] \"PSINA_12_07_110615_DAV_s.dat\" #> #> $solution #> $temperature #> [1] 25 #> #> $pressure #> [1] 1 #> #> $pe #> [1] 4 #> #> $components #> $components$component #> [1] \"C(4)\" #> #> $components$component #> [1] \"Ca\" #> #> #> $charge_balance #> [1] \"pH\" #> #> $fixing_pe #> NULL #> #> $xpath #> [1] \"chemical_system/solution\" #> #> $attr_names #> [1] \"fixing_pe\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_solution\" #> #> $knobs #> $knobs$max_iter #> [1] \"100\" #> #> $knobs$relative_convergence_tolerance #> [1] \"1e-12\" #> #> $knobs$tolerance #> [1] \"1e-15\" #> #> $knobs$step_size #> [1] \"100\" #> #> $knobs$scaling #> [1] \"0\" #> #> #> $kinetic_reactants #> NULL #> #> $rates #> NULL #> #> $equilibrium_reactants #> $equilibrium_reactants$phase_component #> $name #> [1] \"Calcite\" #> #> $saturation_index #> [1] 0 #> #> $initial_amount #> [1] 0.000207 #> #> $xpath #> [1] \"chemical_system/equilibrium_reactants/phase_component\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase_component\" #> #> #> $surface #> NULL #> #> $user_punch #> NULL #> #> $use_high_precision #> NULL #> #> $exchangers #> NULL #> #> $chemical_reactions #> NULL #> #> $number_of_components #> NULL #> #> $xpath #> [1] \"chemical_system\" #> #> $attr_names #> [1] \"chemical_solver\" \"site_unit\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_chemical_system\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_com_property.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_com_property — prj_com_property","title":"prj_com_property — prj_com_property","text":"tag: property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_com_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_com_property — prj_com_property","text":"","code":"prj_com_property( name, type, value = NULL, parameter_name = NULL, reference_diffusion = NULL, activation_energy = NULL, reference_temperature = NULL, triple_temperature = NULL, triple_pressure = NULL, critical_temperature = NULL, critical_pressure = NULL, reference_pressure = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_com_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_com_property — prj_com_property","text":"name string: Property name type string: Property type value Optional: string | double: ... parameter_name Optional: reference_diffusion Optional: character activation_energy Optional: string | double reference_temperature Optional: numeric triple_temperature Optional: numeric triple_pressure Optional: numeric critical_temperature Optional: numeric critical_pressure Optional: numeric reference_pressure Optional: numeric","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_com_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_com_property — prj_com_property","text":"","code":"prj_com_property(name = \"molecular_diffusion\", type = \"Constant\", value = 2e-09) #> $name #> [1] \"molecular_diffusion\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 2e-09 #> #> $parameter_name #> NULL #> #> $reference_diffusion #> NULL #> #> $activation_energy #> NULL #> #> $reference_temperature #> NULL #> #> $triple_temperature #> NULL #> #> $triple_pressure #> NULL #> #> $critical_temperature #> NULL #> #> $critical_pressure #> NULL #> #> $reference_pressure #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/components/component/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_com_property\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_component.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_component — prj_component","title":"prj_component — prj_component","text":"tag: component","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_component.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_component — prj_component","text":"","code":"prj_component(name, properties)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_component.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_component — prj_component","text":"name string: properties list, prj_com_property:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_component.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_component — prj_component","text":"","code":"prj_component( name = \"concentration\", properties = list( property = prj_com_property(name = \"molecular_diffusion\", type = \"Constant\", value = 2e-09) ) ) #> $name #> [1] \"concentration\" #> #> $properties #> $properties$property #> $name #> [1] \"molecular_diffusion\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 2e-09 #> #> $parameter_name #> NULL #> #> $reference_diffusion #> NULL #> #> $activation_energy #> NULL #> #> $reference_temperature #> NULL #> #> $triple_temperature #> NULL #> #> $triple_pressure #> NULL #> #> $critical_temperature #> NULL #> #> $critical_pressure #> NULL #> #> $reference_pressure #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/components/component/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_com_property\" #> #> #> $xpath #> [1] \"media/medium/phases/phase/components/component\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_component\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_constitutive_relation.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_constitutive_relation — prj_constitutive_relation","title":"prj_constitutive_relation — prj_constitutive_relation","text":"tag: constitutive_relation","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_constitutive_relation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_constitutive_relation — prj_constitutive_relation","text":"","code":"prj_constitutive_relation( type, id = NULL, youngs_modulus = NULL, poissons_ratio = NULL, nonlinear_solver = NULL, behaviour = NULL, material_properties = NULL, shear_modulus = NULL, bulk_modulus = NULL, kappa = NULL, beta = NULL, gamma = NULL, hardening_modulus = NULL, alpha = NULL, delta = NULL, eps = NULL, m = NULL, alphap = NULL, deltap = NULL, epsp = NULL, mp = NULL, betap = NULL, gammap = NULL, tangent_type = NULL, damage_properties = NULL, youngs_moduli = NULL, shear_moduli = NULL, poissons_ratios = NULL, a = NULL, n = NULL, sigma0 = NULL, q = NULL, kelvin_shear_modulus = NULL, kelvin_viscosity = NULL, maxwell_shear_modulus = NULL, maxwell_bulk_modulus = NULL, maxwell_viscosity = NULL, dependency_parameter_mk = NULL, dependency_parameter_mvk = NULL, dependency_parameter_mvm = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_constitutive_relation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_constitutive_relation — prj_constitutive_relation","text":"type string: id Optional: youngs_modulus Optional: poissons_ratio Optional: nonlinear_solver Optional: behaviour Optional: material_properties Optional: shear_modulus Optional: bulk_modulus Optional: kappa Optional: beta Optional: gamma Optional: hardening_modulus Optional: alpha Optional: delta Optional: eps Optional: m Optional: alphap Optional: deltap Optional: epsp Optional: mp Optional: betap Optional: gammap Optional: tangent_type Optional: damage_properties Optional: youngs_moduli Optional: shear_moduli Optional: poissons_ratios Optional: Optional: n Optional: sigma0 Optional: q Optional: kelvin_shear_modulus Optional: kelvin_viscosity Optional: maxwell_shear_modulus Optional: maxwell_bulk_modulus Optional: maxwell_viscosity Optional: dependency_parameter_mk Optional: dependency_parameter_mvk Optional: dependency_parameter_mvm Optional:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_constitutive_relation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_constitutive_relation — prj_constitutive_relation","text":"","code":"prj_constitutive_relation( type = \"LinearElasticIsotropic\", youngs_modulus = \"E\", poissons_ratio = \"nu\" ) #> $type #> [1] \"LinearElasticIsotropic\" #> #> $id #> NULL #> #> $youngs_modulus #> [1] \"E\" #> #> $poissons_ratio #> [1] \"nu\" #> #> $nonlinear_solver #> NULL #> #> $behaviour #> NULL #> #> $material_properties #> NULL #> #> $shear_modulus #> NULL #> #> $bulk_modulus #> NULL #> #> $kappa #> NULL #> #> $beta #> NULL #> #> $gamma #> NULL #> #> $hardening_modulus #> NULL #> #> $alpha #> NULL #> #> $delta #> NULL #> #> $eps #> NULL #> #> $m #> NULL #> #> $alphap #> NULL #> #> $deltap #> NULL #> #> $epsp #> NULL #> #> $mp #> NULL #> #> $betap #> NULL #> #> $gammap #> NULL #> #> $tangent_type #> NULL #> #> $damage_properties #> NULL #> #> $youngs_moduli #> NULL #> #> $shear_moduli #> NULL #> #> $poissons_ratios #> NULL #> #> $a #> NULL #> #> $n #> NULL #> #> $sigma0 #> NULL #> #> $q #> NULL #> #> $kelvin_shear_modulus #> NULL #> #> $kelvin_viscosity #> NULL #> #> $maxwell_shear_modulus #> NULL #> #> $maxwell_bulk_modulus #> NULL #> #> $maxwell_viscosity #> NULL #> #> $dependency_parameter_mk #> NULL #> #> $dependency_parameter_mvk #> NULL #> #> $dependency_parameter_mvm #> NULL #> #> $xpath #> [1] \"processes/process/constitutive_relation\" #> #> $attr_names #> [1] \"id\" \"material_property\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_constitutive_relation\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_convergence_criterion.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_convergence_criterion — prj_convergence_criterion","title":"prj_convergence_criterion — prj_convergence_criterion","text":"tag: convergence_criterion","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_convergence_criterion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_convergence_criterion — prj_convergence_criterion","text":"","code":"prj_convergence_criterion( type, norm_type, abstol = NULL, reltol = NULL, abstols = NULL, reltols = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_convergence_criterion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_convergence_criterion — prj_convergence_criterion","text":"type string: Type norm_type string: ... abstol string | double: Absolute tolerance reltol string | double: Relative tolerance abstols string | numeric: Absolute tolerances reltols string | numeric: Relative tolerances","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_convergence_criterion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_convergence_criterion — prj_convergence_criterion","text":"","code":"prj_convergence_criterion( type = \"DeltaX\", norm_type = \"INFINITY_N\", abstol = 1e-08, reltol = 1e-10 ) #> $type #> [1] \"DeltaX\" #> #> $norm_type #> [1] \"INFINITY_N\" #> #> $abstol #> [1] 1e-08 #> #> $reltol #> [1] 1e-10 #> #> $abstols #> NULL #> #> $reltols #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/convergence_criterion\" #> [2] \"time_loop/global_process_coupling/convergence_criteria/convergence_criterion\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"abstols\" \"reltols\" #> #> attr(,\"class\") #> [1] \"prj_convergence_criterion\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_curve.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_curve — prj_curve","title":"prj_curve — prj_curve","text":"tag: curve, curve","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_curve.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_curve — prj_curve","text":"","code":"prj_curve(name, coords, values)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_curve.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_curve — prj_curve","text":"name string: Name curve coords string | numeric: Coordinates curve's values given values string | numeric: Values curve given coordinates","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_curve.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_curve — prj_curve","text":"","code":"prj_curve(name = \"Dirichlet_temporal\", coords = \"0 3\", values = \"200 200\") #> $name #> [1] \"Dirichlet_temporal\" #> #> $coords #> [1] 0 3 #> #> $values #> [1] 200 200 #> #> $xpath #> [1] \"curves/curve\" #> [2] \"processes/process/porous_medium/porous_medium/capillary_pressure/curve\" #> [3] \"processes/process/material_property/porous_medium/porous_medium/capillary_pressure/curve\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"coords\" \"values\" #> #> attr(,\"class\") #> [1] \"prj_curve\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_deactivated_subdomain.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_deactivated_subdomain — prj_deactivated_subdomain","title":"prj_deactivated_subdomain — prj_deactivated_subdomain","text":"tag: deactivated_subdomain","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_deactivated_subdomain.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_deactivated_subdomain — prj_deactivated_subdomain","text":"","code":"prj_deactivated_subdomain( material_ids, time_interval = NULL, time_curve = NULL, line_segment = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_deactivated_subdomain.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_deactivated_subdomain — prj_deactivated_subdomain","text":"material_ids string | double: time_interval Optional: list, numeric: time_curve Optional: line_segment Optional:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_deactivated_subdomain.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_deactivated_subdomain — prj_deactivated_subdomain","text":"","code":"prj_deactivated_subdomain(material_ids = 0, time_interval = list(start = \"0.51\", end = \"1.0\")) #> $material_ids #> [1] 0 #> #> $time_interval #> $time_interval$start #> [1] \"0.51\" #> #> $time_interval$end #> [1] \"1.0\" #> #> #> $time_curve #> NULL #> #> $line_segment #> NULL #> #> $xpath #> [1] \"process_variables/process_variable/deactivated_subdomains/deactivated_subdomain\" #> #> $attr_names #> NULL #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_deactivated_subdomain\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_eigen.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_eigen — prj_eigen","title":"prj_eigen — prj_eigen","text":"tag: eigen","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_eigen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_eigen — prj_eigen","text":"","code":"prj_eigen( solver_type, precon_type = NULL, max_iteration_step = NULL, error_tolerance = NULL, scaling = NULL, restart = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_eigen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_eigen — prj_eigen","text":"solver_type string: precon_type Optional: string: max_iteration_step Optional: string | double: ... error_tolerance Optional: string | double: ... scaling Optional: string | double: ... restart Optional: string | double: ...","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_eigen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_eigen — prj_eigen","text":"","code":"prj_eigen( solver_type = \"BiCGSTAB\", precon_type = \"ILUT\", max_iteration_step = 10000, error_tolerance = 1e-16 ) #> $solver_type #> [1] \"BiCGSTAB\" #> #> $precon_type #> [1] \"ILUT\" #> #> $max_iteration_step #> [1] 10000 #> #> $error_tolerance #> [1] 1e-16 #> #> $scaling #> NULL #> #> $restart #> NULL #> #> $xpath #> [1] \"linear_solvers/linear_solver/eigen\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_eigen\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_exchangers.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_exchangers — prj_exchangers","title":"prj_exchangers — prj_exchangers","text":"tag: exchangers","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_exchangers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_exchangers — prj_exchangers","text":"","code":"prj_exchangers(exchange_site)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_exchangers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_exchangers — prj_exchangers","text":"exchange_site list","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_flow_and_temperature_control.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","title":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","text":"tag: flow_and_temperature_control","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_flow_and_temperature_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","text":"","code":"prj_flow_and_temperature_control( type, flow_rate = NULL, temperature_curve = NULL, power = NULL, power_curve = NULL, flow_rate_curve = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_flow_and_temperature_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","text":"type string: flow_rate Optional: string | double: temperature_curve Optional: string: power Optional: string | double: power_curve Optional: string: flow_rate_curve Optional: string:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_flow_and_temperature_control.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","text":"","code":"prj_flow_and_temperature_control( type = \"TemperatureCurveConstantFlow\", flow_rate = 2e-04, temperature_curve = \"inflow_temperature\" ) #> $type #> [1] \"TemperatureCurveConstantFlow\" #> #> $flow_rate #> [1] 2e-04 #> #> $temperature_curve #> [1] \"inflow_temperature\" #> #> $power #> NULL #> #> $power_curve #> NULL #> #> $flow_rate_curve #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger/flow_and_temperature_control\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_flow_and_temperature_control\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fluid.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_fluid — prj_fluid","title":"prj_fluid — prj_fluid","text":"tag: fluid","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fluid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_fluid — prj_fluid","text":"","code":"prj_fluid( liquid_density, gas_density, liquid_viscosity, gas_viscosity, specific_heat_capacity_solid = NULL, specific_heat_capacity_water = NULL, specific_heat_capacity_air = NULL, specific_heat_capacity_water_vapor = NULL, thermal_conductivity_dry_solid = NULL, thermal_conductivity_wet_solid = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fluid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_fluid — prj_fluid","text":"liquid_density list: gas_density list: liquid_viscosity list: gas_viscosity list: specific_heat_capacity_solid Optional: specific_heat_capacity_water Optional: specific_heat_capacity_air Optional: specific_heat_capacity_water_vapor Optional: thermal_conductivity_dry_solid Optional: thermal_conductivity_wet_solid Optional:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fluid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_fluid — prj_fluid","text":"","code":"prj_fluid( liquid_density = list(type = \"Constant\", value = \" 1.e3 \"), gas_density = list(type = \"IdealGasLaw\", molar_mass = \" 0.002 \"), liquid_viscosity = list(type = \"Constant\", value = \" 3.171e-11 \"), gas_viscosity = list(type = \"Constant\", value = \" 2.8539e-13 \") ) #> $liquid_density #> $liquid_density$type #> [1] \"Constant\" #> #> $liquid_density$value #> [1] \" 1.e3 \" #> #> #> $gas_density #> $gas_density$type #> [1] \"IdealGasLaw\" #> #> $gas_density$molar_mass #> [1] \" 0.002 \" #> #> #> $liquid_viscosity #> $liquid_viscosity$type #> [1] \"Constant\" #> #> $liquid_viscosity$value #> [1] \" 3.171e-11 \" #> #> #> $gas_viscosity #> $gas_viscosity$type #> [1] \"Constant\" #> #> $gas_viscosity$value #> [1] \" 2.8539e-13 \" #> #> #> $specific_heat_capacity_solid #> NULL #> #> $specific_heat_capacity_water #> NULL #> #> $specific_heat_capacity_air #> NULL #> #> $specific_heat_capacity_water_vapor #> NULL #> #> $thermal_conductivity_dry_solid #> NULL #> #> $thermal_conductivity_wet_solid #> NULL #> #> $xpath #> [1] \"processes/process/material_property/fluid\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_fluid\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_model.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_fracture_model — prj_fracture_model","title":"prj_fracture_model — prj_fracture_model","text":"tag: fracture_model","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_model.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_fracture_model — prj_fracture_model","text":"","code":"prj_fracture_model( type, normal_stiffness, shear_stiffness, penalty_aperture_cutoff, tension_cutoff, fracture_toughness = NULL, peak_normal_traction = NULL, friction_angle = NULL, dilatancy_angle = NULL, cohesion = NULL, nonlinear_solver = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_model.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_fracture_model — prj_fracture_model","text":"type string: normal_stiffness string: shear_stiffness string: penalty_aperture_cutoff string | double: tension_cutoff string | double: fracture_toughness Optional: string: peak_normal_traction Optional: string: friction_angle Optional: string: dilatancy_angle Optional: string: cohesion Optional: string: nonlinear_solver Optional: list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_model.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_fracture_model — prj_fracture_model","text":"","code":"prj_fracture_model(type = \"LinearElasticIsotropic\", normal_stiffness = \"Kn\", shear_stiffness = \"Ks\", penalty_aperture_cutoff = 1e-05, tension_cutoff = 1) #> $type #> [1] \"LinearElasticIsotropic\" #> #> $normal_stiffness #> [1] \"Kn\" #> #> $shear_stiffness #> [1] \"Ks\" #> #> $penalty_aperture_cutoff #> [1] 1e-05 #> #> $tension_cutoff #> [1] 1 #> #> $fracture_toughness #> NULL #> #> $peak_normal_traction #> NULL #> #> $friction_angle #> NULL #> #> $dilatancy_angle #> NULL #> #> $cohesion #> NULL #> #> $nonlinear_solver #> NULL #> #> $xpath #> [1] \"processes/process/fracture_model\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_fracture_model\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_properties.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_fracture_properties — prj_fracture_properties","title":"prj_fracture_properties — prj_fracture_properties","text":"tag: fracture_properties","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_properties.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_fracture_properties — prj_fracture_properties","text":"","code":"prj_fracture_properties( material_id, initial_aperture, specific_storage = NULL, biot_coefficient = NULL, permeability_model = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_properties.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_fracture_properties — prj_fracture_properties","text":"material_id string | double: initial_aperture string: specific_storage Optional: string: biot_coefficient Optional: string: permeability_model Optional: list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_properties.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_fracture_properties — prj_fracture_properties","text":"","code":"prj_fracture_properties( material_id = 0, initial_aperture = \"aperture0\", specific_storage = \"S_f\", biot_coefficient = \"biot_f\", permeability_model = list(type = \"CubicLaw\") ) #> $material_id #> [1] 0 #> #> $initial_aperture #> [1] \"aperture0\" #> #> $specific_storage #> [1] \"S_f\" #> #> $biot_coefficient #> [1] \"biot_f\" #> #> $permeability_model #> $permeability_model$type #> [1] \"CubicLaw\" #> #> #> $xpath #> [1] \"processes/process/fracture_properties\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_fracture_properties\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_geometrical_set.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_geometrical_set — prj_geometrical_set","title":"prj_geometrical_set — prj_geometrical_set","text":"tag: geometrical_set","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_geometrical_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_geometrical_set — prj_geometrical_set","text":"","code":"prj_geometrical_set(name, geometry)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_geometrical_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_geometrical_set — prj_geometrical_set","text":"name string geometry string","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_global_process_coupling.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_global_process_coupling — prj_global_process_coupling","title":"prj_global_process_coupling — prj_global_process_coupling","text":"tag: global_process_coupling","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_global_process_coupling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_global_process_coupling — prj_global_process_coupling","text":"","code":"prj_global_process_coupling(max_iter, convergence_criteria)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_global_process_coupling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_global_process_coupling — prj_global_process_coupling","text":"max_iter string | double: Maximal number iterations convergence_criteria list, prj_convergence_criterion: Convergence criteria","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_global_process_coupling.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_global_process_coupling — prj_global_process_coupling","text":"","code":"prj_global_process_coupling( max_iter = 100, convergence_criteria = list( convergence_criterion = prj_convergence_criterion( type = \"DeltaX\", norm_type = \"INFINITY_N\", abstol = 1e-08, reltol = 1e-10 ) ) ) #> $max_iter #> [1] 100 #> #> $convergence_criteria #> $convergence_criteria$convergence_criterion #> $type #> [1] \"DeltaX\" #> #> $norm_type #> [1] \"INFINITY_N\" #> #> $abstol #> [1] 1e-08 #> #> $reltol #> [1] 1e-10 #> #> $abstols #> NULL #> #> $reltols #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/convergence_criterion\" #> [2] \"time_loop/global_process_coupling/convergence_criteria/convergence_criterion\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"abstols\" \"reltols\" #> #> attr(,\"class\") #> [1] \"prj_convergence_criterion\" #> #> #> $xpath #> [1] \"time_loop/global_process_coupling\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_global_process_coupling\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_insitu.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_insitu — prj_insitu","title":"prj_insitu — prj_insitu","text":"tag: insitu","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_insitu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_insitu — prj_insitu","text":"","code":"prj_insitu(scripts)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_insitu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_insitu — prj_insitu","text":"scripts character: Script names","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_insitu.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_insitu — prj_insitu","text":"","code":"prj_insitu(scripts = c(script = \"square_1e1_neumann-insitu.py\")) #> $scripts #> script #> \"square_1e1_neumann-insitu.py\" #> #> $xpath #> [1] \"insitu\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_insitu\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_jacobian_assembler.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_jacobian_assembler — prj_jacobian_assembler","title":"prj_jacobian_assembler — prj_jacobian_assembler","text":"tag: jacobian_assembler","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_jacobian_assembler.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_jacobian_assembler — prj_jacobian_assembler","text":"","code":"prj_jacobian_assembler( type, component_magnitudes = NULL, relative_epsilons = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_jacobian_assembler.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_jacobian_assembler — prj_jacobian_assembler","text":"type string: component_magnitudes Optional: string | double: relative_epsilons Optional: string | double:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_jacobian_assembler.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_jacobian_assembler — prj_jacobian_assembler","text":"","code":"prj_jacobian_assembler( type = \"CentralDifferences\", component_magnitudes = 1, relative_epsilons = 1e-08 ) #> $type #> [1] \"CentralDifferences\" #> #> $component_magnitudes #> [1] 1 #> #> $relative_epsilons #> [1] 1e-08 #> #> $xpath #> [1] \"processes/process/jacobian_assembler\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"component_magnitudes\" \"relative_epsilons\" #> #> attr(,\"class\") #> [1] \"prj_jacobian_assembler\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_kinetic_reactant.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_kinetic_reactant — prj_kinetic_reactant","title":"prj_kinetic_reactant — prj_kinetic_reactant","text":"S3 class describing .prj kinetic_reactant","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_kinetic_reactant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_kinetic_reactant — prj_kinetic_reactant","text":"","code":"prj_kinetic_reactant( name, initial_amount = NULL, chemical_formula = NULL, fix_amount = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_kinetic_reactant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_kinetic_reactant — prj_kinetic_reactant","text":"name component name initial_amount initial amount component chemical_formula chemical formula component fix_amount amount fixed ?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_kinetic_reactant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_kinetic_reactant — prj_kinetic_reactant","text":"","code":"prj_kinetic_reactant(name = \"Productc\", initial_amount = 1e-06) #> $name #> [1] \"Productc\" #> #> $initial_amount #> [1] 1e-06 #> #> $chemical_formula #> NULL #> #> $fix_amount #> NULL #> #> $xpath #> [1] \"chemical_system/kinetic_reactants/kinetic_reactant\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_kinetic_reactant\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_linear_solver.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_linear_solver — prj_linear_solver","title":"prj_linear_solver — prj_linear_solver","text":"tag: linear_solver","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_linear_solver.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_linear_solver — prj_linear_solver","text":"","code":"prj_linear_solver(name, eigen = NULL, lis = NULL, petsc = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_linear_solver.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_linear_solver — prj_linear_solver","text":"name string: name linear solver eigen Optional: list: ... lis Optional: string: ... petsc Optional: character: ...","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_linear_solver.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_linear_solver — prj_linear_solver","text":"","code":"prj_linear_solver( name = \"general_linear_solver\", eigen = prj_eigen( solver_type = \"BiCGSTAB\", precon_type = \"ILUT\", max_iteration_step = 10000, error_tolerance = 1e-16 ), lis = \"-i bicgstab -p ilu -tol 1e-16 -maxiter 10000\" ) #> $name #> [1] \"general_linear_solver\" #> #> $eigen #> $solver_type #> [1] \"BiCGSTAB\" #> #> $precon_type #> [1] \"ILUT\" #> #> $max_iteration_step #> [1] 10000 #> #> $error_tolerance #> [1] 1e-16 #> #> $scaling #> NULL #> #> $restart #> NULL #> #> $xpath #> [1] \"linear_solvers/linear_solver/eigen\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_eigen\" #> #> $lis #> [1] \"-i bicgstab -p ilu -tol 1e-16 -maxiter 10000\" #> #> $petsc #> NULL #> #> $xpath #> [1] \"linear_solvers/linear_solver\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_linear_solver\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_local_coordinate_system.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_local_coordinate_system — prj_local_coordinate_system","title":"prj_local_coordinate_system — prj_local_coordinate_system","text":"tag: local_coordinate_system","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_local_coordinate_system.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_local_coordinate_system — prj_local_coordinate_system","text":"","code":"prj_local_coordinate_system( basis_vector_0, basis_vector_1, basis_vector_2 = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_local_coordinate_system.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_local_coordinate_system — prj_local_coordinate_system","text":"basis_vector_0 string | double: basis vector basis_vector_1 string | double: basis vector basis_vector_2 Optional: string | double: basis vector","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_local_coordinate_system.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_local_coordinate_system — prj_local_coordinate_system","text":"","code":"prj_local_coordinate_system(basis_vector_0 = \"e0\", basis_vector_1 = \"e1\", basis_vector_2 = \"e2\") #> $basis_vector_0 #> [1] \"e0\" #> #> $basis_vector_1 #> [1] \"e1\" #> #> $basis_vector_2 #> [1] \"e2\" #> #> $xpath #> [1] \"local_coordinate_system\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_local_coordinate_system\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_material_property.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_material_property — prj_material_property","title":"prj_material_property — prj_material_property","text":"tag: material_property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_material_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_material_property — prj_material_property","text":"","code":"prj_material_property(fluid, porous_medium)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_material_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_material_property — prj_material_property","text":"fluid prj_fluid: porous_medium prj_porous_medium:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_material_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_material_property — prj_material_property","text":"","code":"prj_material_property( fluid = prj_fluid( liquid_density = list(type = \"Constant\", value = \" 1.e3 \"), gas_density = list(type = \"IdealGasLaw\", molar_mass = \" 0.002 \"), liquid_viscosity = list(type = \"Constant\", value = \" 3.171e-11 \"), gas_viscosity = list(type = \"Constant\", value = \" 2.8539e-13 \") ), porous_medium = list( porous_medium = prj_porous_medium( id = 0, permeability = list(permeability_tensor_entries = \"kappa1\", type = \"Constant\"), porosity = list(type = \"Constant\", porosity_parameter = \"constant_porosity_parameter\"), storage = list(type = \"Constant\", value = \" 0.0 \"), capillary_pressure = prj_capillary_pressure( type = \"vanGenuchten\", pd = 2e+06, sr = 0.4, smax = 1, m = 0.3288590604, pc_max = 2e+07, has_regularized = \"true\" ), relative_permeability = list( relative_permeability = prj_relative_permeability( type = \"NonWettingPhaseVanGenuchten\", sr = 0, smax = 0.6, m = 0.3288590604, krel_min = 0, id = \"0\" ) ) ) ) ) #> $fluid #> $liquid_density #> $liquid_density$type #> [1] \"Constant\" #> #> $liquid_density$value #> [1] \" 1.e3 \" #> #> #> $gas_density #> $gas_density$type #> [1] \"IdealGasLaw\" #> #> $gas_density$molar_mass #> [1] \" 0.002 \" #> #> #> $liquid_viscosity #> $liquid_viscosity$type #> [1] \"Constant\" #> #> $liquid_viscosity$value #> [1] \" 3.171e-11 \" #> #> #> $gas_viscosity #> $gas_viscosity$type #> [1] \"Constant\" #> #> $gas_viscosity$value #> [1] \" 2.8539e-13 \" #> #> #> $specific_heat_capacity_solid #> NULL #> #> $specific_heat_capacity_water #> NULL #> #> $specific_heat_capacity_air #> NULL #> #> $specific_heat_capacity_water_vapor #> NULL #> #> $thermal_conductivity_dry_solid #> NULL #> #> $thermal_conductivity_wet_solid #> NULL #> #> $xpath #> [1] \"processes/process/material_property/fluid\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_fluid\" #> #> $porous_medium #> $porous_medium$porous_medium #> $id #> [1] 0 #> #> $permeability #> $permeability$permeability_tensor_entries #> [1] \"kappa1\" #> #> $permeability$type #> [1] \"Constant\" #> #> #> $porosity #> $porosity$type #> [1] \"Constant\" #> #> $porosity$porosity_parameter #> [1] \"constant_porosity_parameter\" #> #> #> $storage #> $storage$type #> [1] \"Constant\" #> #> $storage$value #> [1] \" 0.0 \" #> #> #> $capillary_pressure #> $type #> [1] \"vanGenuchten\" #> #> $pd #> [1] 2e+06 #> #> $sr #> [1] 0.4 #> #> $smax #> [1] 1 #> #> $m #> [1] 0.3288591 #> #> $pc_max #> [1] 2e+07 #> #> $has_regularized #> [1] \"true\" #> #> $curve #> NULL #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/capillary_pressure\" #> [2] \"processes/process/porous_medium/porous_medium/capillary_pressure\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_capillary_pressure\" #> #> $relative_permeability #> $relative_permeability$relative_permeability #> $type #> [1] \"NonWettingPhaseVanGenuchten\" #> #> $sr #> [1] 0 #> #> $smax #> [1] 0.6 #> #> $m #> [1] 0.3288591 #> #> $krel_min #> [1] 0 #> #> $id #> [1] \"0\" #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/relative_permeability/relative_permeability\" #> [2] \"processes/process/porous_medium/porous_medium/relative_permeability\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_relative_permeability\" #> #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium\" #> [2] \"processes/process/porous_medium/porous_medium\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_porous_medium\" #> #> #> $xpath #> [1] \"processes/process/material_property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_material_property\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_medium.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_medium — prj_medium","title":"prj_medium — prj_medium","text":"tag: medium, specific medium optional id corresponding MaterialIDs","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_medium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_medium — prj_medium","text":"","code":"prj_medium(phases = NULL, properties = NULL, id = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_medium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_medium — prj_medium","text":"phases list, prj_phase: Optional: Medium phases properties list, prj_pr_property: Optional: Medium properties id string | double: Optional: ID corresponding MaterialIDs","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_medium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_medium — prj_medium","text":"","code":"prj_medium( phases = list( phase = prj_phase( type = \"Gas\", properties = list( property = prj_ph_property(name = \"viscosity\", type = \"Constant\", value = 1e-05) ) ), phase = prj_phase( type = \"Solid\", properties = list( property = prj_ph_property(name = \"porosity\", type = \"Constant\", value = 0.3) ) ) ), properties = list( property = prj_pr_property(name = \"reference_temperature\", type = \"Constant\", value = 293.15) ) ) #> $phases #> $phases$phase #> $type #> [1] \"Gas\" #> #> $properties #> $properties$property #> $name #> [1] \"viscosity\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 1e-05 #> #> $dvalue #> list() #> #> $reference_value #> NULL #> #> $independent_variable #> list() #> #> $offset #> NULL #> #> $exponent #> NULL #> #> $parameter_name #> NULL #> #> $swelling_pressures #> NULL #> #> $exponents #> NULL #> #> $lower_saturation_limit #> NULL #> #> $upper_saturation_limit #> NULL #> #> $tortuosity #> NULL #> #> $curve #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" \"exponents\" \"swelling_pressures\" #> #> $unwrap_on_exp #> [1] \"independent_variable\" \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_ph_property\" #> #> #> $components #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase\" #> #> $phases$phase #> $type #> [1] \"Solid\" #> #> $properties #> $properties$property #> $name #> [1] \"porosity\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 0.3 #> #> $dvalue #> list() #> #> $reference_value #> NULL #> #> $independent_variable #> list() #> #> $offset #> NULL #> #> $exponent #> NULL #> #> $parameter_name #> NULL #> #> $swelling_pressures #> NULL #> #> $exponents #> NULL #> #> $lower_saturation_limit #> NULL #> #> $upper_saturation_limit #> NULL #> #> $tortuosity #> NULL #> #> $curve #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" \"exponents\" \"swelling_pressures\" #> #> $unwrap_on_exp #> [1] \"independent_variable\" \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_ph_property\" #> #> #> $components #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase\" #> #> #> $properties #> $properties$property #> $name #> [1] \"reference_temperature\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 293.15 #> #> $parameter_name #> NULL #> #> $exponent #> NULL #> #> $residual_liquid_saturation #> NULL #> #> $residual_gas_saturation #> NULL #> #> $initial_porosity #> NULL #> #> $minimal_porosity #> NULL #> #> $maximal_porosity #> NULL #> #> $p_b #> NULL #> #> $independent_variable #> NULL #> #> $curve #> NULL #> #> $minimum_relative_permeability_liquid #> NULL #> #> $cutoff_value #> NULL #> #> $lambda #> NULL #> #> $min_relative_permeability #> NULL #> #> $initial_permeability #> NULL #> #> $maximum_permeability #> NULL #> #> $intrinsic_permeability #> NULL #> #> $initial_aperture #> NULL #> #> $mean_frac_distance #> NULL #> #> $mean_frac_distances #> NULL #> #> $threshold_strain #> NULL #> #> $threshold_strains #> NULL #> #> $fracture_normal #> NULL #> #> $fracture_normals #> NULL #> #> $fracture_rotation_xy #> NULL #> #> $fracture_rotation_yz #> NULL #> #> $reference_permeability #> NULL #> #> $fitting_factor #> NULL #> #> $cohesion #> NULL #> #> $friction_angle #> NULL #> #> $tensile_strength_parameter #> NULL #> #> $b1 #> NULL #> #> $b2 #> NULL #> #> $b3 #> NULL #> #> $minimum_permeability #> NULL #> #> $entry_pressure #> NULL #> #> $intrinsic_permeabilities #> NULL #> #> $exponents #> NULL #> #> $jacobian_factor #> NULL #> #> $dry_thermal_conductivity #> NULL #> #> $wet_thermal_conductivity #> NULL #> #> $mean_type #> NULL #> #> $dvalue #> list() #> #> $xpath #> [1] \"media/medium/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" #> #> $unwrap_on_exp #> [1] \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_pr_property\" #> #> #> $id #> NULL #> #> $xpath #> [1] \"media/medium\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_medium\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_micro_porosity.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_micro_porosity — prj_micro_porosity","title":"prj_micro_porosity — prj_micro_porosity","text":"tag: micro_porosity","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_micro_porosity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_micro_porosity — prj_micro_porosity","text":"","code":"prj_micro_porosity(mass_exchange_coefficient, nonlinear_solver)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_micro_porosity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_micro_porosity — prj_micro_porosity","text":"mass_exchange_coefficient Required: nonlinear_solver Required:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_nonlinear_solver.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_nonlinear_solver — prj_nonlinear_solver","title":"prj_nonlinear_solver — prj_nonlinear_solver","text":"tag: nonlinear_solver","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_nonlinear_solver.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_nonlinear_solver — prj_nonlinear_solver","text":"","code":"prj_nonlinear_solver(name, type, max_iter, linear_solver, damping = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_nonlinear_solver.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_nonlinear_solver — prj_nonlinear_solver","text":"name string: Name type string: Type max_iter string | double: Maximal number iterations linear_solver string: Name corresponding linear_solver damping Optional: string | double: Damping","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_nonlinear_solver.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_nonlinear_solver — prj_nonlinear_solver","text":"","code":"prj_nonlinear_solver( name = \"basic_newton\", type = \"Newton\", max_iter = 50, linear_solver = \"general_linear_solver\" ) #> $name #> [1] \"basic_newton\" #> #> $type #> [1] \"Newton\" #> #> $max_iter #> [1] 50 #> #> $linear_solver #> [1] \"general_linear_solver\" #> #> $damping #> NULL #> #> $xpath #> [1] \"nonlinear_solvers/nonlinear_solver\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_nonlinear_solver\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_output.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_output — prj_output","title":"prj_output — prj_output","text":"tag: output","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_output — prj_output","text":"","code":"prj_output( type, prefix, variables, suffix = NULL, timesteps = NULL, compress_output = NULL, data_mode = NULL, output_iteration_results = NULL, meshes = NULL, fixed_output_times = NULL, hdf = NULL, geometrical_sets = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_output — prj_output","text":"type string: prefix string: variables vector: suffix Optional: string: timesteps Optional: compress_output Optional: string: output compressed? Either \"true\" \"false\" data_mode Optional: string: output_iteration_results Optional: string: Either \"true\" \"false\" meshes Optional: list: list meshes fixed_output_times Optional: string | numeric: hdf Optional: numeric geometrical_sets Optional: list, prj_geometrical_set","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_output.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_output — prj_output","text":"","code":"prj_output( type = \"VTK\", prefix = \"flow_free_expansion\", variables = list( variable = \"displacement\", variable = \"pressure\" ), suffix = \"_ts_{:timestep}_t_{:time}\", timesteps = list(pair = list(1, each_steps = 1000)) ) #> $type #> [1] \"VTK\" #> #> $prefix #> [1] \"flow_free_expansion\" #> #> $variables #> $variables$variable #> [1] \"displacement\" #> #> $variables$variable #> [1] \"pressure\" #> #> #> $suffix #> [1] \"_ts_{:timestep}_t_{:time}\" #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1 #> #> $timesteps$pair$each_steps #> [1] 1000 #> #> #> #> $compress_output #> NULL #> #> $data_mode #> NULL #> #> $output_iteration_results #> NULL #> #> $meshes #> NULL #> #> $fixed_output_times #> NULL #> #> $hdf #> NULL #> #> $geometrical_sets #> NULL #> #> $xpath #> [1] \"time_loop/output\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"fixed_output_times\" #> #> attr(,\"class\") #> [1] \"prj_output\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_parameter.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_parameter — prj_parameter","title":"prj_parameter — prj_parameter","text":"tag: parameter","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_parameter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_parameter — prj_parameter","text":"","code":"prj_parameter( name, type, value = NULL, values = NULL, curve = NULL, parameter = NULL, group_id_property = NULL, field_name = NULL, mesh = NULL, time_series = NULL, use_local_coordinate_system = NULL, range = NULL, seed = NULL, ... )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_parameter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_parameter — prj_parameter","text":"name string: type string: value Optional: string | double: Parameter value values Optional: string | double: Parameter values curve Optional: string: parameter Optional: string: group_id_property Optional: string: field_name Optional: string: mesh Optional: string: time_series Optional: list: use_local_coordinate_system Optional: string, \"true\" | \"false\": range Optional: list seed Optional: number ... Optional: index_values expression tags (since can multiple)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_parameter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_parameter — prj_parameter","text":"","code":"prj_parameter(name = \"zero\", type = \"Constant\", value = 0) #> $name #> [1] \"zero\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 0 #> #> $values #> NULL #> #> $curve #> NULL #> #> $parameter #> NULL #> #> $group_id_property #> NULL #> #> $index_values #> list() #> #> $field_name #> NULL #> #> $mesh #> NULL #> #> $expression #> list() #> #> $time_series #> NULL #> #> $use_local_coordinate_system #> NULL #> #> $range #> NULL #> #> $seed #> NULL #> #> $xpath #> [1] \"parameters/parameter\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"values\" \"range\" #> #> $unwrap_on_exp #> [1] \"index_values\" \"expression\" #> #> attr(,\"class\") #> [1] \"prj_parameter\" prj_parameter(name = \"flux_in\", type = \"Constant\", value = 1e-04) #> $name #> [1] \"flux_in\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 1e-04 #> #> $values #> NULL #> #> $curve #> NULL #> #> $parameter #> NULL #> #> $group_id_property #> NULL #> #> $index_values #> list() #> #> $field_name #> NULL #> #> $mesh #> NULL #> #> $expression #> list() #> #> $time_series #> NULL #> #> $use_local_coordinate_system #> NULL #> #> $range #> NULL #> #> $seed #> NULL #> #> $xpath #> [1] \"parameters/parameter\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"values\" \"range\" #> #> $unwrap_on_exp #> [1] \"index_values\" \"expression\" #> #> attr(,\"class\") #> [1] \"prj_parameter\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_ph_property.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_ph_property — prj_ph_property","title":"prj_ph_property — prj_ph_property","text":"tag: property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_ph_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_ph_property — prj_ph_property","text":"","code":"prj_ph_property( name, type, value = NULL, reference_value = NULL, offset = NULL, exponent = NULL, parameter_name = NULL, swelling_pressures = NULL, exponents = NULL, lower_saturation_limit = NULL, upper_saturation_limit = NULL, tortuosity = NULL, curve = NULL, ... )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_ph_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_ph_property — prj_ph_property","text":"name string: type string: value Optional: reference_value Optional: offset Optional: exponent Optional: parameter_name Optional: swelling_pressures Optional: exponents Optional: lower_saturation_limit Optional: upper_saturation_limit Optional: tortuosity Optional: curve Optional: ... independent_variable, dvalue","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_ph_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_ph_property — prj_ph_property","text":"","code":"prj_ph_property(name = \"porosity\", type = \"Constant\", value = 0.3) #> $name #> [1] \"porosity\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 0.3 #> #> $dvalue #> list() #> #> $reference_value #> NULL #> #> $independent_variable #> list() #> #> $offset #> NULL #> #> $exponent #> NULL #> #> $parameter_name #> NULL #> #> $swelling_pressures #> NULL #> #> $exponents #> NULL #> #> $lower_saturation_limit #> NULL #> #> $upper_saturation_limit #> NULL #> #> $tortuosity #> NULL #> #> $curve #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" \"exponents\" \"swelling_pressures\" #> #> $unwrap_on_exp #> [1] \"independent_variable\" \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_ph_property\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_phase — prj_phase","title":"prj_phase — prj_phase","text":"tag: phase, coherent material homogeneous properties","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_phase — prj_phase","text":"","code":"prj_phase(type, properties = NULL, components = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_phase — prj_phase","text":"type string: Phase type (get valid types get_valid_phase_types()) properties list, prj_pr_property: Properties components list, components","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_phase — prj_phase","text":"","code":"prj_phase( type = \"Solid\", properties = list( property = prj_ph_property(name = \"porosity\", type = \"Constant\", value = 0.3) ) ) #> $type #> [1] \"Solid\" #> #> $properties #> $properties$property #> $name #> [1] \"porosity\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 0.3 #> #> $dvalue #> list() #> #> $reference_value #> NULL #> #> $independent_variable #> list() #> #> $offset #> NULL #> #> $exponent #> NULL #> #> $parameter_name #> NULL #> #> $swelling_pressures #> NULL #> #> $exponents #> NULL #> #> $lower_saturation_limit #> NULL #> #> $upper_saturation_limit #> NULL #> #> $tortuosity #> NULL #> #> $curve #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" \"exponents\" \"swelling_pressures\" #> #> $unwrap_on_exp #> [1] \"independent_variable\" \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_ph_property\" #> #> #> $components #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase_component.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_phase_component — prj_phase_component","title":"prj_phase_component — prj_phase_component","text":"S3 class describing .prj phase_component","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase_component.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_phase_component — prj_phase_component","text":"","code":"prj_phase_component(name, saturation_index, initial_amount = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase_component.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_phase_component — prj_phase_component","text":"name component name saturation_index saturation index component initial_amount optional: initial amount component","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase_component.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_phase_component — prj_phase_component","text":"","code":"prj_phase_component( name = \"Calcite\", saturation_index = 0, initial_amount = 0.000207 ) #> $name #> [1] \"Calcite\" #> #> $saturation_index #> [1] 0 #> #> $initial_amount #> [1] 0.000207 #> #> $xpath #> [1] \"chemical_system/equilibrium_reactants/phase_component\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase_component\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phasefield_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_phasefield_parameters — prj_phasefield_parameters","title":"prj_phasefield_parameters — prj_phasefield_parameters","text":"tag: phasefield_parameters","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phasefield_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_phasefield_parameters — prj_phasefield_parameters","text":"","code":"prj_phasefield_parameters( residual_stiffness, crack_resistance, crack_length_scale, kinetic_coefficient = NULL, history_field = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phasefield_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_phasefield_parameters — prj_phasefield_parameters","text":"residual_stiffness string: crack_resistance string: crack_length_scale string: kinetic_coefficient string: history_field Optional: string:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phasefield_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_phasefield_parameters — prj_phasefield_parameters","text":"","code":"prj_phasefield_parameters( residual_stiffness = \"k\", crack_resistance = \"gc\", crack_length_scale = \"ls\", kinetic_coefficient = \"M\", history_field = \"H\" ) #> $residual_stiffness #> [1] \"k\" #> #> $crack_resistance #> [1] \"gc\" #> #> $crack_length_scale #> [1] \"ls\" #> #> $kinetic_coefficient #> [1] \"M\" #> #> $history_field #> [1] \"H\" #> #> $xpath #> [1] \"processes/process/phasefield_parameters\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phasefield_parameters\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pipes.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_pipes — prj_pipes","title":"prj_pipes — prj_pipes","text":"tag: pipes","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pipes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_pipes — prj_pipes","text":"","code":"prj_pipes( longitudinal_dispersion_length, inlet = NULL, outlet = NULL, distance_between_pipes = NULL, outer = NULL, inner = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pipes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_pipes — prj_pipes","text":"longitudinal_dispersion_length string | double: inlet Optional: list: outlet Optional: list: distance_between_pipes Optional: string | double: outer Optional: list: inner Optional: list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pipes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_pipes — prj_pipes","text":"","code":"prj_pipes( longitudinal_dispersion_length = 0.001, inlet = list( diameter = \" 0.013665\", wall_thickness = \"0.003035\", wall_thermal_conductivity = \"0.39\" ), outlet = list( diameter = \"0.013665\", wall_thickness = \"0.003035\", wall_thermal_conductivity = \"0.39\" ), distance_between_pipes = 0.053 ) #> $longitudinal_dispersion_length #> [1] 0.001 #> #> $inlet #> $inlet$diameter #> [1] \" 0.013665\" #> #> $inlet$wall_thickness #> [1] \"0.003035\" #> #> $inlet$wall_thermal_conductivity #> [1] \"0.39\" #> #> #> $outlet #> $outlet$diameter #> [1] \"0.013665\" #> #> $outlet$wall_thickness #> [1] \"0.003035\" #> #> $outlet$wall_thermal_conductivity #> [1] \"0.39\" #> #> #> $distance_between_pipes #> [1] 0.053 #> #> $outer #> NULL #> #> $inner #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger/pipes\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_pipes\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_porous_medium.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_porous_medium — prj_porous_medium","title":"prj_porous_medium — prj_porous_medium","text":"tag: porous_medium","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_porous_medium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_porous_medium — prj_porous_medium","text":"","code":"prj_porous_medium( id, permeability, porosity, storage, capillary_pressure, relative_permeability )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_porous_medium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_porous_medium — prj_porous_medium","text":"id string | double: permeability list: porosity list: storage list: capillary_pressure prj_capillary_pressure: relative_permeability list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_porous_medium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_porous_medium — prj_porous_medium","text":"","code":"prj_porous_medium( id = 0, permeability = list(permeability_tensor_entries = \"kappa1\", type = \"Constant\"), porosity = list(type = \"Constant\", porosity_parameter = \"constant_porosity_parameter\"), storage = list(type = \"Constant\", value = \" 0.0 \"), capillary_pressure = prj_capillary_pressure( type = \"vanGenuchten\", pd = 2e+06, sr = 0.4, smax = 1, m = 0.3288590604, pc_max = 2e+07, has_regularized = \"true\" ), relative_permeability = list( relative_permeability = prj_relative_permeability( type = \"NonWettingPhaseVanGenuchten\", sr = 0, smax = 0.6, m = 0.3288590604, krel_min = 0, id = \"0\" ) ) ) #> $id #> [1] 0 #> #> $permeability #> $permeability$permeability_tensor_entries #> [1] \"kappa1\" #> #> $permeability$type #> [1] \"Constant\" #> #> #> $porosity #> $porosity$type #> [1] \"Constant\" #> #> $porosity$porosity_parameter #> [1] \"constant_porosity_parameter\" #> #> #> $storage #> $storage$type #> [1] \"Constant\" #> #> $storage$value #> [1] \" 0.0 \" #> #> #> $capillary_pressure #> $type #> [1] \"vanGenuchten\" #> #> $pd #> [1] 2e+06 #> #> $sr #> [1] 0.4 #> #> $smax #> [1] 1 #> #> $m #> [1] 0.3288591 #> #> $pc_max #> [1] 2e+07 #> #> $has_regularized #> [1] \"true\" #> #> $curve #> NULL #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/capillary_pressure\" #> [2] \"processes/process/porous_medium/porous_medium/capillary_pressure\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_capillary_pressure\" #> #> $relative_permeability #> $relative_permeability$relative_permeability #> $type #> [1] \"NonWettingPhaseVanGenuchten\" #> #> $sr #> [1] 0 #> #> $smax #> [1] 0.6 #> #> $m #> [1] 0.3288591 #> #> $krel_min #> [1] 0 #> #> $id #> [1] \"0\" #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/relative_permeability/relative_permeability\" #> [2] \"processes/process/porous_medium/porous_medium/relative_permeability\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_relative_permeability\" #> #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium\" #> [2] \"processes/process/porous_medium/porous_medium\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_porous_medium\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pr_property.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_pr_property — prj_pr_property","title":"prj_pr_property — prj_pr_property","text":"tag: property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pr_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_pr_property — prj_pr_property","text":"","code":"prj_pr_property( name, type, value = NULL, parameter_name = NULL, exponent = NULL, residual_liquid_saturation = NULL, residual_gas_saturation = NULL, initial_porosity = NULL, minimal_porosity = NULL, maximal_porosity = NULL, p_b = NULL, independent_variable = NULL, curve = NULL, minimum_relative_permeability_liquid = NULL, cutoff_value = NULL, lambda = NULL, min_relative_permeability = NULL, initial_permeability = NULL, maximum_permeability = NULL, intrinsic_permeability = NULL, initial_aperture = NULL, mean_frac_distance = NULL, mean_frac_distances = NULL, threshold_strain = NULL, threshold_strains = NULL, fracture_normal = NULL, fracture_normals = NULL, fracture_rotation_xy = NULL, fracture_rotation_yz = NULL, reference_permeability = NULL, fitting_factor = NULL, cohesion = NULL, friction_angle = NULL, tensile_strength_parameter = NULL, b1 = NULL, b2 = NULL, b3 = NULL, minimum_permeability = NULL, entry_pressure = NULL, intrinsic_permeabilities = NULL, exponents = NULL, jacobian_factor = NULL, dry_thermal_conductivity = NULL, wet_thermal_conductivity = NULL, mean_type = NULL, ... )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pr_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_pr_property — prj_pr_property","text":"name string: type string: value Optional: parameter_name Optional: exponent Optional: residual_liquid_saturation Optional: residual_gas_saturation Optional: initial_porosity Optional: minimal_porosity Optional: maximal_porosity Optional: p_b Optional: independent_variable Optional: curve Optional: minimum_relative_permeability_liquid Optional: cutoff_value Optional: lambda Optional: min_relative_permeability Optional: initial_permeability Optional: maximum_permeability Optional: intrinsic_permeability Optional: initial_aperture Optional: mean_frac_distance Optional: mean_frac_distances Optional: numeric vector threshold_strain Optional: threshold_strains Optional: numeric vector fracture_normal Optional: fracture_normals Optional: numeric vector fracture_rotation_xy Optional: fracture_rotation_yz Optional: reference_permeability Optional: fitting_factor Optional: cohesion Optional: friction_angle Optional: tensile_strength_parameter Optional: b1 Optional: b2 Optional: b3 Optional: minimum_permeability Optional: entry_pressure Optional: intrinsic_permeabilities Optional: exponents Optional: jacobian_factor Optional: dry_thermal_conductivity Optional: wet_thermal_conductivity Optional: mean_type Optional: string ... dvalue","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pr_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_pr_property — prj_pr_property","text":"","code":"prj_pr_property(name = \"reference_temperature\", type = \"Constant\", value = 293.15) #> $name #> [1] \"reference_temperature\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 293.15 #> #> $parameter_name #> NULL #> #> $exponent #> NULL #> #> $residual_liquid_saturation #> NULL #> #> $residual_gas_saturation #> NULL #> #> $initial_porosity #> NULL #> #> $minimal_porosity #> NULL #> #> $maximal_porosity #> NULL #> #> $p_b #> NULL #> #> $independent_variable #> NULL #> #> $curve #> NULL #> #> $minimum_relative_permeability_liquid #> NULL #> #> $cutoff_value #> NULL #> #> $lambda #> NULL #> #> $min_relative_permeability #> NULL #> #> $initial_permeability #> NULL #> #> $maximum_permeability #> NULL #> #> $intrinsic_permeability #> NULL #> #> $initial_aperture #> NULL #> #> $mean_frac_distance #> NULL #> #> $mean_frac_distances #> NULL #> #> $threshold_strain #> NULL #> #> $threshold_strains #> NULL #> #> $fracture_normal #> NULL #> #> $fracture_normals #> NULL #> #> $fracture_rotation_xy #> NULL #> #> $fracture_rotation_yz #> NULL #> #> $reference_permeability #> NULL #> #> $fitting_factor #> NULL #> #> $cohesion #> NULL #> #> $friction_angle #> NULL #> #> $tensile_strength_parameter #> NULL #> #> $b1 #> NULL #> #> $b2 #> NULL #> #> $b3 #> NULL #> #> $minimum_permeability #> NULL #> #> $entry_pressure #> NULL #> #> $intrinsic_permeabilities #> NULL #> #> $exponents #> NULL #> #> $jacobian_factor #> NULL #> #> $dry_thermal_conductivity #> NULL #> #> $wet_thermal_conductivity #> NULL #> #> $mean_type #> NULL #> #> $dvalue #> list() #> #> $xpath #> [1] \"media/medium/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" #> #> $unwrap_on_exp #> [1] \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_pr_property\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_process — prj_process","title":"prj_process — prj_process","text":"tag: process (parent tag: processes)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_process — prj_process","text":"","code":"prj_process( name, type, integration_order, process_variables, secondary_variables = NULL, specific_body_force = NULL, solid_density = NULL, dimension = NULL, coupling_scheme = NULL, darcy_gravity = NULL, reference_temperature = NULL, fracture_model = NULL, jacobian_assembler = NULL, internal_length = NULL, mass_lumping = NULL, porosity = NULL, calculatesurfaceflux = NULL, intrinsic_permeability = NULL, specific_storage = NULL, fluid_viscosity = NULL, biot_coefficient = NULL, fluid_density = NULL, initial_effective_stress = NULL, initial_fracture_effective_stress = NULL, phasefield_parameters = NULL, deactivate_matrix_in_flow = NULL, borehole_heat_exchangers = NULL, temperature = NULL, reactive_system = NULL, fluid_specific_heat_source = NULL, fluid_specific_isobaric_heat_capacity = NULL, solid_hydraulic_permeability = NULL, solid_specific_heat_source = NULL, solid_heat_conductivity = NULL, solid_specific_isobaric_heat_capacity = NULL, tortuosity = NULL, diffusion_coefficient = NULL, solid_density_dry = NULL, solid_density_initial = NULL, characteristic_pressure = NULL, characteristic_temperature = NULL, characteristic_vapour_mass_fraction = NULL, output_element_matrices = NULL, material_property = NULL, diffusion_coeff_component_b = NULL, diffusion_coeff_component_a = NULL, hydro_crack_scheme = NULL, at_num = NULL, initial_stress = NULL, split_method = NULL, reg_param = NULL, thermal_parameters = NULL, non_advective_form = NULL, fluid = NULL, porous_medium = NULL, decay_rate = NULL, fluid_reference_density = NULL, retardation_factor = NULL, solute_dispersivity_longitudinal = NULL, solute_dispersivity_transverse = NULL, molecular_diffusion_coefficient = NULL, pf_irrv = NULL, micro_porosity = NULL, explicit_hm_coupling_in_unsaturated_zone = NULL, simplified_elasticity = NULL, chemically_induced_porosity_change = NULL, use_server_communication = NULL, phasefield_model = NULL, irreversible_threshold = NULL, tabular_file = NULL, temperature_field = NULL, use_stokes_brinkman_form = NULL, energy_split_model = NULL, softening_curve = NULL, characteristic_length = NULL, coupling_scheme_parameter = NULL, numerical_stabilization = NULL, aperture_size = NULL, linear = NULL, pressurized_crack_scheme = NULL, subtype = NULL, apply_body_force_for_deformation = NULL, ... )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_process — prj_process","text":"name string: type string: integration_order string | double: process_variables list, character: secondary_variables Optional: specific_body_force Optional: solid_density Optional: dimension Optional: coupling_scheme Optional: darcy_gravity Optional: reference_temperature Optional: fracture_model Optional: jacobian_assembler Optional: internal_length Optional: mass_lumping Optional: porosity Optional: calculatesurfaceflux Optional: intrinsic_permeability Optional: specific_storage Optional: fluid_viscosity Optional: biot_coefficient Optional: fluid_density Optional: initial_effective_stress Optional: initial_fracture_effective_stress Optional: phasefield_parameters Optional: deactivate_matrix_in_flow Optional: borehole_heat_exchangers Optional: temperature Optional: reactive_system Optional: fluid_specific_heat_source Optional: fluid_specific_isobaric_heat_capacity Optional: solid_hydraulic_permeability Optional: solid_specific_heat_source Optional: solid_heat_conductivity Optional: solid_specific_isobaric_heat_capacity Optional: tortuosity Optional: diffusion_coefficient Optional: solid_density_dry Optional: solid_density_initial Optional: characteristic_pressure Optional: characteristic_temperature Optional: characteristic_vapour_mass_fraction Optional: output_element_matrices Optional: material_property Optional: diffusion_coeff_component_b Optional: diffusion_coeff_component_a Optional: hydro_crack_scheme Optional: at_num Optional: initial_stress Optional: split_method Optional: reg_param Optional: thermal_parameters Optional: non_advective_form Optional: fluid Optional: porous_medium Optional: decay_rate Optional: fluid_reference_density Optional: retardation_factor Optional: solute_dispersivity_longitudinal Optional: solute_dispersivity_transverse Optional: molecular_diffusion_coefficient Optional: pf_irrv Optional: micro_porosity Optional: explicit_hm_coupling_in_unsaturated_zone Optional: simplified_elasticity Optional: character chemically_induced_porosity_change Optional: character use_server_communication Optional: phasefield_model Optional: irreversible_threshold Optional: numeric tabular_file Optional: character temperature_field Optional: character use_stokes_brinkman_form Optional: character energy_split_model Optional: string softening_curve Optional: string characteristic_length Optional: double coupling_scheme_parameter Optional: double numerical_stabilization Optional: list aperture_size Optional: list linear Optional: pressurized_crack_scheme Optional: subtype Optional: apply_body_force_for_deformation Optional: ... Optional: fracture_properties, constitutive_relation","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_process — prj_process","text":"","code":"prj_process( name = \"HM\", type = \"HYDRO_MECHANICS\", integration_order = 3, process_variables = list(displacement = \"displacement\", pressure = \"pressure\"), secondary_variables = list( secondary_variable = c(internal_name = \"sigma_xx\", output_name = \"sigma_xx\"), secondary_variable = c(internal_name = \"sigma_yy\", output_name = \"sigma_yy\") ), specific_body_force = c(0, 0, 0), dimension = 3, constitutive_relation = prj_constitutive_relation( type = \"LinearElasticIsotropic\", youngs_modulus = \"E\", poissons_ratio = \"nu\" ) ) #> $name #> [1] \"HM\" #> #> $type #> [1] \"HYDRO_MECHANICS\" #> #> $integration_order #> [1] 3 #> #> $process_variables #> $process_variables$displacement #> [1] \"displacement\" #> #> $process_variables$pressure #> [1] \"pressure\" #> #> #> $secondary_variables #> $secondary_variables$secondary_variable #> internal_name output_name #> \"sigma_xx\" \"sigma_xx\" #> #> $secondary_variables$secondary_variable #> internal_name output_name #> \"sigma_yy\" \"sigma_yy\" #> #> #> $specific_body_force #> [1] 0 0 0 #> #> $constitutive_relation #> $constitutive_relation$constitutive_relation #> $type #> [1] \"LinearElasticIsotropic\" #> #> $id #> NULL #> #> $youngs_modulus #> [1] \"E\" #> #> $poissons_ratio #> [1] \"nu\" #> #> $nonlinear_solver #> NULL #> #> $behaviour #> NULL #> #> $material_properties #> NULL #> #> $shear_modulus #> NULL #> #> $bulk_modulus #> NULL #> #> $kappa #> NULL #> #> $beta #> NULL #> #> $gamma #> NULL #> #> $hardening_modulus #> NULL #> #> $alpha #> NULL #> #> $delta #> NULL #> #> $eps #> NULL #> #> $m #> NULL #> #> $alphap #> NULL #> #> $deltap #> NULL #> #> $epsp #> NULL #> #> $mp #> NULL #> #> $betap #> NULL #> #> $gammap #> NULL #> #> $tangent_type #> NULL #> #> $damage_properties #> NULL #> #> $youngs_moduli #> NULL #> #> $shear_moduli #> NULL #> #> $poissons_ratios #> NULL #> #> $a #> NULL #> #> $n #> NULL #> #> $sigma0 #> NULL #> #> $q #> NULL #> #> $kelvin_shear_modulus #> NULL #> #> $kelvin_viscosity #> NULL #> #> $maxwell_shear_modulus #> NULL #> #> $maxwell_bulk_modulus #> NULL #> #> $maxwell_viscosity #> NULL #> #> $dependency_parameter_mk #> NULL #> #> $dependency_parameter_mvk #> NULL #> #> $dependency_parameter_mvm #> NULL #> #> $xpath #> [1] \"processes/process/constitutive_relation\" #> #> $attr_names #> [1] \"id\" \"material_property\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_constitutive_relation\" #> #> #> $solid_density #> NULL #> #> $dimension #> [1] 3 #> #> $coupling_scheme #> NULL #> #> $darcy_gravity #> NULL #> #> $reference_temperature #> NULL #> #> $fracture_model #> NULL #> #> $fracture_properties #> named list() #> #> $jacobian_assembler #> NULL #> #> $internal_length #> NULL #> #> $mass_lumping #> NULL #> #> $porosity #> NULL #> #> $calculatesurfaceflux #> NULL #> #> $intrinsic_permeability #> NULL #> #> $specific_storage #> NULL #> #> $fluid_viscosity #> NULL #> #> $biot_coefficient #> NULL #> #> $fluid_density #> NULL #> #> $initial_effective_stress #> NULL #> #> $initial_fracture_effective_stress #> NULL #> #> $phasefield_parameters #> NULL #> #> $deactivate_matrix_in_flow #> NULL #> #> $borehole_heat_exchangers #> NULL #> #> $temperature #> NULL #> #> $reactive_system #> NULL #> #> $fluid_specific_heat_source #> NULL #> #> $fluid_specific_isobaric_heat_capacity #> NULL #> #> $solid_hydraulic_permeability #> NULL #> #> $solid_specific_heat_source #> NULL #> #> $solid_heat_conductivity #> NULL #> #> $solid_specific_isobaric_heat_capacity #> NULL #> #> $tortuosity #> NULL #> #> $diffusion_coefficient #> NULL #> #> $solid_density_dry #> NULL #> #> $solid_density_initial #> NULL #> #> $characteristic_pressure #> NULL #> #> $characteristic_temperature #> NULL #> #> $characteristic_vapour_mass_fraction #> NULL #> #> $output_element_matrices #> NULL #> #> $material_property #> NULL #> #> $diffusion_coeff_component_b #> NULL #> #> $diffusion_coeff_component_a #> NULL #> #> $hydro_crack_scheme #> NULL #> #> $at_num #> NULL #> #> $initial_stress #> NULL #> #> $split_method #> NULL #> #> $reg_param #> NULL #> #> $thermal_parameters #> NULL #> #> $non_advective_form #> NULL #> #> $fluid #> NULL #> #> $porous_medium #> NULL #> #> $decay_rate #> NULL #> #> $fluid_reference_density #> NULL #> #> $retardation_factor #> NULL #> #> $solute_dispersivity_longitudinal #> NULL #> #> $solute_dispersivity_transverse #> NULL #> #> $molecular_diffusion_coefficient #> NULL #> #> $pf_irrv #> NULL #> #> $micro_porosity #> NULL #> #> $explicit_hm_coupling_in_unsaturated_zone #> NULL #> #> $simplified_elasticity #> NULL #> #> $chemically_induced_porosity_change #> NULL #> #> $use_server_communication #> NULL #> #> $phasefield_model #> NULL #> #> $irreversible_threshold #> NULL #> #> $tabular_file #> NULL #> #> $temperature_field #> NULL #> #> $use_stokes_brinkman_form #> NULL #> #> $energy_split_model #> NULL #> #> $softening_curve #> NULL #> #> $characteristic_length #> NULL #> #> $coupling_scheme_parameter #> NULL #> #> $numerical_stabilization #> NULL #> #> $aperture_size #> NULL #> #> $linear #> NULL #> #> $pressurized_crack_scheme #> NULL #> #> $subtype #> NULL #> #> $apply_body_force_for_deformation #> NULL #> #> $xpath #> [1] \"processes/process\" #> #> $attr_names #> [1] \"secondary_variable\" #> #> $flatten_on_exp #> [1] \"specific_body_force\" #> #> $unwrap_on_exp #> [1] \"fracture_properties\" \"constitutive_relation\" #> #> attr(,\"class\") #> [1] \"prj_process\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process_variable.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_process_variable — prj_process_variable","title":"prj_process_variable — prj_process_variable","text":"tag: process_variable","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process_variable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_process_variable — prj_process_variable","text":"","code":"prj_process_variable( name, components, order, initial_condition, boundary_conditions = NULL, source_terms = NULL, mesh = NULL, deactivated_subdomains = NULL, compensate_non_equilibrium_initial_residuum = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process_variable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_process_variable — prj_process_variable","text":"name string: name process variable components string | double: order string | double: initial_condition string: boundary_conditions list, prj_boundary_condition: source_terms Optional: list, prj_source_term: mesh Optional: string: list: deactivated_subdomains Optional: list, prj_deactivated_subdomain: compensate_non_equilibrium_initial_residuum Optional: string","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process_variable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_process_variable — prj_process_variable","text":"","code":"prj_process_variable( name = \"pressure\", components = 1, order = 1, initial_condition = \"pressure0\", boundary_conditions = list( boundary_condition = prj_boundary_condition( type = \"Neumann\", parameter = \"flux_in\", geometrical_set = \"cube_1x1x1_geometry\", geometry = \"left\", component = 0 ) ) ) #> $name #> [1] \"pressure\" #> #> $components #> [1] 1 #> #> $order #> [1] 1 #> #> $initial_condition #> [1] \"pressure0\" #> #> $boundary_conditions #> $boundary_conditions$boundary_condition #> $type #> [1] \"Neumann\" #> #> $parameter #> [1] \"flux_in\" #> #> $geometrical_set #> [1] \"cube_1x1x1_geometry\" #> #> $geometry #> [1] \"left\" #> #> $component #> [1] 0 #> #> $mesh #> NULL #> #> $alpha #> NULL #> #> $u_0 #> NULL #> #> $constraint_type #> NULL #> #> $constraining_process_variable #> NULL #> #> $constraint_threshold #> NULL #> #> $constraint_direction #> NULL #> #> $area_parameter #> NULL #> #> $bc_object #> NULL #> #> $flush_stdout #> NULL #> #> $property_name #> NULL #> #> $initial_value_parameter #> NULL #> #> $constant_name #> NULL #> #> $coefficient_current_variable_name #> NULL #> #> $coefficient_other_variable_name #> NULL #> #> $coefficient_mixed_variables_name #> NULL #> #> $threshold_parameter #> NULL #> #> $comparison_operator #> NULL #> #> $time_interval #> NULL #> #> $xpath #> [1] \"process_variables/process_variable/boundary_conditions/boundary_condition\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_boundary_condition\" #> #> #> $source_terms #> NULL #> #> $mesh #> NULL #> #> $deactivated_subdomains #> NULL #> #> $compensate_non_equilibrium_initial_residuum #> NULL #> #> $xpath #> [1] \"process_variables/process_variable\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_process_variable\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_python_script.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_python_script — prj_python_script","title":"prj_python_script — prj_python_script","text":"tag: python_script","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_python_script.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_python_script — prj_python_script","text":"","code":"prj_python_script(file_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_python_script.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_python_script — prj_python_script","text":"file_path string: Path name python script file (*.py).","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_python_script.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_python_script — prj_python_script","text":"","code":"prj_python_script(file_path = \"bcs_laplace_eq.py\") #> [[1]] #> [1] \"bcs_laplace_eq.py\" #> #> $xpath #> [1] \"python_script\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_python_script\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_rate — prj_rate","title":"prj_rate — prj_rate","text":"S3 class describing .prj rate","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_rate — prj_rate","text":"","code":"prj_rate(kinetic_reactant, expression)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_rate — prj_rate","text":"kinetic_reactant string: References kinetic_reactant object expression character: Statements","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_rate — prj_rate","text":"","code":"prj_rate( kinetic_reactant = \"Productc\", expression = list( statement = \"Km = 10\", statement = \"U = 1e-3\", statement = \"rate = U * TOT(\\\"Synthetica\\\") / (Km + TOT(\\\"Syntheticb\\\"))\", statement = \"moles = - rate * TIME\", statement = \"save moles\" ) ) #> $kinetic_reactant #> [1] \"Productc\" #> #> $expression #> $expression$statement #> [1] \"Km = 10\" #> #> $expression$statement #> [1] \"U = 1e-3\" #> #> $expression$statement #> [1] \"rate = U * TOT(\\\"Synthetica\\\") / (Km + TOT(\\\"Syntheticb\\\"))\" #> #> $expression$statement #> [1] \"moles = - rate * TIME\" #> #> $expression$statement #> [1] \"save moles\" #> #> #> $xpath #> [1] \"chemical_system/rates/rate\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_rate\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_relative_permeability.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_relative_permeability — prj_relative_permeability","title":"prj_relative_permeability — prj_relative_permeability","text":"tag: relative_permeability","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_relative_permeability.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_relative_permeability — prj_relative_permeability","text":"","code":"prj_relative_permeability(type, sr, smax, m, krel_min, id = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_relative_permeability.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_relative_permeability — prj_relative_permeability","text":"type string: sr string | number: smax string | number: m string | number: krel_min string | number: id string: Optional:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_relative_permeability.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_relative_permeability — prj_relative_permeability","text":"","code":"prj_relative_permeability( type = \"NonWettingPhaseVanGenuchten\", sr = 0, smax = 0.6, m = 0.3288590604, krel_min = 0, id = \"0\" ) #> $type #> [1] \"NonWettingPhaseVanGenuchten\" #> #> $sr #> [1] 0 #> #> $smax #> [1] 0.6 #> #> $m #> [1] 0.3288591 #> #> $krel_min #> [1] 0 #> #> $id #> [1] \"0\" #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/relative_permeability/relative_permeability\" #> [2] \"processes/process/porous_medium/porous_medium/relative_permeability\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_relative_permeability\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_search_length_algorithm.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_search_length_algorithm — prj_search_length_algorithm","title":"prj_search_length_algorithm — prj_search_length_algorithm","text":"tag: search_length_algorithm","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_search_length_algorithm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_search_length_algorithm — prj_search_length_algorithm","text":"","code":"prj_search_length_algorithm(type, value = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_search_length_algorithm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_search_length_algorithm — prj_search_length_algorithm","text":"type string: type value string | double: value","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_search_length_algorithm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_search_length_algorithm — prj_search_length_algorithm","text":"","code":"prj_search_length_algorithm(type = \"fixed\", value = 1e-06) #> $type #> [1] \"fixed\" #> #> $value #> [1] 1e-06 #> #> $xpath #> [1] \"search_length_algorithm\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_search_length_algorithm\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_solution.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_solution — prj_solution","title":"prj_solution — prj_solution","text":"tag: solution","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_solution — prj_solution","text":"","code":"prj_solution( temperature, pressure, pe, components, charge_balance = NULL, fixing_pe = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_solution — prj_solution","text":"temperature string | double: Temperature pressure string | double: Pressure pe string | double: pe components list: Components charge_balance Optional: string: Charge balance fixing_pe Optional: string","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_solution — prj_solution","text":"","code":"prj_solution( temperature = 25, pressure = 1, pe = 4, components = list( component = \"C(4)\", component = \"Ca\" ), charge_balance = \"pH\" ) #> $temperature #> [1] 25 #> #> $pressure #> [1] 1 #> #> $pe #> [1] 4 #> #> $components #> $components$component #> [1] \"C(4)\" #> #> $components$component #> [1] \"Ca\" #> #> #> $charge_balance #> [1] \"pH\" #> #> $fixing_pe #> NULL #> #> $xpath #> [1] \"chemical_system/solution\" #> #> $attr_names #> [1] \"fixing_pe\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_solution\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_source_term.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_source_term — prj_source_term","title":"prj_source_term — prj_source_term","text":"tag: source_term","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_source_term.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_source_term — prj_source_term","text":"","code":"prj_source_term( type, parameter = NULL, geometrical_set = NULL, geometry = NULL, mesh = NULL, source_term_object = NULL, flush_stdout = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_source_term.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_source_term — prj_source_term","text":"type string: parameter Optional: string: geometrical_set Optional: string: geometry Optional: string: mesh Optional: string: source_term_object Optional: string: flush_stdout Optional: string:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_source_term.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_source_term — prj_source_term","text":"","code":"prj_source_term( type = \"Nodal\", parameter = \"sourceterm_heat_transfer_coefficient\", geometrical_set = \"geometry\", geometry = \"po0\" ) #> $type #> [1] \"Nodal\" #> #> $parameter #> [1] \"sourceterm_heat_transfer_coefficient\" #> #> $geometrical_set #> [1] \"geometry\" #> #> $geometry #> [1] \"po0\" #> #> $mesh #> NULL #> #> $source_term_object #> NULL #> #> $flush_stdout #> NULL #> #> $xpath #> [1] \"process_variables/process_variable/source_terms/source_term\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_source_term\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_submesh_residuum_output.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_submesh_residuum_output — prj_submesh_residuum_output","title":"prj_submesh_residuum_output — prj_submesh_residuum_output","text":"tag: submesh_residuum_output","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_submesh_residuum_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_submesh_residuum_output — prj_submesh_residuum_output","text":"","code":"prj_submesh_residuum_output( type, prefix, variables, suffix = NULL, timesteps = NULL, compress_output = NULL, data_mode = NULL, output_iteration_results = NULL, meshes = NULL, fixed_output_times = NULL, hdf = NULL, geometrical_sets = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_submesh_residuum_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_submesh_residuum_output — prj_submesh_residuum_output","text":"type string: prefix string: variables vector: suffix Optional: string: timesteps Optional: compress_output Optional: string: output compressed? Either \"true\" \"false\" data_mode Optional: string: output_iteration_results Optional: string: Either \"true\" \"false\" meshes Optional: list: list meshes fixed_output_times Optional: string | numeric: hdf Optional: numeric geometrical_sets Optional: list, prj_geometrical_set","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_surface.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_surface — prj_surface","title":"prj_surface — prj_surface","text":"tag: surface","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_surface.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_surface — prj_surface","text":"","code":"prj_surface(site_unit = NULL, ...)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_surface.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_surface — prj_surface","text":"site_unit Optional: string ... site","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_loop.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_time_loop — prj_time_loop","title":"prj_time_loop — prj_time_loop","text":"tag: time_loop","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_loop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_time_loop — prj_time_loop","text":"","code":"prj_time_loop( processes, output, global_process_coupling = NULL, submesh_residuum_output = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_loop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_time_loop — prj_time_loop","text":"processes list, prj_tl_process: output prj_output: global_process_coupling Optional: prj_global_process_coupling: submesh_residuum_output Optional: prj_submesh_residuum_output:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_loop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_time_loop — prj_time_loop","text":"","code":"prj_time_loop( processes = list( process = prj_tl_process( ref = \"HM\", nonlinear_solver = \"basic_newton\", convergence_criterion = prj_convergence_criterion( type = \"DeltaX\", norm_type = \"NORM2\", reltol = 1e-08 ), time_discretization = list(type = \"BackwardEuler\"), time_stepping = prj_time_stepping( type = \"FixedTimeStepping\", t_initial = 0, t_end = 10000, timesteps = list(pair = list(1000, delta_t = 10)) ) ) ), output = prj_output( type = \"VTK\", prefix = \"flow_free_expansion\", variables = list( variable = \"displacement\", variable = \"pressure\" ), suffix = \"_ts_{:timestep}_t_{:time}\", timesteps = list(pair = list(1, each_steps = 1000)) ) ) #> $processes #> $processes$process #> $ref #> [1] \"HM\" #> #> $nonlinear_solver #> [1] \"basic_newton\" #> #> $convergence_criterion #> $type #> [1] \"DeltaX\" #> #> $norm_type #> [1] \"NORM2\" #> #> $abstol #> NULL #> #> $reltol #> [1] 1e-08 #> #> $abstols #> NULL #> #> $reltols #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/convergence_criterion\" #> [2] \"time_loop/global_process_coupling/convergence_criteria/convergence_criterion\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"abstols\" \"reltols\" #> #> attr(,\"class\") #> [1] \"prj_convergence_criterion\" #> #> $time_discretization #> $time_discretization$type #> [1] \"BackwardEuler\" #> #> #> $time_stepping #> $type #> [1] \"FixedTimeStepping\" #> #> $t_initial #> [1] 0 #> #> $t_end #> [1] 10000 #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1000 #> #> $timesteps$pair$delta_t #> [1] 10 #> #> #> #> $initial_dt #> NULL #> #> $minimum_dt #> NULL #> #> $maximum_dt #> NULL #> #> $number_iterations #> NULL #> #> $multiplier #> NULL #> #> $dt_guess #> NULL #> #> $dt_min #> NULL #> #> $dt_max #> NULL #> #> $rel_dt_min #> NULL #> #> $rel_dt_max #> NULL #> #> $tol #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/time_stepping\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"number_iterations\" \"multiplier\" #> #> attr(,\"class\") #> [1] \"prj_time_stepping\" #> #> $compensate_non_equilibrium_initial_residuum #> NULL #> #> $xpath #> [1] \"time_loop/processes/process\" #> #> $attr_names #> [1] \"ref\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_tl_process\" #> #> #> $output #> $type #> [1] \"VTK\" #> #> $prefix #> [1] \"flow_free_expansion\" #> #> $variables #> $variables$variable #> [1] \"displacement\" #> #> $variables$variable #> [1] \"pressure\" #> #> #> $suffix #> [1] \"_ts_{:timestep}_t_{:time}\" #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1 #> #> $timesteps$pair$each_steps #> [1] 1000 #> #> #> #> $compress_output #> NULL #> #> $data_mode #> NULL #> #> $output_iteration_results #> NULL #> #> $meshes #> NULL #> #> $fixed_output_times #> NULL #> #> $hdf #> NULL #> #> $geometrical_sets #> NULL #> #> $xpath #> [1] \"time_loop/output\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"fixed_output_times\" #> #> attr(,\"class\") #> [1] \"prj_output\" #> #> $global_process_coupling #> NULL #> #> $submesh_residuum_output #> NULL #> #> $xpath #> [1] \"time_loop\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_time_loop\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_stepping.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_time_stepping — prj_time_stepping","title":"prj_time_stepping — prj_time_stepping","text":"tag: time_stepping","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_stepping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_time_stepping — prj_time_stepping","text":"","code":"prj_time_stepping( type, t_initial = NULL, t_end = NULL, timesteps = NULL, initial_dt = NULL, minimum_dt = NULL, maximum_dt = NULL, number_iterations = NULL, multiplier = NULL, dt_guess = NULL, dt_min = NULL, dt_max = NULL, rel_dt_min = NULL, rel_dt_max = NULL, tol = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_stepping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_time_stepping — prj_time_stepping","text":"type string: t_initial Optional: string | double: t_end Optional: string | double: timesteps Optional: list: initial_dt Optional: string | double: minimum_dt Optional: string | double: maximum_dt Optional: string | double: number_iterations Optional: string | numeric: multiplier Optional: string | numeric: dt_guess Optional: string | double: dt_min Optional: string | double: dt_max Optional: string | double: rel_dt_min Optional: string | double: rel_dt_max Optional: string | double: tol Optional: string | double:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_stepping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_time_stepping — prj_time_stepping","text":"","code":"prj_time_stepping( type = \"FixedTimeStepping\", t_initial = 0, t_end = 10000, timesteps = list(pair = list(1000, delta_t = 10)) ) #> $type #> [1] \"FixedTimeStepping\" #> #> $t_initial #> [1] 0 #> #> $t_end #> [1] 10000 #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1000 #> #> $timesteps$pair$delta_t #> [1] 10 #> #> #> #> $initial_dt #> NULL #> #> $minimum_dt #> NULL #> #> $maximum_dt #> NULL #> #> $number_iterations #> NULL #> #> $multiplier #> NULL #> #> $dt_guess #> NULL #> #> $dt_min #> NULL #> #> $dt_max #> NULL #> #> $rel_dt_min #> NULL #> #> $rel_dt_max #> NULL #> #> $tol #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/time_stepping\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"number_iterations\" \"multiplier\" #> #> attr(,\"class\") #> [1] \"prj_time_stepping\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_tl_process.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_tl_process — prj_tl_process","title":"prj_tl_process — prj_tl_process","text":"tag: process (parent: time_loop, processes!)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_tl_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_tl_process — prj_tl_process","text":"","code":"prj_tl_process( ref, nonlinear_solver, convergence_criterion, time_discretization, time_stepping, compensate_non_equilibrium_initial_residuum = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_tl_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_tl_process — prj_tl_process","text":"ref string: References prj_process object name nonlinear_solver string: convergence_criterion prj_convergence_criterion: time_discretization vector: time_stepping prj_time_stepping: compensate_non_equilibrium_initial_residuum string: Optional: Either \"true\" \"false\"","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_tl_process.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_tl_process — prj_tl_process","text":"","code":"prj_tl_process( ref = \"HM\", nonlinear_solver = \"basic_newton\", convergence_criterion = prj_convergence_criterion( type = \"DeltaX\", norm_type = \"NORM2\", reltol = 1e-08 ), time_discretization = list(type = \"BackwardEuler\"), time_stepping = prj_time_stepping( type = \"FixedTimeStepping\", t_initial = 0, t_end = 10000, timesteps = list(pair = list(1000, delta_t = 10)) ) ) #> $ref #> [1] \"HM\" #> #> $nonlinear_solver #> [1] \"basic_newton\" #> #> $convergence_criterion #> $type #> [1] \"DeltaX\" #> #> $norm_type #> [1] \"NORM2\" #> #> $abstol #> NULL #> #> $reltol #> [1] 1e-08 #> #> $abstols #> NULL #> #> $reltols #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/convergence_criterion\" #> [2] \"time_loop/global_process_coupling/convergence_criteria/convergence_criterion\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"abstols\" \"reltols\" #> #> attr(,\"class\") #> [1] \"prj_convergence_criterion\" #> #> $time_discretization #> $time_discretization$type #> [1] \"BackwardEuler\" #> #> #> $time_stepping #> $type #> [1] \"FixedTimeStepping\" #> #> $t_initial #> [1] 0 #> #> $t_end #> [1] 10000 #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1000 #> #> $timesteps$pair$delta_t #> [1] 10 #> #> #> #> $initial_dt #> NULL #> #> $minimum_dt #> NULL #> #> $maximum_dt #> NULL #> #> $number_iterations #> NULL #> #> $multiplier #> NULL #> #> $dt_guess #> NULL #> #> $dt_min #> NULL #> #> $dt_max #> NULL #> #> $rel_dt_min #> NULL #> #> $rel_dt_max #> NULL #> #> $tol #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/time_stepping\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"number_iterations\" \"multiplier\" #> #> attr(,\"class\") #> [1] \"prj_time_stepping\" #> #> $compensate_non_equilibrium_initial_residuum #> NULL #> #> $xpath #> [1] \"time_loop/processes/process\" #> #> $attr_names #> [1] \"ref\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_tl_process\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_vtkdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_vtkdiff — prj_vtkdiff","title":"prj_vtkdiff — prj_vtkdiff","text":"tag: vtkdiff","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_vtkdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_vtkdiff — prj_vtkdiff","text":"","code":"prj_vtkdiff( field, absolute_tolerance, relative_tolerance, file = NULL, regex = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_vtkdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_vtkdiff — prj_vtkdiff","text":"field string: ... absolute_tolerance string | double: Absolute tolerance relative_tolerance string | double: Relative tolerance file string: Optional: File regex string: Optional: regular expression","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_vtkdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_vtkdiff — prj_vtkdiff","text":"","code":"prj_vtkdiff(field = \"displacement\", absolute_tolerance = 1e-15, relative_tolerance = 0, regex = \"gravity_pcs_0_ts_.*_t_.*.vtu\") #> $field #> [1] \"displacement\" #> #> $absolute_tolerance #> [1] 1e-15 #> #> $relative_tolerance #> [1] 0 #> #> $file #> NULL #> #> $regex #> [1] \"gravity_pcs_0_ts_.*_t_.*.vtu\" #> #> $xpath #> [1] \"test_definition/vtkdiff\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_vtkdiff\""},{"path":"https://joboog.github.io/r2ogs6/reference/read_in_prj.html","id":null,"dir":"Reference","previous_headings":"","what":"read_in_prj — read_in_prj","title":"read_in_prj — read_in_prj","text":"Wrapper function read whole .prj file","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/read_in_prj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read_in_prj — read_in_prj","text":"","code":"read_in_prj( ogs6_obj, prj_path, read_in_gml, read_in_vtu = FALSE, read_includes = FALSE )"},{"path":"https://joboog.github.io/r2ogs6/reference/read_in_prj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_in_prj — read_in_prj","text":"ogs6_obj OGS6: Simulation object prj_path string: Path .prj file read read_in_gml flag: Optional: .gml file just copied read ? parameter missing .gml file contains <= options(\"r2ogs6.max_lines_gml\"), .gml read . Else, geometry reference saved. read_in_vtu flag: .vtu file just copied read read_includes flag: files referenced include tages read ?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/set_ogs6_bin_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Set default OpenGeoSys 6 binary path — set_ogs6_bin_path","title":"Set default OpenGeoSys 6 binary path — set_ogs6_bin_path","text":"function automatically detects temporarily sets path OpenGeoSys (OGS) binary within active Python virtual environment. typically called installing OGS using `install_ogs()` function. permanent setting OGS binary path, consider define `r2ogs6.default_ogs6_bin_path` `config.yml` file.'","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/set_ogs6_bin_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set default OpenGeoSys 6 binary path — set_ogs6_bin_path","text":"","code":"set_ogs6_bin_path()"},{"path":"https://joboog.github.io/r2ogs6/reference/set_ogs6_bin_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set default OpenGeoSys 6 binary path — set_ogs6_bin_path","text":"None, sets option `r2ogs6.default_ogs6_bin_path` point detected OGS binary path.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/xpaths_for_classes.html","id":null,"dir":"Reference","previous_headings":"","what":"xpaths_for_classes — xpaths_for_classes","title":"xpaths_for_classes — xpaths_for_classes","text":"Path .xml document containing information .prj file structure","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/xpaths_for_classes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"xpaths_for_classes — xpaths_for_classes","text":"","code":"xpaths_for_classes"},{"path":"https://joboog.github.io/r2ogs6/reference/xpaths_for_classes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"xpaths_for_classes — xpaths_for_classes","text":"list: named list character vectors names r2ogs6 class names values corresponding xpaths","code":""}] +[{"path":"https://joboog.github.io/r2ogs6/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"How to Contribute to r2ogs6","title":"How to Contribute to r2ogs6","text":"happy contributions!","code":""},{"path":"https://joboog.github.io/r2ogs6/CONTRIBUTING.html","id":"bug-reports","dir":"","previous_headings":"","what":"Bug reports?","title":"How to Contribute to r2ogs6","text":"Please open issue bug , set bugfix label, add clear problem description, , possible add minimal working example.","code":""},{"path":"https://joboog.github.io/r2ogs6/CONTRIBUTING.html","id":"new-features","dir":"","previous_headings":"","what":"New features?","title":"How to Contribute to r2ogs6","text":"Open new issue idea.","code":""},{"path":"https://joboog.github.io/r2ogs6/CONTRIBUTING.html","id":"contribute-code","dir":"","previous_headings":"","what":"Contribute code?","title":"How to Contribute to r2ogs6","text":"Clone repo. Add author contributor DESCRIPTION. Add code. Push repo submit merge request.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. 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States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. However, include work’s System Libraries, general-purpose tools generally available free programs used unmodified performing activities part work. example, Corresponding Source includes interface definition files associated source files work, source code shared libraries dynamically linked subprograms work specifically designed require, intimate data communication control flow subprograms parts work. Corresponding Source need include anything users can regenerate automatically parts Corresponding Source. Corresponding Source work source code form work.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"2-basic-permissions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"2. Basic Permissions","title":"GNU General Public License","text":"rights granted License granted term copyright Program, irrevocable provided stated conditions met. License explicitly affirms unlimited permission run unmodified Program. output running covered work covered License output, given content, constitutes covered work. License acknowledges rights fair use equivalent, provided copyright law. may make, run propagate covered works convey, without conditions long license otherwise remains force. may convey covered works others sole purpose make modifications exclusively , provide facilities running works, provided comply terms License conveying material control copyright. thus making running covered works must exclusively behalf, direction control, terms prohibit making copies copyrighted material outside relationship . Conveying circumstances permitted solely conditions stated . Sublicensing allowed; section 10 makes unnecessary.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"3-protecting-users-legal-rights-from-anti-circumvention-law","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"3. Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. Conveying Verbatim Copies","title":"GNU General Public License","text":"may convey verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice; keep intact notices stating License non-permissive terms added accord section 7 apply code; keep intact notices absence warranty; give recipients copy License along Program. may charge price price copy convey, may offer support warranty protection fee.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. 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Conveying Non-Source Forms","title":"GNU General Public License","text":"may convey covered work object code form terms sections 4 5, provided also convey machine-readable Corresponding Source terms License, one ways: ) Convey object code , embodied , physical product (including physical distribution medium), accompanied Corresponding Source fixed durable physical medium customarily used software interchange. b) Convey object code , embodied , physical product (including physical distribution medium), accompanied written offer, valid least three years valid long offer spare parts customer support product model, give anyone possesses object code either (1) copy Corresponding Source software product covered License, durable physical medium customarily used software interchange, price reasonable cost physically performing conveying source, (2) access copy Corresponding Source network server charge. c) Convey individual copies object code copy written offer provide Corresponding Source. alternative allowed occasionally noncommercially, received object code offer, accord subsection 6b. d) Convey object code offering access designated place (gratis charge), offer equivalent access Corresponding Source way place charge. need require recipients copy Corresponding Source along object code. place copy object code network server, Corresponding Source may different server (operated third party) supports equivalent copying facilities, provided maintain clear directions next object code saying find Corresponding Source. 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Access network may denied modification materially adversely affects operation network violates rules protocols communication across network. Corresponding Source conveyed, Installation Information provided, accord section must format publicly documented (implementation available public source code form), must require special password key unpacking, reading copying.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"7-additional-terms","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"7. Additional Terms","title":"GNU General Public License","text":"“Additional permissions” terms supplement terms License making exceptions one conditions. Additional permissions applicable entire Program shall treated though included License, extent valid applicable law. additional permissions apply part Program, part may used separately permissions, entire Program remains governed License without regard additional permissions. convey copy covered work, may option remove additional permissions copy, part . (Additional permissions may written require removal certain cases modify work.) may place additional permissions material, added covered work, can give appropriate copyright permission. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. Termination rights section terminate licenses parties received copies rights License. rights terminated permanently reinstated, qualify receive new licenses material section 10.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"9-acceptance-not-required-for-having-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"9. Acceptance Not Required for Having Copies","title":"GNU General Public License","text":"required accept License order receive run copy Program. Ancillary propagation covered work occurring solely consequence using peer--peer transmission receive copy likewise require acceptance. However, nothing License grants permission propagate modify covered work. actions infringe copyright accept License. Therefore, modifying propagating covered work, indicate acceptance License .","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"10-automatic-licensing-of-downstream-recipients","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"10. Automatic Licensing of Downstream Recipients","title":"GNU General Public License","text":"time convey covered work, recipient automatically receives license original licensors, run, modify propagate work, subject License. responsible enforcing compliance third parties License. “entity transaction” transaction transferring control organization, substantially assets one, subdividing organization, merging organizations. propagation covered work results entity transaction, party transaction receives copy work also receives whatever licenses work party’s predecessor interest give previous paragraph, plus right possession Corresponding Source work predecessor interest, predecessor can get reasonable efforts. may impose restrictions exercise rights granted affirmed License. example, may impose license fee, royalty, charge exercise rights granted License, may initiate litigation (including cross-claim counterclaim lawsuit) alleging patent claim infringed making, using, selling, offering sale, importing Program portion .","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"11-patents","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"11. Patents","title":"GNU General Public License","text":"“contributor” copyright holder authorizes use License Program work Program based. work thus licensed called contributor’s “contributor version”. contributor’s “essential patent claims” patent claims owned controlled contributor, whether already acquired hereafter acquired, infringed manner, permitted License, making, using, selling contributor version, include claims infringed consequence modification contributor version. purposes definition, “control” includes right grant patent sublicenses manner consistent requirements License. contributor grants non-exclusive, worldwide, royalty-free patent license contributor’s essential patent claims, make, use, sell, offer sale, import otherwise run, modify propagate contents contributor version. following three paragraphs, “patent license” express agreement commitment, however denominated, enforce patent (express permission practice patent covenant sue patent infringement). “grant” patent license party means make agreement commitment enforce patent party. convey covered work, knowingly relying patent license, Corresponding Source work available anyone copy, free charge terms License, publicly available network server readily accessible means, must either (1) cause Corresponding Source available, (2) arrange deprive benefit patent license particular work, (3) arrange, manner consistent requirements License, extend patent license downstream recipients. “Knowingly relying” means actual knowledge , patent license, conveying covered work country, recipient’s use covered work country, infringe one identifiable patents country reason believe valid. , pursuant connection single transaction arrangement, convey, propagate procuring conveyance , covered work, grant patent license parties receiving covered work authorizing use, propagate, modify convey specific copy covered work, patent license grant automatically extended recipients covered work works based . patent license “discriminatory” include within scope coverage, prohibits exercise , conditioned non-exercise one rights specifically granted License. may convey covered work party arrangement third party business distributing software, make payment third party based extent activity conveying work, third party grants, parties receive covered work , discriminatory patent license () connection copies covered work conveyed (copies made copies), (b) primarily connection specific products compilations contain covered work, unless entered arrangement, patent license granted, prior 28 March 2007. Nothing License shall construed excluding limiting implied license defenses infringement may otherwise available applicable patent law.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"12-no-surrender-of-others-freedom","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"12. No Surrender of Others’ Freedom","title":"GNU General Public License","text":"conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. convey covered work satisfy simultaneously obligations License pertinent obligations, consequence may convey . example, agree terms obligate collect royalty conveying convey Program, way satisfy terms License refrain entirely conveying Program.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"13-use-with-the-gnu-affero-general-public-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"13. Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://joboog.github.io/r2ogs6/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":"`r2ogs6` is an R-API to the open-source multiphysics simulator [OpenGeoSys 6](https://www.opengeosys.org). Copyright (C) 2021 Helmholtz Centre for Environmental Research - UFZ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . r2ogs6 Copyright (C) 2021 Helmholtz Centre for Environmental Research - UFZ This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"hi-there","dir":"Articles","previous_headings":"","what":"Hi there!","title":"r2ogs6 Developer Guide","text":"Welcome dev guide r2ogs6. collection tips, useful info (admittedly warnings) hopefully make life bit easier developing package.","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"the-basics","dir":"Articles","previous_headings":"","what":"The basics","title":"r2ogs6 Developer Guide","text":"dive implementation details, take look exactly package structured first. r2ogs6 developed using workflow described . strongly recommend keeping way save time headaches. … main folder R/ find lot scripts, can grouped following categories: export_*.R export functions generate_*.R code generation read_in_*.R import functions ogs6_*.R simulation class definitions prj_*.R class definitions XML tags found .prj file *_utils.R utility functions used multiple scripts","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"the-classes","dir":"Articles","previous_headings":"","what":"The classes","title":"r2ogs6 Developer Guide","text":"r2ogs6 largely built top S3 classes moment. reasons elaborate later, viable switch R6 classes. let’s look first. ….","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"generating-new-classes","dir":"Articles","previous_headings":"","what":"Generating new classes","title":"r2ogs6 Developer Guide","text":"’ve familiarized OpenGeoSys 6, know lot, lot mean LOT parameters special cases regarding .prj XML tags. nice new class based tag, consider . save () bit typing, ’ve written useful functions .","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"analyse_xml","dir":"Articles","previous_headings":"Generating new classes","what":"analyse_xml()","title":"r2ogs6 Developer Guide","text":"first arguably important one analyse_xml(). matches files folder, reads XML searches XML elements given name. analyses elements returns useful information , namely names attributes child elements. prints summary findings also returns list look moment. used function two things: Analysing … . Secondly, soon decided tags represented class, used function output class generation.","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"generate_","dir":"Articles","previous_headings":"Generating new classes","what":"generate_*()","title":"r2ogs6 Developer Guide","text":"say .prj files stored folder. show workflow small dataset (, folder two .prj files) , path usually passed analyse_xml() directory containing benchmark files OpenGeoSys 6 can downloaded . Now say decided going make class based element tag name nonlinear_solver. readability reasons, store results analyse_xml() variable pass generator function. want, can skip step call analyse_xml() generator function directly. First, define path specify files ending .prj parsed. ’m looking elements named nonlinear_solver, ’m looking whole document. often isn’t best option since sometimes nodes may name contain different things depending exact position document, also case . narrow , change xpath accordingly. Now can sure future class generated correct parameters. analyse_xml() returns named list invisibly, let’s short look . can see list contains xpath parameter passed analyse_xml(), along three named logical vectors called children, attributes both_sorted respectively. can read like : attribute child element specified xpath always occurred, required parameter new class. Else, optional parameter. logical vectors sorted occurrency, rarest children attributes go end logical vector. Now, let’s generate code! S3 classes, generate constructor like : S3 classes, generate helper like : R6 classes, generate constructor like : Ta-daa, now nice stubs. Copy script R folder package, add documentation validation ’re almost done.","code":"test_folder <- system.file(\"extdata/vignettes_data/analyse_xml_demo\", package = \"r2ogs6\") analysis_results <- analyse_xml(path = test_folder, pattern = \"\\\\.prj$\", xpath = \"//nonlinear_solver\", print_findings = TRUE) #> #> I parsed 2 valid XML files matching your pattern. #> #> I found at least one element named nonlinear_solver in the following file(s): #> beam.prj #> beam3d.prj #> #> In total, I found 5 element(s) named nonlinear_solver. #> #> These are the child elements I found: #> name ex_occ p_occ total total_mean #> 1 name 2 0.4 2 0.4 #> 2 type 2 0.4 2 0.4 #> 3 max_iter 2 0.4 2 0.4 #> 4 linear_solver 2 0.4 2 0.4 #> 5 maximum_iterations 1 0.2 1 0.2 #> 6 error_tolerance 1 0.2 1 0.2 #> 7 damping 1 0.2 1 0.2 analysis_results <- analyse_xml(path = test_folder, pattern = \"\\\\.prj$\", xpath = \"/OpenGeoSysProject/nonlinear_solvers/nonlinear_solver\", print_findings = TRUE) #> #> I parsed 2 valid XML files matching your pattern. #> #> I found at least one element named nonlinear_solver in the following file(s): #> beam.prj #> beam3d.prj #> #> In total, I found 2 element(s) named nonlinear_solver. #> #> These are the child elements I found: #> name ex_occ p_occ total total_mean #> 1 name 2 1.0 2 1.0 #> 2 type 2 1.0 2 1.0 #> 3 max_iter 2 1.0 2 1.0 #> 4 linear_solver 2 1.0 2 1.0 #> 5 damping 1 0.5 1 0.5 analysis_results #> $xpath #> [1] \"/OpenGeoSysProject/nonlinear_solvers/nonlinear_solver\" #> #> $children #> name type max_iter linear_solver damping #> TRUE TRUE TRUE TRUE FALSE #> #> $attributes #> logical(0) #> #> $both_sorted #> name type max_iter linear_solver damping #> TRUE TRUE TRUE TRUE FALSE generate_constructor(params = analysis_results, print_result = TRUE) #> new_prj_nonlinear_solver <- function(name, #> type, #> max_iter, #> linear_solver, #> damping = NULL) { #> structure(list(name = name, #> type = type, #> max_iter = max_iter, #> linear_solver = linear_solver, #> damping = damping, #> xpath = \"nonlinear_solvers/nonlinear_solver\", #> attr_names = c(), #> flatten_on_exp = character() #> ), #> class = \"prj_nonlinear_solver\" #> ) #> } #> generate_helper(params = analysis_results, print_result = TRUE) #> #'prj_nonlinear_solver #> #'@description tag: nonlinear_solver #> #'@param name #> #'@param type #> #'@param max_iter #> #'@param linear_solver #> #'@param damping Optional: #> #'@export #> prj_nonlinear_solver <- function(name, #> type, #> max_iter, #> linear_solver, #> damping = NULL) { #> #> # Add coercing utility here #> #> new_prj_nonlinear_solver(name, #> type, #> max_iter, #> linear_solver, #> damping) #> } #> generate_R6(params = analysis_results, print_result = TRUE) #> OGS6_nonlinear_solver <- R6::R6Class(\"OGS6_nonlinear_solver\", #> public = list( #> #'@description #> #'Creates new OGS6_nonlinear_solverobject #> #'@param name #> #'@param type #> #'@param max_iter #> #'@param linear_solver #> #'@param damping Optional: initialize = function(name, #> type, #> max_iter, #> linear_solver, #> damping = NULL){ #> self$name <- name #> self$type <- type #> self$max_iter <- max_iter #> self$linear_solver <- linear_solver #> self$damping <- damping #> } #> ), #> #> active = list( #> #'@field name #> #'Access to private parameter '.name' #> name = function(value) { #> if(missing(value)) { #> private$.name #> }else{ #> private$.name <- value #> } #> }, #> #> #'@field type #> #'Access to private parameter '.type' #> type = function(value) { #> if(missing(value)) { #> private$.type #> }else{ #> private$.type <- value #> } #> }, #> #> #'@field max_iter #> #'Access to private parameter '.max_iter' #> max_iter = function(value) { #> if(missing(value)) { #> private$.max_iter #> }else{ #> private$.max_iter <- value #> } #> }, #> #> #'@field linear_solver #> #'Access to private parameter '.linear_solver' #> linear_solver = function(value) { #> if(missing(value)) { #> private$.linear_solver #> }else{ #> private$.linear_solver <- value #> } #> }, #> #> #'@field damping #> #'Access to private parameter '.damping' #> damping = function(value) { #> if(missing(value)) { #> private$.damping #> }else{ #> private$.damping <- value #> } #> }, #> #> #'@field is_subclass #> #'Access to private parameter '.is_subclass' #> is_subclass = function() { #> private$.is_subclass #> }, #> #> #'@field subclasses_names #> #'Access to private parameter '.subclasses_names' #> subclasses_names = function() { #> private$.subclasses_names #> }, #> #> #'@field attr_names #> #'Access to private parameter '.attr_names' #> attr_names = function() { #> private$.attr_names #> } #> ), #> #> private = list( #> .name = NULL, #> .type = NULL, #> .max_iter = NULL, #> .linear_solver = NULL, #> .damping = NULL, #> .is_subclass = TRUE, #> .subclasses_names = character(), #> .attr_names = c(), #> ) #> )"},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"integrating-new-classes","dir":"Articles","previous_headings":"","what":"Integrating new classes","title":"r2ogs6 Developer Guide","text":"Now class, need tell package exists. ’re reading exporting .prj file, knows automatically turn content nonlinear_solver tag object new class way around. achieve , execute code data_raw/xpaths_for_classes.R. update xpaths_for_classes parameter, adding entry class. Afterwards, run xpaths_for_classes[[\"your_class_name\"]]. return xpath parameter class like : class ’ve created .prj top level class child top level wrapper node like processes, add corresponding OGS6 private parameter active field. example, processes node represented list, added private parameter .processes = list() active field processes. lot things r2ogs6 package work way bit “meta”. Often times, functions called via eval(parse(text = call_string)) call_string example concatenated info parameter names certain class. saves lot code regarding import, export script generation requires ’ve made respective info available shown . ’ve analysed files, generated code, created new class registered package… now? ’s actually, ’s workflow. Well, least ’s supposed .","code":"xpaths_for_classes[[\"prj_process\"]] # A class can have multiple xpaths if the represented node occurs at different positions. xpaths_for_classes[[\"prj_convergence_criterion\"]]"},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"recursive-function-guide","dir":"Articles","previous_headings":"","what":"Recursive function guide","title":"r2ogs6 Developer Guide","text":"wasn’t , ’m afraid might take look functions handling import, export benchmark script generation. bit tricky use recursion far proven efficient structure-wise exactly fun think .","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/articles/dev_workflow_vignette.html","id":"conclusion","dir":"Articles","previous_headings":"","what":"Conclusion","title":"r2ogs6 Developer Guide","text":"hope ’ve taken away helpful information short guide. make changes improve workflow, please update vignette next dev!","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"r2ogs6 Ensemble Guide","text":"Hi ! practical guide OGS6_Ensemble class r2ogs6 package. show can use class set ensemble runs OpenGeoSys 6, extract results plot . want follow tutorial, ’ll need r2ogs6 installed loaded. prerequisites r2ogs6 described detail r2ogs6 User Guide vignette. Additionally, ’ll need following benchmark files: Theis’ Problem described Theis solution well pumping described General instructions download OpenGeoSys 6 benchmark files can found .","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"theis-problem","dir":"Articles","previous_headings":"","what":"Theis’ problem","title":"r2ogs6 Ensemble Guide","text":"consider following parameters sensitivity analysis: permeability porosity storage","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"setup","dir":"Articles","previous_headings":"Theis’ problem","what":"Setup","title":"r2ogs6 Ensemble Guide","text":"First, create simulation object base ensemble read .prj file.","code":"# Change this to fit your system testdir_path <- tempdir() sim_path <- paste0(testdir_path, \"/axisym_theis_sim\") ogs6_obj <- OGS6$new(sim_name = \"axisym_theis\", sim_path = sim_path) # Change this to fit your system prj_path <- system.file(\"extdata/benchmarks/AxiSymTheis/\", \"axisym_theis.prj\", package = \"r2ogs6\") read_in_prj(ogs6_obj, prj_path, read_in_gml = T)"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"single-parameter-sequential-run","dir":"Articles","previous_headings":"Theis’ problem","what":"Single-parameter sequential run","title":"r2ogs6 Ensemble Guide","text":"Let’s create small ensemble alter value storage. Say don’t want hardcode values, instead examine effects changing storage 1%, 10% 50%. can use percentages_mode parameter OGS6_Ensemble . already defaults TRUE, ’m merely explicit demonstration purposes. Now can start simulation.","code":"# Assign percentages percentages <- c(-50, -10, -1, 0, 1, 10, 50) # Define an ensemble object ogs6_ens <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list(list(ogs6_obj$media[[1]]$properties[[4]]$value, percentages)), percentages_mode = TRUE) ogs6_ens$run_simulation() lapply(ogs6_ens$ensemble, ogs6_read_output_files)"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"plot-results-for-single-simulation","dir":"Articles","previous_headings":"Theis’ problem > Single-parameter sequential run","what":"Plot results for single simulation","title":"r2ogs6 Ensemble Guide","text":"simulations (hopefully) ran successfully - great! Now ’d nice see results. Say ’re interested pressure data. may leave point_ids parameter. defaults points dataset - specify ’s 500 slow building vignette. can see ’s one row per timestep point ID. Say want plot average pressure timestep, , mean pressure values rows timestep. ’ll consider first simulation now. plot chunk p-t-first-plot","code":"# This will get a combined dataframe storage_tbl <- ogs6_ens$get_point_data(point_ids = c(0, 1, 2), keys = c(\"pressure\")) # Let's look at the first 10 rows of the dataset head(storage_tbl, 10) #> # A tibble: 10 × 8 #> id x y z pressure timestep sim_id perc #> #> 1 0 0.305 0 0 0 0 1 -50 #> 2 0 0.305 0 0 6.99 8.64 1 -50 #> 3 0 0.305 0 0 9.77 86.4 1 -50 #> 4 0 0.305 0 0 13.3 1728 1 -50 #> 5 0 0.305 0 0 16.2 24192 1 -50 #> 6 0 0.305 0 0 16.6 172800 1 -50 #> 7 0 0.305 0 0 16.6 604800 1 -50 #> 8 0 0.305 0 0 16.6 864000 1 -50 #> 9 1 305. 0 0 0 0 1 -50 #> 10 1 305. 0 0 0 8.64 1 -50 # Get average pressure from first simulation avg_pr_first_sim <- storage_tbl[storage_tbl$sim_id == 1,] %>% group_by(timestep) %>% summarize(avg_pressure = mean(pressure)) # Plot pressure over time for first simulation ggplot(data = avg_pr_first_sim) + geom_point(mapping = aes(x = as.numeric(row.names(avg_pr_first_sim)), y = avg_pressure)) + xlab(\"Timestep\")"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"plot-results-for-multiple-simulations","dir":"Articles","previous_headings":"Theis’ problem > Single-parameter sequential run","what":"Plot results for multiple simulations","title":"r2ogs6 Ensemble Guide","text":"plot chunk p-t--plot Now average pressure time simulations (rows). Since ’re pretty similar, let’s put plot better comparison. plot chunk p-t--combined-plot","code":"# Get average pressure for all simulations avg_pr_df <- storage_tbl %>% group_by(sim_id, timestep) %>% summarise(avg_pressure = mean(pressure)) # Plot pressure over time for all simulations ggplot(avg_pr_df, aes(x = as.numeric(as.factor(timestep)), y = avg_pressure)) + geom_point(aes(color = as.factor(sim_id))) + geom_line(aes(color = as.factor(sim_id))) + xlab(\"Timestep\") + labs(color = \"sim id\") + facet_grid(rows = vars(sim_id)) ggplot(avg_pr_df, aes(x = as.numeric(as.factor(timestep)), y = avg_pressure, group = sim_id)) + geom_point(aes(color = as.factor(sim_id))) + geom_line(aes(color = as.factor(sim_id))) + labs(color = \"sim id\") + xlab(\"Timestep\")"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"multi-parameter-sequential-run","dir":"Articles","previous_headings":"Theis’ problem","what":"Multi-parameter sequential run","title":"r2ogs6 Ensemble Guide","text":"far ’ve considered storage parameter. Now want look two parameters influence simulation, let’s put ensemble together. permeability can reuse percentages already . porosity, doesn’t work - original value 1 values can range 0 1, ’ll supply shorter vector. time ’s important set OGS6_Ensemble parameter sequential_mode TRUE change supplied parameters sequentially means end 18 (7 + 7 + 4) simulations equal sum elements value vectors supply (’ve named values clarity, naming optional though). default FALSE give error message value vectors length even , wouldn’t want - number simulations equal length one value vector (thus requiring length). Generally, set sequential_mode TRUE want examine influence parameters simulation independently. want examine parameters influence wanting test parameter combinations, default mode way go. Now can start simulation. take short time. soon simulations done, can extract point data much like . time want plot point x coodinates x axis ’re leaving point_ids get points. Also just want data last timestep. Plotting time! Since set sequential_mode TRUE, dataframe just created contains name column allows us group parameters. ’ve also set percentages_mode TRUE, also column perc allows us group percentages. Now can simply use facet grid plot. plot chunk p-t-group-plot Ta-Daa! can see permeability influence pressure. Though may seem suspicious, porosity storage plotted correctly - points just placed right top . Since porosity can’t go value 1 original value, value vector went -50% 0% line colors porosity storage differ. Maybe want try use logarithmic approach storage. won’t work built-functionality OGS6_Ensemble ’ll set Ensemble little differently. , can run simulation right away. Let’s check can observe influence storage pressure now. plot chunk p-t-log-plot","code":"# Change this to fit your system sim_path <- paste0(testdir_path, \"/axisym_theis_sim_big\") ogs6_obj$sim_path <- sim_path ogs6_ens_big <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list(per = list(ogs6_obj$media[[1]]$properties[[1]]$value, values = percentages), por = list(ogs6_obj$media[[1]]$properties[[3]]$value, c(-50, -10, -1, 0)), sto = list(ogs6_obj$media[[1]]$properties[[4]]$value, values = percentages)), sequential_mode = TRUE) ogs6_ens_big$run_simulation() lapply(ogs6_ens_big$ensemble, ogs6_read_output_files) # Get combined dataframe per_por_sto_df <- ogs6_ens_big$get_point_data( keys = c(\"pressure\"), start_at_timestep = ogs6_ens_big$ensemble[[1]]$pvds[[1]]$last_timestep) # Make plot ggplot(per_por_sto_df, aes(x = x, y = -pressure, # Flip pressure because source term was positive group = perc)) + geom_point(aes(color = as.factor(perc))) + xlab(\"Radius (m)\") + ylab(\"Head (m)\") + labs(color = \"%\") + facet_grid(cols = vars(name), labeller = as_labeller(c(per = \"permeability\", por = \"porosity\", sto = \"storage\"))) # Calculate log value log_val <- log(as.numeric( ogs6_obj$media[[1]]$properties[[4]]$value), base = 10) # Apply changes to log value log_vals <- vapply(percentages, function(x){ log_val + (log_val * (x / 100)) }, FUN.VALUE = numeric(1)) # Transfer back to non-logarithmic scale back_transf_vals <- 10^log_vals # Change sim_path to fit your system ogs6_obj$sim_path <- paste0(testdir_path, \"/axisym_theis_sim_log_storage\") # Set up new ensemble ogs6_ens_sto <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list( sto = list( ogs6_obj$media[[1]]$properties[[4]]$value, values = back_transf_vals) ), percentages_mode = FALSE, sequential_mode = TRUE ) ogs6_ens_sto$run_simulation() lapply(ogs6_ens_sto$ensemble, ogs6_read_output_files) # Get combined dataframe sto_df <- ogs6_ens_sto$get_point_data( keys = c(\"pressure\"), start_at_timestep = ogs6_ens_sto$ensemble[[1]]$pvds[[1]]$last_timestep) # Supply percentages manually since we couldn't use `percentages_mode` percs <- vapply(sto_df$sim_id, function(x){percentages[[x]]}, FUN.VALUE = numeric(1)) ggplot(sto_df, aes(x = x, y = -pressure)) + geom_point(aes(color = as.factor(percs))) + xlab(\"Radius (m)\") + ylab(\"Head (m)\") + labs(color = \"%\")"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"theis-solution-for-well-pumping","dir":"Articles","previous_headings":"","what":"Theis solution for well pumping","title":"r2ogs6 Ensemble Guide","text":"consider following parameters sensitivity analysis: permeability porosity slope","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"setup-1","dir":"Articles","previous_headings":"Theis solution for well pumping","what":"Setup","title":"r2ogs6 Ensemble Guide","text":"First, create simulation object base ensemble read .prj file. time want specify output file gets written last timestep.","code":"# Change this to fit your system sim_path <- paste0(testdir_path, \"/theis_sim\") ogs6_obj <- OGS6$new(sim_name = \"theis\", sim_path = sim_path) # Change this to fit your system prj_path <- system.file(\"extdata/benchmarks/theis_well_pumping/\", \"theis.prj\", package = \"r2ogs6\") read_in_prj(ogs6_obj, prj_path, read_in_gml = T) # Increase each_steps ogs6_obj$time_loop$output$timesteps$pair$each_steps <- 200"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"multi-parameter-sequential-run-1","dir":"Articles","previous_headings":"Theis solution for well pumping","what":"Multi-parameter sequential run","title":"r2ogs6 Ensemble Guide","text":"Now can start simulation. simulations run, can extract plot results like . avoid cluttering plot, extract pressure values single line. , get IDs points x axis. plot chunk p-x-plot Let’s take closer look permeability. plot chunk p-x-subset-plot Maybe want try use logarithmic approach slope. won’t work built-functionality OGS6_Ensemble ’ll set Ensemble little differently. , can run simulation right away. Let’s check can observe influence slope pressure now. plot chunk p-x-log-plot","code":"# Assign percentages percentages <- c(-50, -10, -1, 0, 1, 10, 50) ogs6_ens_theis_2 <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list( per = list(ogs6_obj$parameters[[3]]$values, values = percentages), por = list(ogs6_obj$parameters[[2]]$value, values = percentages), slo = list( ogs6_obj$media[[1]]$phases[[1]]$properties[[1]]$independent_variable[[2]]$slope, values = percentages) ), sequential_mode = TRUE ) ogs6_ens_theis_2$run_simulation() lapply(ogs6_ens_theis_2$ensemble, ogs6_read_output_files) # Extract point ids get_point_ids_x <- function(points){ x_axis_ids <- numeric() for(i in seq_len(dim(points)[[1]])) { if (points[i, ][[2]] == 0 && points[i, ][[3]] == 0) { x_axis_ids <- c(x_axis_ids, (i - 1)) } } return(x_axis_ids) } point_ids_x <- get_point_ids_x( ogs6_ens_theis_2$ensemble[[1]]$pvds[[1]]$OGS6_vtus[[1]]$points) # Get combined dataframe per_por_slo_df <- ogs6_ens_theis_2$get_point_data( point_ids = point_ids_x, keys = c(\"pressure\"), start_at_timestep = ogs6_ens_theis_2$ensemble[[1]]$pvds[[1]]$last_timestep) # Make plot ggplot(per_por_slo_df, aes(x = x, y = pressure / 9806.65, # 1mH2O = 9806.65 kPa group = perc)) + geom_point(aes(color = as.factor(perc))) + xlab(\"Radius (m)\") + ylab(\"Absenkung (m)\") + labs(color = \"%\") + facet_grid(cols = vars(name), labeller = as_labeller(c(per = \"permeability\", por = \"porosity\", slo = \"slope\" ))) per_df <- subset(per_por_slo_df, name == \"per\") # Make plot ggplot(per_df, aes(x = x, y = pressure)) + geom_point(aes(color = as.factor(perc))) + xlab(\"Radius (m)\") + ylab(\"Head (m)\") + labs(color = \"%\") # Calculate log value log_val <- log(as.numeric( ogs6_obj$media[[1]]$phases[[1]]$properties[[1]]$independent_variable[[2]]$slope), base = 10) # Apply changes to log value log_vals <- vapply(percentages, function(x){ log_val + (log_val * (x / 100)) }, FUN.VALUE = numeric(1)) # Transfer back to non-logarithmic scale back_transf_vals <- 10^log_vals # Change sim_path to fit your system ogs6_obj$sim_path <- paste0(testdir_path, \"/theis_sim_log_slope\") # Set up new ensemble ogs6_ens_slo <- OGS6_Ensemble$new( ogs6_obj = ogs6_obj, parameters = list( slo = list( ogs6_obj$media[[1]]$phases[[1]]$properties[[1]]$independent_variable[[2]]$slope, values = back_transf_vals) ), percentages_mode = FALSE, sequential_mode = TRUE ) ogs6_ens_slo$run_simulation() lapply(ogs6_ens_slo$ensemble, ogs6_read_output_files) # Filter point ids point_ids_x <- get_point_ids_x( ogs6_ens_slo$ensemble[[1]]$pvds[[1]]$OGS6_vtus[[1]]$points) # Get combined dataframe slo_df <- ogs6_ens_slo$get_point_data( point_ids = point_ids_x, keys = c(\"pressure\"), start_at_timestep = ogs6_ens_slo$ensemble[[1]]$pvds[[1]]$last_timestep) # Supply percentages manually since we couldn't use `percentages_mode` percs <- vapply(slo_df$sim_id, function(x){percentages[[x]]}, FUN.VALUE = numeric(1)) ggplot(slo_df, aes(x = x, y = pressure / 9806.65)) + # 1mH2O = 9806.65 kPa geom_point(aes(color = as.factor(percs))) + xlab(\"Radius (m)\") + ylab(\"Head (m)\") + labs(color = \"%\")"},{"path":"https://joboog.github.io/r2ogs6/articles/ensemble_workflow_vignette.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"r2ogs6 Ensemble Guide","text":"OGS6_Ensemble class useful tool set ensemble runs sensitivity analyses. vignette, learned create OGS6_Ensemble objects. looked parameters sequential_mode percentages_mode influence ensemble object initialised. started simulations via OGS6_Ensemble$run_simulation() extracted information output files plot .","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"prerequisites","dir":"Articles","previous_headings":"","what":"Prerequisites","title":"User Guide","text":"guide assumes r2ogs6 dependencies installed. ’s case, please take look installation instructions provided README.md file repository. loading r2ogs6, first need set package options knows look OpenGeoSys 6.","code":"# Set path for OpenGeoSys 6 options(\"r2ogs6.default_ogs6_bin_path\" = \"your_ogs6_bin_path\")"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"creating-your-simulation-object","dir":"Articles","previous_headings":"","what":"Creating your simulation object","title":"User Guide","text":"represent simulation object, r2ogs6 uses R6 class called OGS6. ’re new R6 objects, don’t worry. Creating simulation object easy. call class constructor provide parameters: sim_name name simulation sim_path relevant files simulation ’s , now simulation object.","code":"# Change this to fit your system # sim_path <- system.file(\"extdata/benchmarks/flow_no_strain\", # package = \"r2ogs6\") sim_path <- tempdir() ogs6_obj <- OGS6$new(sim_name = \"my_simulation\", sim_path = sim_path)"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"defining-the-simulation-parameters","dir":"Articles","previous_headings":"","what":"Defining the simulation parameters","title":"User Guide","text":"’s two ways can define simulation parameters. Either load benchmark file define simulation manually.","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"loading-a-benchmark-file","dir":"Articles","previous_headings":"Defining the simulation parameters","what":"Loading a benchmark file","title":"User Guide","text":"quickest easiest way define simulation using already existing benchmark. take look OpenGeoSys documentation, ’ll find plenty benchmarks choose along link project file GitLab top respective page. demonstration purposes, use project HydroMechanics benchmarks, can found . NOTE: r2ogs6 tested every existing benchmark. Due large number input parameters, might encounter cases import fails.","code":"# Change this to fit your system #prj_path <- paste0(sim_path, \"/flow_no_strain.prj\") prj_path <- system.file(\"extdata/benchmarks/flow_no_strain/flow_no_strain.prj\", package = \"r2ogs6\") read_in_prj(ogs6_obj, prj_path = prj_path, read_in_gml = T)"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"setting-up-your-own-opengeosys-6-simulation","dir":"Articles","previous_headings":"Defining the simulation parameters","what":"Setting up your own OpenGeoSys 6 simulation","title":"User Guide","text":"Setting simulation possible . Since ’s plenty required optional input parameters, might want call get_status() occasionally get brief overview simulation. tells input parameters missing can run simulation. Since haven’t defined anything far, ’ll see lot red . results gave us hint can add. ’ll go try find possible input data. Say want find process objects. rule thumb, classes named prefix prj_ followed XML tag name .prj file. exceptions rule subclasses lead duplicate class names. class prj_time_loop example contains subclass representing process child element confused process children first level processes node directly root node .prj file. , subclass named prj_tl_process. Let’s try adding something now. add data simulation object, use OGS6$add(). can use method top level .prj element, means ’re limited prj_parameter objects. Since already read .prj file earlier, won’t run snippet. ’d like complete example manually defining simulation parameters, ’s script flow_free_expansion.R examples/workflow_demos folder.","code":"# Call on the OGS6 object (note the R6 style) ogs6_obj$get_status() #> ✓ 'processes' has at least one element #> ✓ 'time_loop' is defined #> ✓ 'nonlinear_solvers' has at least one element #> ✓ 'linear_solvers' has at least one element #> ✓ 'parameters' has at least one element #> ✓ 'process_variables' has at least one element #> ✗ 'mesh' is defined #> ✗ 'geometry' is defined #> ✓ 'media' has at least one element #> ✗ 'test_definition' has at least one element #> ✗ 'curves' has at least one element #> ✓ 'meshes' has at least one element #> ✗ 'local_coordinate_system' is defined #> ✗ 'search_length_algorithm' is defined #> ✗ 'chemical_system' is defined #> ✗ 'python_script' is defined #> ✗ 'insitu' is definedYour OGS6 object has all necessary components. #> You can try calling ogs6_run_simulation().Note that this calls more validation functions, so you may not be done just yet. # To take a look at the documentation, use ? followed by the name of a class ?prj_process # Add a parameter ogs6_obj$add(prj_parameter(name = \"E\", type = \"Constant\", value = 1e+10)) # Add a process variable ogs6_obj$add( prj_process_variable( name = \"pressure\", components = 1, order = 1, initial_condition = \"pressure0\", boundary_conditions = list( boundary_condition = prj_boundary_condition( type = \"Neumann\", parameter = \"flux_in\", geometrical_set = \"cube_1x1x1_geometry\", geometry = \"left\", component = 0 ) ) ) )"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"running-the-simulation","dir":"Articles","previous_headings":"","what":"Running the simulation","title":"User Guide","text":"soon ’ve added necessary parameters, can try starting simulation. run additional checks start OpenGeoSys 6. write_logfile set FALSE, output OpenGeoSys 6 shown console.","code":"ogs6_run_simulation(ogs6_obj)"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"retrieve-the-results","dir":"Articles","previous_headings":"","what":"Retrieve the results","title":"User Guide","text":"simulation finished, might want plot results. retrieve ? went expected, don’t need call extra function ogs6_run_simulation() already calls ogs6_read_output_files() internally. need decide information want extract. Say ’re interested pressure Parameter last timestep. easy example, one .pvd file produced. plot chunk user-guide-plot Similar idea .pvd output, hdf5 files automatically referenced $h5s returned simulation. , added file artificially benchmark library demonstration. can seen, hdf5 files particular structure. work data, simple method get_h5() allows access different data elements raw starting point post processing data. functions HDF5 handles dataset processing can used directly rhdf5 package, course. path hd5 file available active field h5_path can accessed changed OGS6 object. file reasonably “clean” structure, convenient way importing data using method get_df returns tibble table.","code":"ogs6_read_output_files(ogs6_obj) # Extract relevant info into dataframe result_df <- ogs6_obj$pvds[[1]]$get_point_data(keys = c(\"pressure\")) result_df <- result_df[(result_df$timestep!=0),] # Plot results ggplot(result_df, aes(x = x, y = y, color = pressure)) + geom_point() + #geom_raster(interpolate = T)+ #geom_contour_filled()+ xlab(\"x coordinate\") + ylab(\"y coordinate\") + theme_bw() ogs6_obj$h5s #> [[1]] #> OGS6_h5 #> h5 path: #> /work/ufz/r2ogs6/inst/extdata/benchmarks/EllipticPETSc/cube_1e3_np3.h5 #> #> # h5 file structure ------------------------------------------------------ #> group name otype dclass dim #> 0 / t_0 H5I_GROUP #> 1 /t_0 D1_left_front_N1_right H5I_DATASET FLOAT 1895 #> 2 /t_0 Linear_1_to_minus1 H5I_DATASET FLOAT 1895 #> 3 /t_0 MaterialIDs H5I_DATASET INTEGER 1233 #> 4 /t_0 geometry H5I_DATASET FLOAT 3 x 1895 #> 5 /t_0 pressure H5I_DATASET FLOAT 1895 #> 6 /t_0 topology H5I_DATASET INTEGER 11097 #> 7 /t_0 v H5I_DATASET FLOAT 3 x 1895 #> 8 / t_1 H5I_GROUP #> 9 /t_1 pressure H5I_DATASET FLOAT 1895 #> 10 /t_1 v H5I_DATASET FLOAT 3 x 1895 h5_list <- ogs6_obj$h5s[[1]]$get_h5(\"/\") example_h5 <- rhdf5::H5Fopen(ogs6_obj$h5s[[1]]$h5_path) example_h5 #> HDF5 FILE #> name / #> filename #> #> name otype dclass dim #> 0 t_0 H5I_GROUP #> 1 t_1 H5I_GROUP str(example_h5$t_0) #> List of 7 #> $ D1_left_front_N1_right: num [1:1895(1d)] 1 1 1 1 1.01 ... #> $ Linear_1_to_minus1 : num [1:1895(1d)] 1 0.8 0.6 1 0.8 0.6 1 0.8 0.6 1 ... #> $ MaterialIDs : int [1:1233(1d)] 0 0 0 0 0 0 0 0 0 0 ... #> $ geometry : num [1:3, 1:1895] 0 0 0 0.1 0 0 0.2 0 0 0 ... #> $ pressure : num [1:1895(1d)] 0 0 0 0 0 0 0 0 0 0 ... #> $ topology : int [1:11097(1d)] 9 0 1 4 3 49 50 53 52 9 ... #> $ v : num [1:3, 1:1895] 0 0 0 0 0 0 0 0 0 0 ... rhdf5::h5closeAll() df <- ogs6_obj$h5s[[1]]$get_df(group = \"/t_0\", names = \"pressure\") df #> # A tibble: 1,895 × 5 #> x y z time pressure #> #> 1 0 0 0 0 0 #> 2 0.1 0 0 0 0 #> 3 0.2 0 0 0 0 #> 4 0 0.1 0 0 0 #> 5 0.1 0.1 0 0 0 #> 6 0.2 0.1 0 0 0 #> 7 0 0.2 0 0 0 #> 8 0.1 0.2 0 0 0 #> 9 0.2 0.2 0 0 0 #> 10 0 0.3 0 0 0 #> # … with 1,885 more rows"},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"running-multiple-simulations","dir":"Articles","previous_headings":"","what":"Running multiple simulations","title":"User Guide","text":"want run one multiple simulations, can use simulation object just created blueprint ensemble run. workflow described detail .","code":""},{"path":"https://joboog.github.io/r2ogs6/articles/user_workflow_vignette.html","id":"benchmark-script-generation","dir":"Articles","previous_headings":"","what":"Benchmark script generation","title":"User Guide","text":"Another feature r2ogs6 benchmark script generation. , two functions. ogs6_generate_benchmark_script() creates R script .prj file ogs6_generate_benchmark_scripts() wrapper former. Instead single .prj file path, takes directory path argument. Let’s look parameters ogs6_generate_benchmark_script() first. Say project file sim_file.prj want generate script . Please, make sure directories referencing exist. Now defined parameters, can generate benchmark script. hand, want generate R scripts multiple () benchmarks, can use wrapper function ogs6_generate_benchmark_scripts(). parameters basically , time supply directory path instead .prj path start . can download benchmarks (subfolder need) set path location system. ’re set! Note ogs6_generate_benchmark_scripts() reconstruct structure folder benchmarks stored , e. g. ’s file path//file.prj, find corresponding R script sim_path//file.R. , can generate scripts benchmarks single call. course can modify path liking ’re interested generating scripts certain subfolders. Furthermore, can restrict script generation benchmarks used test OGS 6. NOTE: New benchmarks .prj parameters constantly added OGS6. benchmark contains parameters added r2ogs6 yet, script generation functions work. case, skipped original error message displayed console.","code":"# The path to the project file you want to generate a script from prj_path <- \"your_path/sim_file.prj\" # The path you want to save the simulation files to sim_path <- \"your_sim_directory/\" # The path to your `ogs.exe` (if not already specified in `r2ogs6` options) ogs6_bin_path <- \"your_ogs6_bin_path/\" # The path you want your benchmark script to be saved to script_path <- \"your_script_directory/\" ogs6_generate_benchmark_script(prj_path = prj_path, sim_path = sim_path, ogs6_bin_path = ogs6_bin_path, script_path = script_path) # The path to the directory you want to generate R scripts from path <- \"path/to/ogs/Tests/Data/Elliptic/\" # The path you want to save the simulation files to sim_path <- \"your_sim_directory/\" # The path you want your benchmark scripts to be saved to script_path <- sim_path # Optional: Use if you want to start from a specific `.prj` file starting_from_prj_path <- \"\" # Optional: Use if you want to skip specific `.prj` files skip_prj_paths <- character() # Optional: Use if you want to skip specific `.prj` files skip_prj_paths <- character() # Optional: Use if you want to restrict scripting to specific `.prj` files only_prj_files <- character() ogs6_generate_benchmark_scripts(path = path, sim_path = sim_path, script_path = script_path, starting_from_prj_path = starting_from_prj_path, skip_prj_paths = skip_prj_paths, only_prj_files = only_prj_files) # extract *.prj files that are used as tests rel_testbm_paths <- get_benchmark_paths(\"path/to/ogs-source-code/ProcessLib/\") rel_testbm_paths <- sapply(rel_testbm_paths, basename) ogs6_generate_benchmark_scripts(path = path, sim_path = sim_path, script_path = script_path, only_prj_files = rel_testbm_paths)"},{"path":"https://joboog.github.io/r2ogs6/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Ruben Heinrich. Author. Johannes Boog. Author, maintainer. Philipp Schad. Author. Helmholtz Centre Environmental Research - UFZ. Copyright holder, funder.","code":""},{"path":"https://joboog.github.io/r2ogs6/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Heinrich R, Boog J, Schad P (2024). r2ogs6: API multi-physics simulator OpenGeoSys-v6. R package version 0.4.644.","code":"@Manual{, title = {r2ogs6: An API to the multi-physics simulator OpenGeoSys-v6}, author = {Ruben Heinrich and Johannes Boog and Philipp Schad}, year = {2024}, note = {R package version 0.4.644}, }"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"r2ogs6","dir":"","previous_headings":"","what":"An API to the multi-physics simulator OpenGeoSys-v6","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"r2ogs6 R-API multiphysics simulator OpenGeoSys 6. r2ogs6 allows pre-processing (preparing input files), executing simulation runs, retrieving, post-processing visualizing output data R. Furthermore, package comes functionality define ensemble runs.","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"setup","dir":"","previous_headings":"","what":"Setup","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"r2ogs6 requires installation OpenGeoSys 6. Furthermore, Python including libraries numpy vtk required read .vtu .pvd files produced OpenGeoSys 6. can install installed r2ogs6. r2ogs6 tested following environment: python==3.10.12, vtk==9.3.0, numpy==1.26.4","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"r2ogs6-installation","dir":"","previous_headings":"Setup","what":"r2ogs6 Installation","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"First, open terminal clone r2ogs6 repository local machine. install r2ogs6, first need R-packages remotes BiocManager. remotes used installing r2ogs6 BiocManager set URLs search dependencies CRAN bioconductor.org. instance, dependency rhdf5 available bioconductor.org. Open R console specific project: remotes, can now install r2ogs6 preferred library.","code":"git clone https://gitlab.opengeosys.org/ogs/tools/r2ogs6.git cd r2ogs6 # Now checkout the latest stable release git checkout tags/v0.4.643 install.packages(c(\"remotes\", \"BiocManager\")) # Install r2ogs6. Change the path to that of the cloned repository! remotes::install_local( path=\"path/to/r2ogs6\", dependencies=\"Imports\", repos=BiocManager::repositories() )"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"set-up-python","dir":"","previous_headings":"Setup > r2ogs6 Installation","what":"Set-up Python","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"OpenGeoSys 6 requires Python installation version 3.8–3.11.","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"linux-systems","dir":"","previous_headings":"Setup > r2ogs6 Installation > Set-up Python","what":"Linux systems","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"Python installed yet can reticulate library R console. Otherwise can use package manager linux distribution.","code":"reticulate::install_python(version = \"3.10:latest\")"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"windows","dir":"","previous_headings":"Setup > r2ogs6 Installation > Set-up Python","what":"Windows","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"Ideally, install Python Python Windows installer. course also try:","code":"reticulate::install_python(version = \"3.10:latest\")"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"install-python-dependencies-and-opengeosys-6","dir":"","previous_headings":"Setup > r2ogs6 Installation","what":"Install Python dependencies and OpenGeoSys 6","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"Create Python virtual environment specific name (e.g. \"r2ogs6) path Python executable just installed. Make sure reticulate::py_config()$python points python executable newly installed Python virtual environment. can try force reticulate use executable environment : work, quit R session create .Renviron file project folder: file read start-R forces reticulate use specific Python executable. Double check: can install OpenGeoSys 6 (Python dependencies numpy vtk installed alongside) Python module. aware, install OpenGeoSys 6 version compatible r2ogs6 version, see releases. Check OpenGeoSys 6 installed correctly. OpenGeoSys 6 binary located /path///python_env/bin/ogs (Linux) /path///python_env/Scripts/ogs (Windows). active R session can temporarily set path default using r2ogs6 (sets options(\"r2ogs6.default_ogs6_bin_path\").) setting permanently, create config.yml file project directory.","code":"reticulate::virtualenv_create(envname=\"r2ogs6\", python=\"/path/to/python\") reticulate::use_virtualenv(envname=\"r2ogs6\") # .Renviron linux RETICULATE_PYTHON=/path/to/your/virtualenv/bin/python reticulate::py_config() library(r2ogs6) install_ogs(ogs_version = \"6.4.4\", envname = \"r2ogs6\") reticulate::py_module_available(\"ogs\") set_ogs6_bin_path() # config.yml for linux default: r2ogs6.default_ogs6_bin_path: /path/to/python_env/bin/ogs"},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"alternative-manual-setup-of-python-environment","dir":"","previous_headings":"Setup > r2ogs6 Installation","what":"Alternative manual setup of Python environment","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"Alternatively, can set python environment including OpenGeoSys 6 without reticulate; look . aware, download install OpenGeoSys 6 version compatible r2ogs6 version, see releases. Nevertheless r2ogs6 uses reticulate hood. make sure reticulate::py_config() shows correct Python environment configured.","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"tutorials use r2ogs6 package, look vignettes: User Guide Ensemble Guide Developer Guide","code":""},{"path":"https://joboog.github.io/r2ogs6/index.html","id":"links","dir":"","previous_headings":"","what":"Links","title":"An API to the multi-physics simulator OpenGeoSys-v6","text":"OpenGeoSys Project OpenGeoSys source code OpenGeoSys documentation","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6 — OGS6","title":"OGS6 — OGS6","text":"Constructor OGS6 base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6 — OGS6","text":"sim_name Simulation name. value must string sim_path Simulation path. value must string logfile Logfile path. value must string gml .gml. read-geometry .prj geometry tag. value must string meshes .prj meshes tag. value must list strings vtus .vtus. value must list OGS6_vtu objects python_script .prj python_script tag. value must string search_length_algorithm .prj search_length_algorithm tag. value must prj_search_length_algorithm object processes .prj processes tag. value must list prj_process objects time_loop .prj time_loop tag. value must prj_time_loop object local_coordinate_system .prj local_coordinate_system tag. value must prj_local_coordinate_system object media .prj media tag. value must list prj_medium objects parameters .prj parameters tag. value must list prj_parameter objects chemical_system .prj chemical_system tag. value must prj_chemical_system object curves .prj curves tag. value must list prj_curve objects process_variables .prj process_variables tag. value must list prj_process_variable objects nonlinear_solvers .prj nonlinear_solvers tag. value must list prj_nonlinear_solver objects linear_solvers .prj linear_solvers tag. value must list prj_linear_solver objects test_definition .prj test_definition tag. value must list prj_vtkdiff objects insitu .prj insitu tag. value must prj_insitu object pvds .pvds. value must list OGS6_pvd objects h5s h5s value must class H5IdComponent returned rhdf5::h5read(). mshs mshs value must object class OGS6_msh. include include value must string.","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6 — OGS6","text":"OGS6$new() OGS6$add() OGS6$add_gml() OGS6$add_mesh() OGS6$update_component() OGS6$get_status() OGS6$print() OGS6$print_log() OGS6$clear() OGS6$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6 — OGS6","text":"Creates new OGS6 object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$new(sim_name, sim_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"sim_name string: Simulation name sim_path string: Path files simulation saved","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\")"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-add-","dir":"Reference","previous_headings":"","what":"Method add()","title":"OGS6 — OGS6","text":"Adds .prj simulation component","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$add(x)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"x object .prj `prj` class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-1","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add(prj_parameter(name = \"foo\", type = \"bar\"))"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-add-gml-","dir":"Reference","previous_headings":"","what":"Method add_gml()","title":"OGS6 — OGS6","text":"Adds reference file ending .gml optionally, OGS6_gml object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$add_gml(gml)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"gml string | OGS6_gml: Either path file extension .gml OGS6_gml object.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-2","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add_gml(\"this_works.gml\") \\dontrun{ogs6_obj$add_gml(\"this_doesnt.oops\")}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-add-mesh-","dir":"Reference","previous_headings":"","what":"Method add_mesh()","title":"OGS6 — OGS6","text":"Adds reference .vtu file optionally, OGS6_vtu object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$add_mesh(path, axisym = FALSE, read_in_vtu = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"path string: path axisym flag: mesh axially symmetrical? read_in_vtu flag: Optional: .vtu file just copied read ?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-3","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add_mesh(\"this_works.vtu\") \\dontrun{ogs6_obj$add_mesh(\"this_doesnt.oops\")}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-update-component-","dir":"Reference","previous_headings":"","what":"Method update_component()","title":"OGS6 — OGS6","text":"Update component OGS6 object.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$update_component(cmpts)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"cmpts list(sublist, length(sublist) == 2): first element sublist character calls OGS6 component, second one corresponding value.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-4","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"\\dontrun{ogs6_obj$update_component(list( list(\"ogs6_obj$parameters[[1]]$value\", 2.3), list(\"ogs6_obj$media[[1]]$properties[[2]]$value\", 1.0e-3)))}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-get-status-","dir":"Reference","previous_headings":"","what":"Method get_status()","title":"OGS6 — OGS6","text":"Checks OGS6 object necessary parameters starting simulation","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$get_status(print_status = TRUE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"print_status flag: status printed console?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"examples-5","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$get_status()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6 — OGS6","text":"Overrides default printing behaviour print_log","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-print-log-","dir":"Reference","previous_headings":"","what":"Method print_log()","title":"OGS6 — OGS6","text":"Prints logfile console (exists)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$print_log()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-clear-","dir":"Reference","previous_headings":"","what":"Method clear()","title":"OGS6 — OGS6","text":"Clears components OGS6 object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$clear(which)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"character: names components (default). want delete components, run names(ogs6_prj_top_level_classes()) available options.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6 — OGS6","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6 — OGS6","text":"","code":"OGS6$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6 — OGS6","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6 — OGS6","text":"","code":"## ------------------------------------------------ ## Method `OGS6$new` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ## ------------------------------------------------ ## Method `OGS6$add` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add(prj_parameter(name = \"foo\", type = \"bar\")) ## ------------------------------------------------ ## Method `OGS6$add_gml` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add_gml(\"this_works.gml\") if (FALSE) ogs6_obj$add_gml(\"this_doesnt.oops\") ## ------------------------------------------------ ## Method `OGS6$add_mesh` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$add_mesh(\"this_works.vtu\") if (FALSE) ogs6_obj$add_mesh(\"this_doesnt.oops\") ## ------------------------------------------------ ## Method `OGS6$update_component` ## ------------------------------------------------ if (FALSE) ogs6_obj$update_component(list( list(\"ogs6_obj$parameters[[1]]$value\", 2.3), list(\"ogs6_obj$media[[1]]$properties[[2]]$value\", 1.0e-3))) ## ------------------------------------------------ ## Method `OGS6$get_status` ## ------------------------------------------------ ogs6_obj <- OGS6$new(sim_name = \"my_sim\", sim_path = \"my/path\") ogs6_obj$get_status() #> ✗ 'processes' has at least one element #> ✗ 'time_loop' is defined #> ✗ 'nonlinear_solvers' has at least one element #> ✗ 'linear_solvers' has at least one element #> ✗ 'parameters' has at least one element #> ✗ 'process_variables' has at least one element #> ✗ 'mesh' is defined #> ✗ 'geometry' is defined #> ✗ 'media' has at least one element #> ✗ 'test_definition' has at least one element #> ✗ 'curves' has at least one element #> ✗ 'meshes' has at least one element #> ✗ 'local_coordinate_system' is defined #> ✗ 'search_length_algorithm' is defined #> ✗ 'chemical_system' is defined #> ✗ 'python_script' is defined #> ✗ 'insitu' is defined"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_Chain — OGS6_Chain","title":"OGS6_Chain — OGS6_Chain","text":"Constructor OGS6_Chain base class","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_Chain — OGS6_Chain","text":"OGS6_Chain$new() OGS6_Chain$ogs6_run_simulation() OGS6_Chain$print_log() OGS6_Chain$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_Chain — OGS6_Chain","text":"Creates new OGS6_Chain object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Chain — OGS6_Chain","text":"","code":"OGS6_Chain$new(ogs6_obj, iter_n)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Chain — OGS6_Chain","text":"ogs6_obj OGS6: simulation object. iter_n number: Number iterations (length chain)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"method-ogs-run-simulation-","dir":"Reference","previous_headings":"","what":"Method ogs6_run_simulation()","title":"OGS6_Chain — OGS6_Chain","text":"Runs simulation. calls r2ogs6::ogs6_run_simulation() internally. chains, output written logfiles.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Chain — OGS6_Chain","text":"","code":"OGS6_Chain$ogs6_run_simulation()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"method-print-log-","dir":"Reference","previous_headings":"","what":"Method print_log()","title":"OGS6_Chain — OGS6_Chain","text":"Reads logfile simulation prints console. calls print_log internally. index specified, print logfile last object chain.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Chain — OGS6_Chain","text":"","code":"OGS6_Chain$print_log(index)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Chain — OGS6_Chain","text":"index number: chain index OGS6 object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_Chain — OGS6_Chain","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Chain — OGS6_Chain","text":"","code":"OGS6_Chain$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Chain.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Chain — OGS6_Chain","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_Ensemble — OGS6_Ensemble","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Constructor OGS6_Ensemble base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_Ensemble — OGS6_Ensemble","text":"dp_parameters Getter private parameter '.dp_parameters' parameter_percs Getter private parameter '.parameter_percs' parameter_values Getter private parameter '.parameter_values' ens_path Getter private parameter '.ens_path' ensemble Getter private parameter '.ensemble'","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_Ensemble — OGS6_Ensemble","text":"OGS6_Ensemble$new() OGS6_Ensemble$print() OGS6_Ensemble$run_simulation() OGS6_Ensemble$get_point_data() OGS6_Ensemble$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Creates new OGS6_Ensemble object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$new( ogs6_obj, parameters, sequential_mode = FALSE, percentages_mode = TRUE )"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Ensemble — OGS6_Ensemble","text":"ogs6_obj OGS6: simulation object. parameters list(sublist, length(sublist) == 2): first element sublist references OGS6 parameter, second one list vector values. Note second elements sublists must length. sequential_mode flag: Defaults `FALSE` percentages_mode flag: Defaults `TRUE`","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Overrides default printing behaviour","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-run-simulation-","dir":"Reference","previous_headings":"","what":"Method run_simulation()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Runs simulation. calls r2ogs6::ogs6_run_simulation() internally. ensembles, output always written logfiles.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$run_simulation(parallel = FALSE, overwrite = T, verbose = F)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Ensemble — OGS6_Ensemble","text":"parallel flag: function run parallel? implementented via 'parallel' package. overwrite flag: existing files overwritten? verbose flag","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-get-point-data-","dir":"Reference","previous_headings":"","what":"Method get_point_data()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"Wrapper `OGS6_pvd$get_point_data()` Returns combined dataframe extra `name` / `perc` column depending `sequential_mode` / `percentages_mode` used.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$get_point_data( pvd_id = 1, point_ids, keys, start_at_timestep, end_at_timestep )"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Ensemble — OGS6_Ensemble","text":"pvd_id number: Optional: .pvd consider OGS6$pvds. Defaults 1. point_ids numeric: Optional: Point IDs. Defaults . keys character: Optional: `Name` attributes `DataArray` elements. Defaults . start_at_timestep number: Optional: Timestep start . Defaults first timestep. end_at_timestep number: Optional: Timestep end . Defaults last timestep.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_Ensemble — OGS6_Ensemble","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_Ensemble — OGS6_Ensemble","text":"","code":"OGS6_Ensemble$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_Ensemble.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_Ensemble — OGS6_Ensemble","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_gml — OGS6_gml","title":"OGS6_gml — OGS6_gml","text":"Constructor OGS6_gml base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_gml — OGS6_gml","text":"gml_path Getter private parameter '.gml_path' name Access private parameter '.name' points Access private parameter '.points' polylines Access private parameter '.polylines' surfaces Access private parameter '.surfaces' attr_names Getter private parameter '.attr_names' flatten_on_exp Getter private parameter '.flatten_on_exp'","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_gml — OGS6_gml","text":"OGS6_gml$new() OGS6_gml$print() OGS6_gml$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_gml — OGS6_gml","text":"Creates new OGS6_gml object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_gml — OGS6_gml","text":"","code":"OGS6_gml$new( gml_path = NULL, name = NULL, points = NULL, polylines = NULL, surfaces = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_gml — OGS6_gml","text":"gml_path string: Optional: Path .gml file name string: Geometry name points tibble: Must 3 vectors named 'x', 'y' 'z', may optional 'name' vector polylines list(list(\"foo\", c(1, 2))): surfaces list(list(\"foo\", c(1, 2, 3), c(2, 3, 4)))","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_gml — OGS6_gml","text":"Overrides default printing behaviour","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_gml — OGS6_gml","text":"","code":"OGS6_gml$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_gml — OGS6_gml","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_gml — OGS6_gml","text":"","code":"OGS6_gml$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_gml — OGS6_gml","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_gml.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"OGS6_gml — OGS6_gml","text":"","code":"OGS6_gml$new( name = \"cube_1x1x1_geometry\", points = tibble::tibble( x = c(0, 0, 0, 0), y = c(0, 0, 1, 1), z = c(0, 1, 1, 0), name = c(\"origin\", \"\", \"\", \"\") ), polylines = list(polyline = list(\"front_left\", c( pnt = 0, pnt = 1 ))), surfaces = list(surface = list( name = \"left\", element = c(p1 = 0, p2 = 1, p3 = 2), element = c(p1 = 0, p2 = 3, p3 = 2) )) ) #> OGS6_gml #> path: #> name: cube_1x1x1_geometry #> #> points #> # A tibble: 4 × 4 #> x y z name #> #> 1 0 0 0 \"origin\" #> 2 0 0 1 \"\" #> 3 0 1 1 \"\" #> 4 0 1 0 \"\" #> #> polylines #> $polyline #> $polyline$name #> [1] \"front_left\" #> #> $polyline$ #> pnt pnt #> 0 1 #> #> #> #> surfaces #> $surface #> $surface$name #> [1] \"left\" #> #> $surface$element #> p1 p2 p3 #> 0 1 2 #> #> $surface$element #> p1 p2 p3 #> 0 3 2 #> #>"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":null,"dir":"Reference","previous_headings":"","what":"wrapper for rhdf5::h5read() — OGS6_h5","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"Small class wrap h5 data r2ogs6 workflow.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"OGS6_h5 NOTE: beta-version guaranteed work current three existing [benchmarks](https://doxygen.opengeosys.org/d9/d28/ogs_file_param__prj__time_loop__output__hdf.html) contain *.h5 files. complicated files can always handled method $get_h5 may refer package rhdf5.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"h5_path Getter/setter private parameter `.h5_path`","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"OGS6_h5$new() OGS6_h5$print() OGS6_h5$get_h5() OGS6_h5$get_df() OGS6_h5$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"function called automatically simulation run give overview h5 output data.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$new(h5_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"h5_path path *.h5 file.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"Overrides default print method","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"examples-1","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) ogs6_h5 \\dontrun{ogs6_obj$h5s}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-get-h-","dir":"Reference","previous_headings":"","what":"Method get_h5()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"return h5 object processing rhdf5 package.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$get_h5(name = \"/\", ...)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"name Optional: *character* indicates element h5 file access. Default *\"/\"* return entire file list. ... Optional: arguments passed function h5read.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"list data elements element accessed name","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"examples-2","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"\\dontrun{h5_list <- ogs6_obj$h5s[[1]]$get_h5(\"/times\")}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-get-df-","dir":"Reference","previous_headings":"","what":"Method get_df()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"Method retrieve HDF5 output tibble assuming standardized structure OGS6 HDF5 output. times geometry added default.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$get_df(group, names = \"geometry\")"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"group *character* names *character* names hdf5 element displayed printing OGS5_h5 object, without leading \"/\".","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"examples-3","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) df <- ogs6_h5$get_df(\"/t_0\", \"pressure\") \\dontrun{df <- ogs6_obj$h5s[[1]]$get_df(\"/t_0\", \"pressure\")}"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"OGS6_h5$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_h5.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"wrapper for rhdf5::h5read() — OGS6_h5","text":"","code":"## ------------------------------------------------ ## Method `OGS6_h5$new` ## ------------------------------------------------ h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) ## ------------------------------------------------ ## Method `OGS6_h5$print` ## ------------------------------------------------ h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) ogs6_h5 #> OGS6_h5 #> h5 path: #> /tmp/RtmpBchsQP/temp_libpathaca2226b66ea/r2ogs6//extdata/benchmarks/EllipticPETSc/cube_1e3_np3.h5 #> #> # h5 file structure ------------------------------------------------------------ #> group name otype dclass dim #> 0 / t_0 H5I_GROUP #> 1 /t_0 D1_left_front_N1_right H5I_DATASET FLOAT 1895 #> 2 /t_0 Linear_1_to_minus1 H5I_DATASET FLOAT 1895 #> 3 /t_0 MaterialIDs H5I_DATASET INTEGER 1233 #> 4 /t_0 geometry H5I_DATASET FLOAT 3 x 1895 #> 5 /t_0 pressure H5I_DATASET FLOAT 1895 #> 6 /t_0 topology H5I_DATASET INTEGER 11097 #> 7 /t_0 v H5I_DATASET FLOAT 3 x 1895 #> 8 / t_1 H5I_GROUP #> 9 /t_1 pressure H5I_DATASET FLOAT 1895 #> 10 /t_1 v H5I_DATASET FLOAT 3 x 1895 if (FALSE) ogs6_obj$h5s ## ------------------------------------------------ ## Method `OGS6_h5$get_h5` ## ------------------------------------------------ if (FALSE) h5_list <- ogs6_obj$h5s[[1]]$get_h5(\"/times\") ## ------------------------------------------------ ## Method `OGS6_h5$get_df` ## ------------------------------------------------ h5_path <- system.file(\"/extdata/benchmarks/EllipticPETSc\", \"cube_1e3_np3.h5\", package = \"r2ogs6\") ogs6_h5 <- OGS6_h5$new(h5_path) df <- ogs6_h5$get_df(\"/t_0\", \"pressure\") if (FALSE) df <- ogs6_obj$h5s[[1]]$get_df(\"/t_0\", \"pressure\")"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_msh — OGS6_msh","title":"OGS6_msh — OGS6_msh","text":"Small class support MSH mesh files. Note MSH files legacy format OGS5. recommended switch VTU files.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_msh — OGS6_msh","text":"msh_path Getter/setter private parameter `.msh_path`","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_msh — OGS6_msh","text":"OGS6_msh$new() OGS6_msh$print() OGS6_msh$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_msh — OGS6_msh","text":"reates new OGS6_vtu object..","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_msh — OGS6_msh","text":"","code":"OGS6_msh$new(msh_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_msh — OGS6_msh","text":"msh_path path *.msh file.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_msh — OGS6_msh","text":"Overrides default print method","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_msh — OGS6_msh","text":"","code":"OGS6_msh$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_msh — OGS6_msh","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_msh — OGS6_msh","text":"","code":"OGS6_msh$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_msh.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_msh — OGS6_msh","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_pvd — OGS6_pvd","title":"OGS6_pvd — OGS6_pvd","text":"Constructor OGS6_pvd base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_pvd — OGS6_pvd","text":"pvd_path Getter private parameter '.pvd_path' datasets Getter private parameter '.datasets' vtu_paths Getter `datasets` `file` abs_vtu_paths Gets absolute .vtu paths, e.g. `dirname(pvd_path)` + `datasets` `file` last_timestep Gets last timestep timesteps Gets timesteps private parameter `datasets` OGS6_vtus Getter private parameter `.OGS6_vtus`","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_pvd — OGS6_pvd","text":"OGS6_pvd$new() OGS6_pvd$print() OGS6_pvd$vtu_by_timestep() OGS6_pvd$timestep_by_vtu() OGS6_pvd$get_point_data_at() OGS6_pvd$get_point_data() OGS6_pvd$get_cell_data() OGS6_pvd$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_pvd — OGS6_pvd","text":"Creates new OGS6_pvd object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$new(pvd_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"pvd_path string: Path .pvd file","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_pvd — OGS6_pvd","text":"Overrides default printing behaviour","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-vtu-by-timestep-","dir":"Reference","previous_headings":"","what":"Method vtu_by_timestep()","title":"OGS6_pvd — OGS6_pvd","text":"Returns .vtu path specified timestep","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$vtu_by_timestep(timestep)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"timestep string: Timestep","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-timestep-by-vtu-","dir":"Reference","previous_headings":"","what":"Method timestep_by_vtu()","title":"OGS6_pvd — OGS6_pvd","text":"Returns timestep specified .vtu path","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$timestep_by_vtu(vtu_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"vtu_path string: .vtu path","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-get-point-data-at-","dir":"Reference","previous_headings":"","what":"Method get_point_data_at()","title":"OGS6_pvd — OGS6_pvd","text":"Returns tibble containing point data","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$get_point_data_at( coordinates, keys, start_at_timestep, end_at_timestep )"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"coordinates list(numeric): List coordinates (coordinate numeric vector length 3) keys character: Optional: `Name` attributes `DataArray` elements. Defaults . start_at_timestep number: Optional: Timestep start . Defaults first timestep. end_at_timestep number: Optional: Timestep end . Defaults last timestep.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-get-point-data-","dir":"Reference","previous_headings":"","what":"Method get_point_data()","title":"OGS6_pvd — OGS6_pvd","text":"Returns tibble containing point data","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$get_point_data(point_ids, keys, start_at_timestep, end_at_timestep)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"point_ids numeric: Optional: Point IDs. Defaults . keys character: Optional: `Name` attributes `DataArray` elements. Defaults . start_at_timestep number: Optional: Timestep start . Defaults first timestep. end_at_timestep number: Optional: Timestep end . Defaults last timestep.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-get-cell-data-","dir":"Reference","previous_headings":"","what":"Method get_cell_data()","title":"OGS6_pvd — OGS6_pvd","text":"Returns tibble containing cell data","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$get_cell_data(cell_ids, keys, start_at_timestep, end_at_timestep)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"cell_ids numeric: Optional: Cell IDs. Defaults . keys character: Optional: `Name` attributes `DataArray` elements. Defaults . start_at_timestep number: Optional: Timestep start . Defaults first timestep. end_at_timestep number: Optional: Timestep end . Defaults last timestep.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_pvd — OGS6_pvd","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_pvd — OGS6_pvd","text":"","code":"OGS6_pvd$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_pvd.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_pvd — OGS6_pvd","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":null,"dir":"Reference","previous_headings":"","what":"OGS6_vtu — OGS6_vtu","title":"OGS6_vtu — OGS6_vtu","text":"Constructor `OGS6_vtu` base class","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"OGS6_vtu — OGS6_vtu","text":"vtu_path Getter private parameter `.vtu_path` number_of_points Getter NumberOfPoints parameter `.vtkUnstructuredGrid` number_of_cells Getter NumberOfCells parameter `.vtkUnstructuredGrid` points Getter Points parameter `.dsa_vtkUnstructuredGrid` cells Getter Cells parameter `.dsa_vtkUnstructuredGrid` field_data Getter FieldData parameter `.dsa_vtkUnstructuredGrid` point_data Getter PointData parameter `.dsa_vtkUnstructuredGrid` cell_data Getter CellData parameter `.dsa_vtkUnstructuredGrid` vtkPointLocator Getter private parameter `.vtkPointLocator` vtkUnstructuredGrid Access private parameter `.vtkUnstructuredGrid` dsa_vtkUnstructuredGrid Getter private parameter `.dsa_vtkUnstructuredGrid`","code":""},{"path":[]},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"OGS6_vtu — OGS6_vtu","text":"OGS6_vtu$new() OGS6_vtu$print() OGS6_vtu$get_field_data() OGS6_vtu$get_point_coords() OGS6_vtu$get_point_data_at() OGS6_vtu$get_point_data() OGS6_vtu$get_cell_data() OGS6_vtu$clone()","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"OGS6_vtu — OGS6_vtu","text":"Creates new OGS6_vtu object.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$new(vtu_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"vtu_path string: Path .vtu file","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"OGS6_vtu — OGS6_vtu","text":"Overrides default printing behaviour.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$print()"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-field-data-","dir":"Reference","previous_headings":"","what":"Method get_field_data()","title":"OGS6_vtu — OGS6_vtu","text":"Gets FieldData.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_field_data(keys)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"keys character: Optional: `Name` attributes `DataArray` elements, defaults `FieldData`.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"OGS6_vtu — OGS6_vtu","text":"list format list(value_a = 1, value_b = 2), names reference `Name` attributes `DataArray` elements.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-point-coords-","dir":"Reference","previous_headings":"","what":"Method get_point_coords()","title":"OGS6_vtu — OGS6_vtu","text":"Gets coordinates specific points IDs.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_point_coords(point_ids)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"point_ids numeric: Point IDs","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"OGS6_vtu — OGS6_vtu","text":"`point_ids` number, coordinate array. point_ids` numeric vector length > 1, list coordinate arrays.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-point-data-at-","dir":"Reference","previous_headings":"","what":"Method get_point_data_at()","title":"OGS6_vtu — OGS6_vtu","text":"Gets PointData specified coordinates.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_point_data_at(coordinates, keys)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"coordinates list(numeric): List coordinates (coordinate numeric vector length 3) keys character: Optional: `Name` attributes `DataArray` elements, defaults `PointData`","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-point-data-","dir":"Reference","previous_headings":"","what":"Method get_point_data()","title":"OGS6_vtu — OGS6_vtu","text":"Gets PointData points IDs `point_ids`.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_point_data(point_ids, keys)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"point_ids numeric: Optional: Point IDs, defaults keys character: Optional: `Name` attributes `DataArray` elements, defaults `PointData`","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"OGS6_vtu — OGS6_vtu","text":"tibble::tibble row represents point.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-get-cell-data-","dir":"Reference","previous_headings":"","what":"Method get_cell_data()","title":"OGS6_vtu — OGS6_vtu","text":"Gets CellData cells IDs `cell_ids`.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$get_cell_data(cell_ids, keys)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"cell_ids numeric: Optional: Cell IDs, defaults keys character: Optional: `Name` attributes `DataArray` elements, defaults `CellData`","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"OGS6_vtu — OGS6_vtu","text":"tibble::tibble row represents cell.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"OGS6_vtu — OGS6_vtu","text":"objects class cloneable method.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"OGS6_vtu — OGS6_vtu","text":"","code":"OGS6_vtu$clone(deep = FALSE)"},{"path":"https://joboog.github.io/r2ogs6/reference/OGS6_vtu.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"OGS6_vtu — OGS6_vtu","text":"deep Whether make deep clone.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/construct_ogs_command.html","id":null,"dir":"Reference","previous_headings":"","what":"construct_ogs_command — construct_ogs_command","title":"construct_ogs_command — construct_ogs_command","text":"Constructs call string 'system2()'.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/construct_ogs_command.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"construct_ogs_command — construct_ogs_command","text":"","code":"construct_ogs_command(ogs6_bin_path, singularity_opts)"},{"path":"https://joboog.github.io/r2ogs6/reference/construct_ogs_command.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"construct_ogs_command — construct_ogs_command","text":"ogs6_bin_path string: Optional: Path OpenGeoSys 6 executable OpenGeoSys container (singularity image) file. Defaults options(\"r2ogs6.default_ogs6_bin_path\") singularity_opts string: Optional: Options singularity exec command. Defaults options(\"r2ogs6.singularity_opts\")","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/construct_ogs_command.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"construct_ogs_command — construct_ogs_command","text":"string: Call object.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/install_ogs.html","id":null,"dir":"Reference","previous_headings":"","what":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","title":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","text":"Install specific version OpenGeoSys 6 (OGS) along necessary Python packages `vtk` `numpy` specified Python virtual environment. Note, work `conda` environments.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/install_ogs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","text":"","code":"install_ogs(..., ogs_version = \"6.4.4\", envname = \"r2ogs6\")"},{"path":"https://joboog.github.io/r2ogs6/reference/install_ogs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","text":"... Rest arguments passed \"py_install()\" ogs_version version OGS install (default: 6.4.4). envname name Python virtual environment (default: r2ogs6).","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/install_ogs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install specific version of OpenGeoSys 6 (OGS) along with necessary Python packages `vtk` and `numpy` into a specified Python virtual environment. Note, this does not work with `conda` environments. — install_ogs","text":"None.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_call_ogs6.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_call_ogs6 — ogs6_call_ogs6","title":"ogs6_call_ogs6 — ogs6_call_ogs6","text":"Makes system call OpenGeoSys 6 retrieves exit code.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_call_ogs6.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_call_ogs6 — ogs6_call_ogs6","text":"","code":"ogs6_call_ogs6( ogs6_obj, write_logfile = TRUE, ogs6_bin_path, verbose = F, singularity_opts )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_call_ogs6.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_call_ogs6 — ogs6_call_ogs6","text":"ogs6_obj OGS6: Simulation object write_logfile flag: output written logfile? FALSE, output written console. TRUE, logfile directory created ogs6$sim_path directory ogs6_bin_path string: Optional: Path OpenGeoSys 6 executable OpenGeoSys container (singularity image) file. Defaults options(\"r2ogs6.default_ogs6_bin_path\") verbose flag singularity_opts string: Optional: Options singularity exec command. Defaults options(\"r2ogs6.singularity_opts\")","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_export_sim_files.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_export_sim_files — ogs6_export_sim_files","title":"ogs6_export_sim_files — ogs6_export_sim_files","text":"Creates ogs6$sim_path directory exist yet exports / copies simulation files .","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_export_sim_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_export_sim_files — ogs6_export_sim_files","text":"","code":"ogs6_export_sim_files( ogs6_obj, overwrite = T, copy_ext_files = F, test_mode = F )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_export_sim_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_export_sim_files — ogs6_export_sim_files","text":"ogs6_obj OGS6: Simulation object overwrite flag: existing files overwritten? copy_ext_files flag: external files references ogs6_obj copied ogs6_obj$sim_path? test_mode flag: TRUE, check status ogs6_obj exporting files. Defaults FALSE","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_script.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate benchmark script — ogs6_generate_benchmark_script","title":"Generate benchmark script — ogs6_generate_benchmark_script","text":"Generates R script existing `.prj` benchmark file.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_script.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate benchmark script — ogs6_generate_benchmark_script","text":"","code":"ogs6_generate_benchmark_script( prj_path, sim_path, ogs6_bin_path, script_path, read_in_gml = FALSE, read_in_vtu = FALSE )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_script.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate benchmark script — ogs6_generate_benchmark_script","text":"prj_path string: `.prj` file script based sim_path string: Path simulation files saved ogs6_bin_path string: Path OpenGeoSys executable. Defaults options(\"r2ogs6.default_ogs6_bin_path\"). script_path string: Path benchmark script saved read_in_gml flag: Optional: `.gml` file just copied read ? read_in_vtu flag: Optional: `.vtu` file(s) just copied read ?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_scripts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate benchmark scripts — ogs6_generate_benchmark_scripts","title":"Generate benchmark scripts — ogs6_generate_benchmark_scripts","text":"wrapper function `ogs6_generate_benchmark_script()`.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_scripts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate benchmark scripts — ogs6_generate_benchmark_scripts","text":"","code":"ogs6_generate_benchmark_scripts( path, sim_path, script_path, read_in_gml, read_in_vtu = FALSE, starting_from_prj_path = \"\", skip_prj_paths = character(), only_prj_files = character() )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_benchmark_scripts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate benchmark scripts — ogs6_generate_benchmark_scripts","text":"path string: Path benchmark directory generate scripts sim_path string: Path simulation files saved script_path string: Path benchmark script saved read_in_gml flag: Optional: `.gml` file just copied read ? read_in_vtu flag: Optional: `.vtu` file(s) just copied read ? starting_from_prj_path string: Optional: `.prj` path start skip_prj_paths character: Optional: `.prj` paths skip only_prj_files character: Optional: `.prj` files limit .","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_structured_mesh.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","title":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","text":"Wrapper function call generateStructuredMesh.exe (VTK mesh generator). full documentation see https://www.opengeosys.org/docs/tools/meshing/structured-mesh-generation/","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_structured_mesh.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","text":"","code":"ogs6_generate_structured_mesh(args_str, ogs6_utils_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_structured_mesh.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","text":"args_str string: arguments script called ogs6_utils_path string: Optional: Path OpenGeoSys6 utils folder. Defaults options(\"r2ogs6.default_ogs6_utils_path\")","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_generate_structured_mesh.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ogs6_generate_structured_mesh — ogs6_generate_structured_mesh","text":"string: .vtu file path","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_combinations.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_get_combinations — ogs6_get_combinations","title":"ogs6_get_combinations — ogs6_get_combinations","text":"Gets possible combinations supplied vectors","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_combinations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_get_combinations — ogs6_get_combinations","text":"","code":"ogs6_get_combinations(...)"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_combinations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_get_combinations — ogs6_get_combinations","text":"... vector:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_medium_property.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_get_medium_property — ogs6_get_medium_property","title":"ogs6_get_medium_property — ogs6_get_medium_property","text":"Returns medium property based property name","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_medium_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_get_medium_property — ogs6_get_medium_property","text":"","code":"ogs6_get_medium_property(medium, name)"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_medium_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_get_medium_property — ogs6_get_medium_property","text":"medium prj_medium name string: property name","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_get_medium_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ogs6_get_medium_property — ogs6_get_medium_property","text":"prj_pr_property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_prj_top_level_classes.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_prj_top_level_classes — ogs6_prj_top_level_classes","title":"ogs6_prj_top_level_classes — ogs6_prj_top_level_classes","text":"Returns named character vector OGS6 top level .prj tags (names) represented r2ogs6 classes along class names (values).","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_prj_top_level_classes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_prj_top_level_classes — ogs6_prj_top_level_classes","text":"","code":"ogs6_prj_top_level_classes()"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_prj_top_level_classes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ogs6_prj_top_level_classes — ogs6_prj_top_level_classes","text":"character","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_read_output_files.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_read_output_files — ogs6_read_output_files","title":"ogs6_read_output_files — ogs6_read_output_files","text":"Read generated .pvd files add ogs6_obj","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_read_output_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_read_output_files — ogs6_read_output_files","text":"","code":"ogs6_read_output_files(ogs6_obj)"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_read_output_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_read_output_files — ogs6_read_output_files","text":"ogs6_obj OGS6: Simulation object","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_run_simulation.html","id":null,"dir":"Reference","previous_headings":"","what":"ogs6_run_simulation — ogs6_run_simulation","title":"ogs6_run_simulation — ogs6_run_simulation","text":"Wrapper function calls ogs6_export_sim_files(), ogs6_call_ogs6() ogs6_read_output_files().","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_run_simulation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ogs6_run_simulation — ogs6_run_simulation","text":"","code":"ogs6_run_simulation( ogs6_obj, write_logfile = TRUE, ogs6_bin_path, overwrite = T, copy_ext_files = F, verbose = F, singularity_opts )"},{"path":"https://joboog.github.io/r2ogs6/reference/ogs6_run_simulation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ogs6_run_simulation — ogs6_run_simulation","text":"ogs6_obj OGS6: Simulation object write_logfile flag: output written logfile? FALSE, output written console. TRUE, logfile directory created ogs6$sim_path directory ogs6_bin_path string: Optional: OpenGeoSys 6 executable path. Defaults options(\"r2ogs6.default_ogs6_bin_path\") overwrite flag: existing files overwritten? copy_ext_files flag: external files references ogs6_obj copied ogs6_obj$sim_path? verbose flag singularity_opts string: Optional: Options singularity exec command. Defaults options(\"r2ogs6.singularity_opts\")","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_borehole_heat_exchanger.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","title":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","text":"tag: borehole_heat_exchanger","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_borehole_heat_exchanger.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","text":"","code":"prj_borehole_heat_exchanger( type, flow_and_temperature_control, borehole, grout, pipes, refrigerant, use_bhe_pipe_network = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_borehole_heat_exchanger.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","text":"type string: flow_and_temperature_control prj_flow_and_temperature_control: borehole list: grout list: pipes prj_pipes: refrigerant list: use_bhe_pipe_network Optional: string (\"true\" | \"false\"):","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_borehole_heat_exchanger.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_borehole_heat_exchanger — prj_borehole_heat_exchanger","text":"","code":"prj_borehole_heat_exchanger( type = \"1U\", flow_and_temperature_control = prj_flow_and_temperature_control( type = \"TemperatureCurveConstantFlow\", flow_rate = 2e-04, temperature_curve = \"inflow_temperature\" ), borehole = list(length = \"18.0\", diameter = \"0.13\"), grout = list( density = \"2190.0\", porosity = \"0.0\", heat_capacity = \"1735.160\", thermal_conductivity = \"0.806\" ), pipes = prj_pipes( longitudinal_dispersion_length = 0.001, inlet = list( diameter = \" 0.013665\", wall_thickness = \"0.003035\", wall_thermal_conductivity = \"0.39\" ), outlet = list( diameter = \"0.013665\", wall_thickness = \"0.003035\", wall_thermal_conductivity = \"0.39\" ), distance_between_pipes = 0.053 ), refrigerant = list( density = \"992.92\", viscosity = \"0.00067418\", specific_heat_capacity = \"4068\", thermal_conductivity = \"0.62863\", reference_temperature = \"298.15\" ) ) #> Renaming elements of vector to fit their default names: 'density', 'porosity', 'specific_heat_capacity', 'thermal_conductivity' #> $type #> [1] \"1U\" #> #> $flow_and_temperature_control #> $type #> [1] \"TemperatureCurveConstantFlow\" #> #> $flow_rate #> [1] 2e-04 #> #> $temperature_curve #> [1] \"inflow_temperature\" #> #> $power #> NULL #> #> $power_curve #> NULL #> #> $flow_rate_curve #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger/flow_and_temperature_control\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_flow_and_temperature_control\" #> #> $borehole #> $borehole$length #> [1] \"18.0\" #> #> $borehole$diameter #> [1] \"0.13\" #> #> #> $grout #> $grout$density #> [1] \"2190.0\" #> #> $grout$porosity #> [1] \"0.0\" #> #> $grout$specific_heat_capacity #> [1] \"1735.160\" #> #> $grout$thermal_conductivity #> [1] \"0.806\" #> #> #> $pipes #> $longitudinal_dispersion_length #> [1] 0.001 #> #> $inlet #> $inlet$diameter #> [1] \" 0.013665\" #> #> $inlet$wall_thickness #> [1] \"0.003035\" #> #> $inlet$wall_thermal_conductivity #> [1] \"0.39\" #> #> #> $outlet #> $outlet$diameter #> [1] \"0.013665\" #> #> $outlet$wall_thickness #> [1] \"0.003035\" #> #> $outlet$wall_thermal_conductivity #> [1] \"0.39\" #> #> #> $distance_between_pipes #> [1] 0.053 #> #> $outer #> NULL #> #> $inner #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger/pipes\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_pipes\" #> #> $refrigerant #> $refrigerant$density #> [1] \"992.92\" #> #> $refrigerant$viscosity #> [1] \"0.00067418\" #> #> $refrigerant$specific_heat_capacity #> [1] \"4068\" #> #> $refrigerant$thermal_conductivity #> [1] \"0.62863\" #> #> $refrigerant$reference_temperature #> [1] \"298.15\" #> #> #> $use_bhe_pipe_network #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_borehole_heat_exchanger\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_boundary_condition.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_boundary_condition — prj_boundary_condition","title":"prj_boundary_condition — prj_boundary_condition","text":"tag: boundary_condition","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_boundary_condition.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_boundary_condition — prj_boundary_condition","text":"","code":"prj_boundary_condition( type, parameter = NULL, geometrical_set = NULL, geometry = NULL, component = NULL, mesh = NULL, alpha = NULL, u_0 = NULL, constraint_type = NULL, constraining_process_variable = NULL, constraint_threshold = NULL, constraint_direction = NULL, area_parameter = NULL, bc_object = NULL, flush_stdout = NULL, property_name = NULL, initial_value_parameter = NULL, constant_name = NULL, coefficient_current_variable_name = NULL, coefficient_other_variable_name = NULL, coefficient_mixed_variables_name = NULL, threshold_parameter = NULL, comparison_operator = NULL, time_interval = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_boundary_condition.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_boundary_condition — prj_boundary_condition","text":"type string: parameter string: geometrical_set Optional: string: geometry Optional: string: component Optional: string | double: mesh Optional: string: alpha Optional: string: u_0 Optional: string: constraint_type Optional: string: constraining_process_variable Optional: string: constraint_threshold Optional: string | double: constraint_direction Optional: string: area_parameter Optional: string: bc_object Optional: string: flush_stdout Optional: string: property_name Optional: string: initial_value_parameter Optional: string: constant_name Optional: string: coefficient_current_variable_name Optional: string: coefficient_other_variable_name Optional: string: coefficient_mixed_variables_name Optional: string: threshold_parameter Optional: string: comparison_operator Optional: string: time_interval Optional: list 2, character:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_boundary_condition.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_boundary_condition — prj_boundary_condition","text":"","code":"prj_boundary_condition( type = \"Neumann\", parameter = \"flux_in\", geometrical_set = \"cube_1x1x1_geometry\", geometry = \"left\", component = 0 ) #> $type #> [1] \"Neumann\" #> #> $parameter #> [1] \"flux_in\" #> #> $geometrical_set #> [1] \"cube_1x1x1_geometry\" #> #> $geometry #> [1] \"left\" #> #> $component #> [1] 0 #> #> $mesh #> NULL #> #> $alpha #> NULL #> #> $u_0 #> NULL #> #> $constraint_type #> NULL #> #> $constraining_process_variable #> NULL #> #> $constraint_threshold #> NULL #> #> $constraint_direction #> NULL #> #> $area_parameter #> NULL #> #> $bc_object #> NULL #> #> $flush_stdout #> NULL #> #> $property_name #> NULL #> #> $initial_value_parameter #> NULL #> #> $constant_name #> NULL #> #> $coefficient_current_variable_name #> NULL #> #> $coefficient_other_variable_name #> NULL #> #> $coefficient_mixed_variables_name #> NULL #> #> $threshold_parameter #> NULL #> #> $comparison_operator #> NULL #> #> $time_interval #> NULL #> #> $xpath #> [1] \"process_variables/process_variable/boundary_conditions/boundary_condition\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_boundary_condition\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_capillary_pressure.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_capillary_pressure — prj_capillary_pressure","title":"prj_capillary_pressure — prj_capillary_pressure","text":"tag: capillary_pressure","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_capillary_pressure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_capillary_pressure — prj_capillary_pressure","text":"","code":"prj_capillary_pressure( type, pd = NULL, sr = NULL, smax = NULL, m = NULL, pc_max = NULL, has_regularized = NULL, curve = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_capillary_pressure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_capillary_pressure — prj_capillary_pressure","text":"type string: pd Optional: string | double: sr Optional: string | double: smax Optional: string | double: m Optional: string | double: pc_max Optional: string | double: has_regularized Optional: string, \"true\" | \"false\": curve Optional: list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_capillary_pressure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_capillary_pressure — prj_capillary_pressure","text":"","code":"prj_capillary_pressure( type = \"vanGenuchten\", pd = 2e+06, sr = 0.4, smax = 1, m = 0.3288590604, pc_max = 2e+07, has_regularized = \"true\" ) #> $type #> [1] \"vanGenuchten\" #> #> $pd #> [1] 2e+06 #> #> $sr #> [1] 0.4 #> #> $smax #> [1] 1 #> #> $m #> [1] 0.3288591 #> #> $pc_max #> [1] 2e+07 #> #> $has_regularized #> [1] \"true\" #> #> $curve #> NULL #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/capillary_pressure\" #> [2] \"processes/process/porous_medium/porous_medium/capillary_pressure\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_capillary_pressure\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_reaction.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_chemical_reaction — prj_chemical_reaction","title":"prj_chemical_reaction — prj_chemical_reaction","text":"tag: chemical_reaction","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_reaction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_chemical_reaction — prj_chemical_reaction","text":"","code":"prj_chemical_reaction( stoichiometric_coefficients, reaction_type, first_order_rate_constant )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_reaction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_chemical_reaction — prj_chemical_reaction","text":"stoichiometric_coefficients numeric: reaction_type string: first_order_rate_constant double:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_system.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_chemical_system — prj_chemical_system","title":"prj_chemical_system — prj_chemical_system","text":"tag: chemical_system","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_system.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_chemical_system — prj_chemical_system","text":"","code":"prj_chemical_system( chemical_solver, mesh, linear_solver = NULL, database = NULL, solution = NULL, knobs = NULL, kinetic_reactants = NULL, rates = NULL, equilibrium_reactants = NULL, surface = NULL, user_punch = NULL, use_high_precision = NULL, exchangers = NULL, chemical_reactions = NULL, number_of_components = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_system.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_chemical_system — prj_chemical_system","text":"chemical_solver string: Either \"Phreeqc\" \"SelfContained\". mesh string: linear_solver Optional: string: database string: Required chemical_solver == \"Phreeqc\" . solution prj_solution: Required chemical_solver == \"Phreeqc\". knobs Optional: list: kinetic_reactants Optional: list, prj_kinetic_reactant: rates Optional: list, prj_rate: equilibrium_reactants Optional: list, prj_phase_component: surface Optional: user_punch Optional: use_high_precision Optional: exchangers Optional: prj_exchangers chemical_reactions list: Required chemical_solver == \"SelfContained\". number_of_components integer: Required chemical_solver == \"SelfContained\".","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_chemical_system.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_chemical_system — prj_chemical_system","text":"","code":"prj_chemical_system( chemical_solver = \"Phreeqc\", database = \"PSINA_12_07_110615_DAV_s.dat\", solution = prj_solution( temperature = 25, pressure = 1, pe = 4, components = list( component = \"C(4)\", component = \"Ca\" ), charge_balance = \"pH\" ), mesh = \"calcite_ReactiveDomain\", knobs = list( max_iter = \"100\", relative_convergence_tolerance = \"1e-12\", tolerance = \"1e-15\", step_size = \"100\", scaling = \"0\" ), equilibrium_reactants = list( phase_component = prj_phase_component( name = \"Calcite\", saturation_index = 0, initial_amount = 0.000207 ) ) ) #> $chemical_solver #> [1] \"Phreeqc\" #> #> $mesh #> [1] \"calcite_ReactiveDomain\" #> #> $linear_solver #> NULL #> #> $database #> [1] \"PSINA_12_07_110615_DAV_s.dat\" #> #> $solution #> $temperature #> [1] 25 #> #> $pressure #> [1] 1 #> #> $pe #> [1] 4 #> #> $components #> $components$component #> [1] \"C(4)\" #> #> $components$component #> [1] \"Ca\" #> #> #> $charge_balance #> [1] \"pH\" #> #> $fixing_pe #> NULL #> #> $xpath #> [1] \"chemical_system/solution\" #> #> $attr_names #> [1] \"fixing_pe\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_solution\" #> #> $knobs #> $knobs$max_iter #> [1] \"100\" #> #> $knobs$relative_convergence_tolerance #> [1] \"1e-12\" #> #> $knobs$tolerance #> [1] \"1e-15\" #> #> $knobs$step_size #> [1] \"100\" #> #> $knobs$scaling #> [1] \"0\" #> #> #> $kinetic_reactants #> NULL #> #> $rates #> NULL #> #> $equilibrium_reactants #> $equilibrium_reactants$phase_component #> $name #> [1] \"Calcite\" #> #> $saturation_index #> [1] 0 #> #> $initial_amount #> [1] 0.000207 #> #> $xpath #> [1] \"chemical_system/equilibrium_reactants/phase_component\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase_component\" #> #> #> $surface #> NULL #> #> $user_punch #> NULL #> #> $use_high_precision #> NULL #> #> $exchangers #> NULL #> #> $chemical_reactions #> NULL #> #> $number_of_components #> NULL #> #> $xpath #> [1] \"chemical_system\" #> #> $attr_names #> [1] \"chemical_solver\" \"site_unit\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_chemical_system\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_com_property.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_com_property — prj_com_property","title":"prj_com_property — prj_com_property","text":"tag: property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_com_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_com_property — prj_com_property","text":"","code":"prj_com_property( name, type, value = NULL, parameter_name = NULL, reference_diffusion = NULL, activation_energy = NULL, reference_temperature = NULL, triple_temperature = NULL, triple_pressure = NULL, critical_temperature = NULL, critical_pressure = NULL, reference_pressure = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_com_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_com_property — prj_com_property","text":"name string: Property name type string: Property type value Optional: string | double: ... parameter_name Optional: reference_diffusion Optional: character activation_energy Optional: string | double reference_temperature Optional: numeric triple_temperature Optional: numeric triple_pressure Optional: numeric critical_temperature Optional: numeric critical_pressure Optional: numeric reference_pressure Optional: numeric","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_com_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_com_property — prj_com_property","text":"","code":"prj_com_property(name = \"molecular_diffusion\", type = \"Constant\", value = 2e-09) #> $name #> [1] \"molecular_diffusion\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 2e-09 #> #> $parameter_name #> NULL #> #> $reference_diffusion #> NULL #> #> $activation_energy #> NULL #> #> $reference_temperature #> NULL #> #> $triple_temperature #> NULL #> #> $triple_pressure #> NULL #> #> $critical_temperature #> NULL #> #> $critical_pressure #> NULL #> #> $reference_pressure #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/components/component/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_com_property\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_component.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_component — prj_component","title":"prj_component — prj_component","text":"tag: component","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_component.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_component — prj_component","text":"","code":"prj_component(name, properties)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_component.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_component — prj_component","text":"name string: properties list, prj_com_property:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_component.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_component — prj_component","text":"","code":"prj_component( name = \"concentration\", properties = list( property = prj_com_property(name = \"molecular_diffusion\", type = \"Constant\", value = 2e-09) ) ) #> $name #> [1] \"concentration\" #> #> $properties #> $properties$property #> $name #> [1] \"molecular_diffusion\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 2e-09 #> #> $parameter_name #> NULL #> #> $reference_diffusion #> NULL #> #> $activation_energy #> NULL #> #> $reference_temperature #> NULL #> #> $triple_temperature #> NULL #> #> $triple_pressure #> NULL #> #> $critical_temperature #> NULL #> #> $critical_pressure #> NULL #> #> $reference_pressure #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/components/component/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_com_property\" #> #> #> $xpath #> [1] \"media/medium/phases/phase/components/component\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_component\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_constitutive_relation.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_constitutive_relation — prj_constitutive_relation","title":"prj_constitutive_relation — prj_constitutive_relation","text":"tag: constitutive_relation","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_constitutive_relation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_constitutive_relation — prj_constitutive_relation","text":"","code":"prj_constitutive_relation( type, id = NULL, youngs_modulus = NULL, poissons_ratio = NULL, nonlinear_solver = NULL, behaviour = NULL, material_properties = NULL, shear_modulus = NULL, bulk_modulus = NULL, kappa = NULL, beta = NULL, gamma = NULL, hardening_modulus = NULL, alpha = NULL, delta = NULL, eps = NULL, m = NULL, alphap = NULL, deltap = NULL, epsp = NULL, mp = NULL, betap = NULL, gammap = NULL, tangent_type = NULL, damage_properties = NULL, youngs_moduli = NULL, shear_moduli = NULL, poissons_ratios = NULL, a = NULL, n = NULL, sigma0 = NULL, q = NULL, kelvin_shear_modulus = NULL, kelvin_viscosity = NULL, maxwell_shear_modulus = NULL, maxwell_bulk_modulus = NULL, maxwell_viscosity = NULL, dependency_parameter_mk = NULL, dependency_parameter_mvk = NULL, dependency_parameter_mvm = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_constitutive_relation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_constitutive_relation — prj_constitutive_relation","text":"type string: id Optional: youngs_modulus Optional: poissons_ratio Optional: nonlinear_solver Optional: behaviour Optional: material_properties Optional: shear_modulus Optional: bulk_modulus Optional: kappa Optional: beta Optional: gamma Optional: hardening_modulus Optional: alpha Optional: delta Optional: eps Optional: m Optional: alphap Optional: deltap Optional: epsp Optional: mp Optional: betap Optional: gammap Optional: tangent_type Optional: damage_properties Optional: youngs_moduli Optional: shear_moduli Optional: poissons_ratios Optional: Optional: n Optional: sigma0 Optional: q Optional: kelvin_shear_modulus Optional: kelvin_viscosity Optional: maxwell_shear_modulus Optional: maxwell_bulk_modulus Optional: maxwell_viscosity Optional: dependency_parameter_mk Optional: dependency_parameter_mvk Optional: dependency_parameter_mvm Optional:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_constitutive_relation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_constitutive_relation — prj_constitutive_relation","text":"","code":"prj_constitutive_relation( type = \"LinearElasticIsotropic\", youngs_modulus = \"E\", poissons_ratio = \"nu\" ) #> $type #> [1] \"LinearElasticIsotropic\" #> #> $id #> NULL #> #> $youngs_modulus #> [1] \"E\" #> #> $poissons_ratio #> [1] \"nu\" #> #> $nonlinear_solver #> NULL #> #> $behaviour #> NULL #> #> $material_properties #> NULL #> #> $shear_modulus #> NULL #> #> $bulk_modulus #> NULL #> #> $kappa #> NULL #> #> $beta #> NULL #> #> $gamma #> NULL #> #> $hardening_modulus #> NULL #> #> $alpha #> NULL #> #> $delta #> NULL #> #> $eps #> NULL #> #> $m #> NULL #> #> $alphap #> NULL #> #> $deltap #> NULL #> #> $epsp #> NULL #> #> $mp #> NULL #> #> $betap #> NULL #> #> $gammap #> NULL #> #> $tangent_type #> NULL #> #> $damage_properties #> NULL #> #> $youngs_moduli #> NULL #> #> $shear_moduli #> NULL #> #> $poissons_ratios #> NULL #> #> $a #> NULL #> #> $n #> NULL #> #> $sigma0 #> NULL #> #> $q #> NULL #> #> $kelvin_shear_modulus #> NULL #> #> $kelvin_viscosity #> NULL #> #> $maxwell_shear_modulus #> NULL #> #> $maxwell_bulk_modulus #> NULL #> #> $maxwell_viscosity #> NULL #> #> $dependency_parameter_mk #> NULL #> #> $dependency_parameter_mvk #> NULL #> #> $dependency_parameter_mvm #> NULL #> #> $xpath #> [1] \"processes/process/constitutive_relation\" #> #> $attr_names #> [1] \"id\" \"material_property\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_constitutive_relation\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_convergence_criterion.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_convergence_criterion — prj_convergence_criterion","title":"prj_convergence_criterion — prj_convergence_criterion","text":"tag: convergence_criterion","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_convergence_criterion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_convergence_criterion — prj_convergence_criterion","text":"","code":"prj_convergence_criterion( type, norm_type, abstol = NULL, reltol = NULL, abstols = NULL, reltols = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_convergence_criterion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_convergence_criterion — prj_convergence_criterion","text":"type string: Type norm_type string: ... abstol string | double: Absolute tolerance reltol string | double: Relative tolerance abstols string | numeric: Absolute tolerances reltols string | numeric: Relative tolerances","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_convergence_criterion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_convergence_criterion — prj_convergence_criterion","text":"","code":"prj_convergence_criterion( type = \"DeltaX\", norm_type = \"INFINITY_N\", abstol = 1e-08, reltol = 1e-10 ) #> $type #> [1] \"DeltaX\" #> #> $norm_type #> [1] \"INFINITY_N\" #> #> $abstol #> [1] 1e-08 #> #> $reltol #> [1] 1e-10 #> #> $abstols #> NULL #> #> $reltols #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/convergence_criterion\" #> [2] \"time_loop/global_process_coupling/convergence_criteria/convergence_criterion\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"abstols\" \"reltols\" #> #> attr(,\"class\") #> [1] \"prj_convergence_criterion\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_curve.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_curve — prj_curve","title":"prj_curve — prj_curve","text":"tag: curve, curve","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_curve.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_curve — prj_curve","text":"","code":"prj_curve(name, coords, values)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_curve.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_curve — prj_curve","text":"name string: Name curve coords string | numeric: Coordinates curve's values given values string | numeric: Values curve given coordinates","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_curve.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_curve — prj_curve","text":"","code":"prj_curve(name = \"Dirichlet_temporal\", coords = \"0 3\", values = \"200 200\") #> $name #> [1] \"Dirichlet_temporal\" #> #> $coords #> [1] 0 3 #> #> $values #> [1] 200 200 #> #> $xpath #> [1] \"curves/curve\" #> [2] \"processes/process/porous_medium/porous_medium/capillary_pressure/curve\" #> [3] \"processes/process/material_property/porous_medium/porous_medium/capillary_pressure/curve\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"coords\" \"values\" #> #> attr(,\"class\") #> [1] \"prj_curve\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_deactivated_subdomain.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_deactivated_subdomain — prj_deactivated_subdomain","title":"prj_deactivated_subdomain — prj_deactivated_subdomain","text":"tag: deactivated_subdomain","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_deactivated_subdomain.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_deactivated_subdomain — prj_deactivated_subdomain","text":"","code":"prj_deactivated_subdomain( material_ids, time_interval = NULL, time_curve = NULL, line_segment = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_deactivated_subdomain.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_deactivated_subdomain — prj_deactivated_subdomain","text":"material_ids string | double: time_interval Optional: list, numeric: time_curve Optional: line_segment Optional:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_deactivated_subdomain.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_deactivated_subdomain — prj_deactivated_subdomain","text":"","code":"prj_deactivated_subdomain(material_ids = 0, time_interval = list(start = \"0.51\", end = \"1.0\")) #> $material_ids #> [1] 0 #> #> $time_interval #> $time_interval$start #> [1] \"0.51\" #> #> $time_interval$end #> [1] \"1.0\" #> #> #> $time_curve #> NULL #> #> $line_segment #> NULL #> #> $xpath #> [1] \"process_variables/process_variable/deactivated_subdomains/deactivated_subdomain\" #> #> $attr_names #> NULL #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_deactivated_subdomain\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_eigen.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_eigen — prj_eigen","title":"prj_eigen — prj_eigen","text":"tag: eigen","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_eigen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_eigen — prj_eigen","text":"","code":"prj_eigen( solver_type, precon_type = NULL, max_iteration_step = NULL, error_tolerance = NULL, scaling = NULL, restart = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_eigen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_eigen — prj_eigen","text":"solver_type string: precon_type Optional: string: max_iteration_step Optional: string | double: ... error_tolerance Optional: string | double: ... scaling Optional: string | double: ... restart Optional: string | double: ...","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_eigen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_eigen — prj_eigen","text":"","code":"prj_eigen( solver_type = \"BiCGSTAB\", precon_type = \"ILUT\", max_iteration_step = 10000, error_tolerance = 1e-16 ) #> $solver_type #> [1] \"BiCGSTAB\" #> #> $precon_type #> [1] \"ILUT\" #> #> $max_iteration_step #> [1] 10000 #> #> $error_tolerance #> [1] 1e-16 #> #> $scaling #> NULL #> #> $restart #> NULL #> #> $xpath #> [1] \"linear_solvers/linear_solver/eigen\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_eigen\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_exchangers.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_exchangers — prj_exchangers","title":"prj_exchangers — prj_exchangers","text":"tag: exchangers","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_exchangers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_exchangers — prj_exchangers","text":"","code":"prj_exchangers(exchange_site)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_exchangers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_exchangers — prj_exchangers","text":"exchange_site list","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_flow_and_temperature_control.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","title":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","text":"tag: flow_and_temperature_control","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_flow_and_temperature_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","text":"","code":"prj_flow_and_temperature_control( type, flow_rate = NULL, temperature_curve = NULL, power = NULL, power_curve = NULL, flow_rate_curve = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_flow_and_temperature_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","text":"type string: flow_rate Optional: string | double: temperature_curve Optional: string: power Optional: string | double: power_curve Optional: string: flow_rate_curve Optional: string:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_flow_and_temperature_control.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_flow_and_temperature_control — prj_flow_and_temperature_control","text":"","code":"prj_flow_and_temperature_control( type = \"TemperatureCurveConstantFlow\", flow_rate = 2e-04, temperature_curve = \"inflow_temperature\" ) #> $type #> [1] \"TemperatureCurveConstantFlow\" #> #> $flow_rate #> [1] 2e-04 #> #> $temperature_curve #> [1] \"inflow_temperature\" #> #> $power #> NULL #> #> $power_curve #> NULL #> #> $flow_rate_curve #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger/flow_and_temperature_control\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_flow_and_temperature_control\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fluid.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_fluid — prj_fluid","title":"prj_fluid — prj_fluid","text":"tag: fluid","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fluid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_fluid — prj_fluid","text":"","code":"prj_fluid( liquid_density, gas_density, liquid_viscosity, gas_viscosity, specific_heat_capacity_solid = NULL, specific_heat_capacity_water = NULL, specific_heat_capacity_air = NULL, specific_heat_capacity_water_vapor = NULL, thermal_conductivity_dry_solid = NULL, thermal_conductivity_wet_solid = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fluid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_fluid — prj_fluid","text":"liquid_density list: gas_density list: liquid_viscosity list: gas_viscosity list: specific_heat_capacity_solid Optional: specific_heat_capacity_water Optional: specific_heat_capacity_air Optional: specific_heat_capacity_water_vapor Optional: thermal_conductivity_dry_solid Optional: thermal_conductivity_wet_solid Optional:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fluid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_fluid — prj_fluid","text":"","code":"prj_fluid( liquid_density = list(type = \"Constant\", value = \" 1.e3 \"), gas_density = list(type = \"IdealGasLaw\", molar_mass = \" 0.002 \"), liquid_viscosity = list(type = \"Constant\", value = \" 3.171e-11 \"), gas_viscosity = list(type = \"Constant\", value = \" 2.8539e-13 \") ) #> $liquid_density #> $liquid_density$type #> [1] \"Constant\" #> #> $liquid_density$value #> [1] \" 1.e3 \" #> #> #> $gas_density #> $gas_density$type #> [1] \"IdealGasLaw\" #> #> $gas_density$molar_mass #> [1] \" 0.002 \" #> #> #> $liquid_viscosity #> $liquid_viscosity$type #> [1] \"Constant\" #> #> $liquid_viscosity$value #> [1] \" 3.171e-11 \" #> #> #> $gas_viscosity #> $gas_viscosity$type #> [1] \"Constant\" #> #> $gas_viscosity$value #> [1] \" 2.8539e-13 \" #> #> #> $specific_heat_capacity_solid #> NULL #> #> $specific_heat_capacity_water #> NULL #> #> $specific_heat_capacity_air #> NULL #> #> $specific_heat_capacity_water_vapor #> NULL #> #> $thermal_conductivity_dry_solid #> NULL #> #> $thermal_conductivity_wet_solid #> NULL #> #> $xpath #> [1] \"processes/process/material_property/fluid\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_fluid\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_model.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_fracture_model — prj_fracture_model","title":"prj_fracture_model — prj_fracture_model","text":"tag: fracture_model","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_model.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_fracture_model — prj_fracture_model","text":"","code":"prj_fracture_model( type, normal_stiffness, shear_stiffness, penalty_aperture_cutoff, tension_cutoff, fracture_toughness = NULL, peak_normal_traction = NULL, friction_angle = NULL, dilatancy_angle = NULL, cohesion = NULL, nonlinear_solver = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_model.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_fracture_model — prj_fracture_model","text":"type string: normal_stiffness string: shear_stiffness string: penalty_aperture_cutoff string | double: tension_cutoff string | double: fracture_toughness Optional: string: peak_normal_traction Optional: string: friction_angle Optional: string: dilatancy_angle Optional: string: cohesion Optional: string: nonlinear_solver Optional: list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_model.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_fracture_model — prj_fracture_model","text":"","code":"prj_fracture_model(type = \"LinearElasticIsotropic\", normal_stiffness = \"Kn\", shear_stiffness = \"Ks\", penalty_aperture_cutoff = 1e-05, tension_cutoff = 1) #> $type #> [1] \"LinearElasticIsotropic\" #> #> $normal_stiffness #> [1] \"Kn\" #> #> $shear_stiffness #> [1] \"Ks\" #> #> $penalty_aperture_cutoff #> [1] 1e-05 #> #> $tension_cutoff #> [1] 1 #> #> $fracture_toughness #> NULL #> #> $peak_normal_traction #> NULL #> #> $friction_angle #> NULL #> #> $dilatancy_angle #> NULL #> #> $cohesion #> NULL #> #> $nonlinear_solver #> NULL #> #> $xpath #> [1] \"processes/process/fracture_model\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_fracture_model\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_properties.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_fracture_properties — prj_fracture_properties","title":"prj_fracture_properties — prj_fracture_properties","text":"tag: fracture_properties","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_properties.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_fracture_properties — prj_fracture_properties","text":"","code":"prj_fracture_properties( material_id, initial_aperture, specific_storage = NULL, biot_coefficient = NULL, permeability_model = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_properties.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_fracture_properties — prj_fracture_properties","text":"material_id string | double: initial_aperture string: specific_storage Optional: string: biot_coefficient Optional: string: permeability_model Optional: list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_fracture_properties.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_fracture_properties — prj_fracture_properties","text":"","code":"prj_fracture_properties( material_id = 0, initial_aperture = \"aperture0\", specific_storage = \"S_f\", biot_coefficient = \"biot_f\", permeability_model = list(type = \"CubicLaw\") ) #> $material_id #> [1] 0 #> #> $initial_aperture #> [1] \"aperture0\" #> #> $specific_storage #> [1] \"S_f\" #> #> $biot_coefficient #> [1] \"biot_f\" #> #> $permeability_model #> $permeability_model$type #> [1] \"CubicLaw\" #> #> #> $xpath #> [1] \"processes/process/fracture_properties\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_fracture_properties\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_geometrical_set.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_geometrical_set — prj_geometrical_set","title":"prj_geometrical_set — prj_geometrical_set","text":"tag: geometrical_set","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_geometrical_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_geometrical_set — prj_geometrical_set","text":"","code":"prj_geometrical_set(name, geometry)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_geometrical_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_geometrical_set — prj_geometrical_set","text":"name string geometry string","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_global_process_coupling.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_global_process_coupling — prj_global_process_coupling","title":"prj_global_process_coupling — prj_global_process_coupling","text":"tag: global_process_coupling","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_global_process_coupling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_global_process_coupling — prj_global_process_coupling","text":"","code":"prj_global_process_coupling(max_iter, convergence_criteria)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_global_process_coupling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_global_process_coupling — prj_global_process_coupling","text":"max_iter string | double: Maximal number iterations convergence_criteria list, prj_convergence_criterion: Convergence criteria","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_global_process_coupling.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_global_process_coupling — prj_global_process_coupling","text":"","code":"prj_global_process_coupling( max_iter = 100, convergence_criteria = list( convergence_criterion = prj_convergence_criterion( type = \"DeltaX\", norm_type = \"INFINITY_N\", abstol = 1e-08, reltol = 1e-10 ) ) ) #> $max_iter #> [1] 100 #> #> $convergence_criteria #> $convergence_criteria$convergence_criterion #> $type #> [1] \"DeltaX\" #> #> $norm_type #> [1] \"INFINITY_N\" #> #> $abstol #> [1] 1e-08 #> #> $reltol #> [1] 1e-10 #> #> $abstols #> NULL #> #> $reltols #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/convergence_criterion\" #> [2] \"time_loop/global_process_coupling/convergence_criteria/convergence_criterion\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"abstols\" \"reltols\" #> #> attr(,\"class\") #> [1] \"prj_convergence_criterion\" #> #> #> $xpath #> [1] \"time_loop/global_process_coupling\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_global_process_coupling\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_insitu.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_insitu — prj_insitu","title":"prj_insitu — prj_insitu","text":"tag: insitu","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_insitu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_insitu — prj_insitu","text":"","code":"prj_insitu(scripts)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_insitu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_insitu — prj_insitu","text":"scripts character: Script names","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_insitu.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_insitu — prj_insitu","text":"","code":"prj_insitu(scripts = c(script = \"square_1e1_neumann-insitu.py\")) #> $scripts #> script #> \"square_1e1_neumann-insitu.py\" #> #> $xpath #> [1] \"insitu\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_insitu\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_jacobian_assembler.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_jacobian_assembler — prj_jacobian_assembler","title":"prj_jacobian_assembler — prj_jacobian_assembler","text":"tag: jacobian_assembler","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_jacobian_assembler.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_jacobian_assembler — prj_jacobian_assembler","text":"","code":"prj_jacobian_assembler( type, component_magnitudes = NULL, relative_epsilons = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_jacobian_assembler.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_jacobian_assembler — prj_jacobian_assembler","text":"type string: component_magnitudes Optional: string | double: relative_epsilons Optional: string | double:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_jacobian_assembler.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_jacobian_assembler — prj_jacobian_assembler","text":"","code":"prj_jacobian_assembler( type = \"CentralDifferences\", component_magnitudes = 1, relative_epsilons = 1e-08 ) #> $type #> [1] \"CentralDifferences\" #> #> $component_magnitudes #> [1] 1 #> #> $relative_epsilons #> [1] 1e-08 #> #> $xpath #> [1] \"processes/process/jacobian_assembler\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"component_magnitudes\" \"relative_epsilons\" #> #> attr(,\"class\") #> [1] \"prj_jacobian_assembler\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_kinetic_reactant.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_kinetic_reactant — prj_kinetic_reactant","title":"prj_kinetic_reactant — prj_kinetic_reactant","text":"S3 class describing .prj kinetic_reactant","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_kinetic_reactant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_kinetic_reactant — prj_kinetic_reactant","text":"","code":"prj_kinetic_reactant( name, initial_amount = NULL, chemical_formula = NULL, fix_amount = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_kinetic_reactant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_kinetic_reactant — prj_kinetic_reactant","text":"name component name initial_amount initial amount component chemical_formula chemical formula component fix_amount amount fixed ?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_kinetic_reactant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_kinetic_reactant — prj_kinetic_reactant","text":"","code":"prj_kinetic_reactant(name = \"Productc\", initial_amount = 1e-06) #> $name #> [1] \"Productc\" #> #> $initial_amount #> [1] 1e-06 #> #> $chemical_formula #> NULL #> #> $fix_amount #> NULL #> #> $xpath #> [1] \"chemical_system/kinetic_reactants/kinetic_reactant\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_kinetic_reactant\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_linear_solver.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_linear_solver — prj_linear_solver","title":"prj_linear_solver — prj_linear_solver","text":"tag: linear_solver","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_linear_solver.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_linear_solver — prj_linear_solver","text":"","code":"prj_linear_solver(name, eigen = NULL, lis = NULL, petsc = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_linear_solver.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_linear_solver — prj_linear_solver","text":"name string: name linear solver eigen Optional: list: ... lis Optional: string: ... petsc Optional: character: ...","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_linear_solver.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_linear_solver — prj_linear_solver","text":"","code":"prj_linear_solver( name = \"general_linear_solver\", eigen = prj_eigen( solver_type = \"BiCGSTAB\", precon_type = \"ILUT\", max_iteration_step = 10000, error_tolerance = 1e-16 ), lis = \"-i bicgstab -p ilu -tol 1e-16 -maxiter 10000\" ) #> $name #> [1] \"general_linear_solver\" #> #> $eigen #> $solver_type #> [1] \"BiCGSTAB\" #> #> $precon_type #> [1] \"ILUT\" #> #> $max_iteration_step #> [1] 10000 #> #> $error_tolerance #> [1] 1e-16 #> #> $scaling #> NULL #> #> $restart #> NULL #> #> $xpath #> [1] \"linear_solvers/linear_solver/eigen\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_eigen\" #> #> $lis #> [1] \"-i bicgstab -p ilu -tol 1e-16 -maxiter 10000\" #> #> $petsc #> NULL #> #> $xpath #> [1] \"linear_solvers/linear_solver\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_linear_solver\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_local_coordinate_system.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_local_coordinate_system — prj_local_coordinate_system","title":"prj_local_coordinate_system — prj_local_coordinate_system","text":"tag: local_coordinate_system","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_local_coordinate_system.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_local_coordinate_system — prj_local_coordinate_system","text":"","code":"prj_local_coordinate_system( basis_vector_0, basis_vector_1, basis_vector_2 = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_local_coordinate_system.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_local_coordinate_system — prj_local_coordinate_system","text":"basis_vector_0 string | double: basis vector basis_vector_1 string | double: basis vector basis_vector_2 Optional: string | double: basis vector","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_local_coordinate_system.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_local_coordinate_system — prj_local_coordinate_system","text":"","code":"prj_local_coordinate_system(basis_vector_0 = \"e0\", basis_vector_1 = \"e1\", basis_vector_2 = \"e2\") #> $basis_vector_0 #> [1] \"e0\" #> #> $basis_vector_1 #> [1] \"e1\" #> #> $basis_vector_2 #> [1] \"e2\" #> #> $xpath #> [1] \"local_coordinate_system\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_local_coordinate_system\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_material_property.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_material_property — prj_material_property","title":"prj_material_property — prj_material_property","text":"tag: material_property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_material_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_material_property — prj_material_property","text":"","code":"prj_material_property(fluid, porous_medium)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_material_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_material_property — prj_material_property","text":"fluid prj_fluid: porous_medium prj_porous_medium:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_material_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_material_property — prj_material_property","text":"","code":"prj_material_property( fluid = prj_fluid( liquid_density = list(type = \"Constant\", value = \" 1.e3 \"), gas_density = list(type = \"IdealGasLaw\", molar_mass = \" 0.002 \"), liquid_viscosity = list(type = \"Constant\", value = \" 3.171e-11 \"), gas_viscosity = list(type = \"Constant\", value = \" 2.8539e-13 \") ), porous_medium = list( porous_medium = prj_porous_medium( id = 0, permeability = list(permeability_tensor_entries = \"kappa1\", type = \"Constant\"), porosity = list(type = \"Constant\", porosity_parameter = \"constant_porosity_parameter\"), storage = list(type = \"Constant\", value = \" 0.0 \"), capillary_pressure = prj_capillary_pressure( type = \"vanGenuchten\", pd = 2e+06, sr = 0.4, smax = 1, m = 0.3288590604, pc_max = 2e+07, has_regularized = \"true\" ), relative_permeability = list( relative_permeability = prj_relative_permeability( type = \"NonWettingPhaseVanGenuchten\", sr = 0, smax = 0.6, m = 0.3288590604, krel_min = 0, id = \"0\" ) ) ) ) ) #> $fluid #> $liquid_density #> $liquid_density$type #> [1] \"Constant\" #> #> $liquid_density$value #> [1] \" 1.e3 \" #> #> #> $gas_density #> $gas_density$type #> [1] \"IdealGasLaw\" #> #> $gas_density$molar_mass #> [1] \" 0.002 \" #> #> #> $liquid_viscosity #> $liquid_viscosity$type #> [1] \"Constant\" #> #> $liquid_viscosity$value #> [1] \" 3.171e-11 \" #> #> #> $gas_viscosity #> $gas_viscosity$type #> [1] \"Constant\" #> #> $gas_viscosity$value #> [1] \" 2.8539e-13 \" #> #> #> $specific_heat_capacity_solid #> NULL #> #> $specific_heat_capacity_water #> NULL #> #> $specific_heat_capacity_air #> NULL #> #> $specific_heat_capacity_water_vapor #> NULL #> #> $thermal_conductivity_dry_solid #> NULL #> #> $thermal_conductivity_wet_solid #> NULL #> #> $xpath #> [1] \"processes/process/material_property/fluid\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_fluid\" #> #> $porous_medium #> $porous_medium$porous_medium #> $id #> [1] 0 #> #> $permeability #> $permeability$permeability_tensor_entries #> [1] \"kappa1\" #> #> $permeability$type #> [1] \"Constant\" #> #> #> $porosity #> $porosity$type #> [1] \"Constant\" #> #> $porosity$porosity_parameter #> [1] \"constant_porosity_parameter\" #> #> #> $storage #> $storage$type #> [1] \"Constant\" #> #> $storage$value #> [1] \" 0.0 \" #> #> #> $capillary_pressure #> $type #> [1] \"vanGenuchten\" #> #> $pd #> [1] 2e+06 #> #> $sr #> [1] 0.4 #> #> $smax #> [1] 1 #> #> $m #> [1] 0.3288591 #> #> $pc_max #> [1] 2e+07 #> #> $has_regularized #> [1] \"true\" #> #> $curve #> NULL #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/capillary_pressure\" #> [2] \"processes/process/porous_medium/porous_medium/capillary_pressure\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_capillary_pressure\" #> #> $relative_permeability #> $relative_permeability$relative_permeability #> $type #> [1] \"NonWettingPhaseVanGenuchten\" #> #> $sr #> [1] 0 #> #> $smax #> [1] 0.6 #> #> $m #> [1] 0.3288591 #> #> $krel_min #> [1] 0 #> #> $id #> [1] \"0\" #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/relative_permeability/relative_permeability\" #> [2] \"processes/process/porous_medium/porous_medium/relative_permeability\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_relative_permeability\" #> #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium\" #> [2] \"processes/process/porous_medium/porous_medium\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_porous_medium\" #> #> #> $xpath #> [1] \"processes/process/material_property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_material_property\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_medium.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_medium — prj_medium","title":"prj_medium — prj_medium","text":"tag: medium, specific medium optional id corresponding MaterialIDs","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_medium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_medium — prj_medium","text":"","code":"prj_medium(phases = NULL, properties = NULL, id = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_medium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_medium — prj_medium","text":"phases list, prj_phase: Optional: Medium phases properties list, prj_pr_property: Optional: Medium properties id string | double: Optional: ID corresponding MaterialIDs","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_medium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_medium — prj_medium","text":"","code":"prj_medium( phases = list( phase = prj_phase( type = \"Gas\", properties = list( property = prj_ph_property(name = \"viscosity\", type = \"Constant\", value = 1e-05) ) ), phase = prj_phase( type = \"Solid\", properties = list( property = prj_ph_property(name = \"porosity\", type = \"Constant\", value = 0.3) ) ) ), properties = list( property = prj_pr_property(name = \"reference_temperature\", type = \"Constant\", value = 293.15) ) ) #> $phases #> $phases$phase #> $type #> [1] \"Gas\" #> #> $properties #> $properties$property #> $name #> [1] \"viscosity\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 1e-05 #> #> $dvalue #> list() #> #> $reference_value #> NULL #> #> $independent_variable #> list() #> #> $offset #> NULL #> #> $exponent #> NULL #> #> $parameter_name #> NULL #> #> $swelling_pressures #> NULL #> #> $exponents #> NULL #> #> $lower_saturation_limit #> NULL #> #> $upper_saturation_limit #> NULL #> #> $tortuosity #> NULL #> #> $curve #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" \"exponents\" \"swelling_pressures\" #> #> $unwrap_on_exp #> [1] \"independent_variable\" \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_ph_property\" #> #> #> $components #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase\" #> #> $phases$phase #> $type #> [1] \"Solid\" #> #> $properties #> $properties$property #> $name #> [1] \"porosity\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 0.3 #> #> $dvalue #> list() #> #> $reference_value #> NULL #> #> $independent_variable #> list() #> #> $offset #> NULL #> #> $exponent #> NULL #> #> $parameter_name #> NULL #> #> $swelling_pressures #> NULL #> #> $exponents #> NULL #> #> $lower_saturation_limit #> NULL #> #> $upper_saturation_limit #> NULL #> #> $tortuosity #> NULL #> #> $curve #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" \"exponents\" \"swelling_pressures\" #> #> $unwrap_on_exp #> [1] \"independent_variable\" \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_ph_property\" #> #> #> $components #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase\" #> #> #> $properties #> $properties$property #> $name #> [1] \"reference_temperature\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 293.15 #> #> $parameter_name #> NULL #> #> $exponent #> NULL #> #> $residual_liquid_saturation #> NULL #> #> $residual_gas_saturation #> NULL #> #> $initial_porosity #> NULL #> #> $minimal_porosity #> NULL #> #> $maximal_porosity #> NULL #> #> $p_b #> NULL #> #> $independent_variable #> NULL #> #> $curve #> NULL #> #> $minimum_relative_permeability_liquid #> NULL #> #> $cutoff_value #> NULL #> #> $lambda #> NULL #> #> $min_relative_permeability #> NULL #> #> $initial_permeability #> NULL #> #> $maximum_permeability #> NULL #> #> $intrinsic_permeability #> NULL #> #> $initial_aperture #> NULL #> #> $mean_frac_distance #> NULL #> #> $mean_frac_distances #> NULL #> #> $threshold_strain #> NULL #> #> $threshold_strains #> NULL #> #> $fracture_normal #> NULL #> #> $fracture_normals #> NULL #> #> $fracture_rotation_xy #> NULL #> #> $fracture_rotation_yz #> NULL #> #> $reference_permeability #> NULL #> #> $fitting_factor #> NULL #> #> $cohesion #> NULL #> #> $friction_angle #> NULL #> #> $tensile_strength_parameter #> NULL #> #> $b1 #> NULL #> #> $b2 #> NULL #> #> $b3 #> NULL #> #> $minimum_permeability #> NULL #> #> $entry_pressure #> NULL #> #> $intrinsic_permeabilities #> NULL #> #> $exponents #> NULL #> #> $jacobian_factor #> NULL #> #> $dry_thermal_conductivity #> NULL #> #> $wet_thermal_conductivity #> NULL #> #> $mean_type #> NULL #> #> $dvalue #> list() #> #> $xpath #> [1] \"media/medium/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" #> #> $unwrap_on_exp #> [1] \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_pr_property\" #> #> #> $id #> NULL #> #> $xpath #> [1] \"media/medium\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_medium\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_micro_porosity.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_micro_porosity — prj_micro_porosity","title":"prj_micro_porosity — prj_micro_porosity","text":"tag: micro_porosity","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_micro_porosity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_micro_porosity — prj_micro_porosity","text":"","code":"prj_micro_porosity(mass_exchange_coefficient, nonlinear_solver)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_micro_porosity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_micro_porosity — prj_micro_porosity","text":"mass_exchange_coefficient Required: nonlinear_solver Required:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_nonlinear_solver.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_nonlinear_solver — prj_nonlinear_solver","title":"prj_nonlinear_solver — prj_nonlinear_solver","text":"tag: nonlinear_solver","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_nonlinear_solver.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_nonlinear_solver — prj_nonlinear_solver","text":"","code":"prj_nonlinear_solver(name, type, max_iter, linear_solver, damping = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_nonlinear_solver.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_nonlinear_solver — prj_nonlinear_solver","text":"name string: Name type string: Type max_iter string | double: Maximal number iterations linear_solver string: Name corresponding linear_solver damping Optional: string | double: Damping","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_nonlinear_solver.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_nonlinear_solver — prj_nonlinear_solver","text":"","code":"prj_nonlinear_solver( name = \"basic_newton\", type = \"Newton\", max_iter = 50, linear_solver = \"general_linear_solver\" ) #> $name #> [1] \"basic_newton\" #> #> $type #> [1] \"Newton\" #> #> $max_iter #> [1] 50 #> #> $linear_solver #> [1] \"general_linear_solver\" #> #> $damping #> NULL #> #> $xpath #> [1] \"nonlinear_solvers/nonlinear_solver\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_nonlinear_solver\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_output.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_output — prj_output","title":"prj_output — prj_output","text":"tag: output","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_output — prj_output","text":"","code":"prj_output( type, prefix, variables, suffix = NULL, timesteps = NULL, compress_output = NULL, data_mode = NULL, output_iteration_results = NULL, meshes = NULL, fixed_output_times = NULL, hdf = NULL, geometrical_sets = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_output — prj_output","text":"type string: prefix string: variables vector: suffix Optional: string: timesteps Optional: compress_output Optional: string: output compressed? Either \"true\" \"false\" data_mode Optional: string: output_iteration_results Optional: string: Either \"true\" \"false\" meshes Optional: list: list meshes fixed_output_times Optional: string | numeric: hdf Optional: numeric geometrical_sets Optional: list, prj_geometrical_set","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_output.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_output — prj_output","text":"","code":"prj_output( type = \"VTK\", prefix = \"flow_free_expansion\", variables = list( variable = \"displacement\", variable = \"pressure\" ), suffix = \"_ts_{:timestep}_t_{:time}\", timesteps = list(pair = list(1, each_steps = 1000)) ) #> $type #> [1] \"VTK\" #> #> $prefix #> [1] \"flow_free_expansion\" #> #> $variables #> $variables$variable #> [1] \"displacement\" #> #> $variables$variable #> [1] \"pressure\" #> #> #> $suffix #> [1] \"_ts_{:timestep}_t_{:time}\" #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1 #> #> $timesteps$pair$each_steps #> [1] 1000 #> #> #> #> $compress_output #> NULL #> #> $data_mode #> NULL #> #> $output_iteration_results #> NULL #> #> $meshes #> NULL #> #> $fixed_output_times #> NULL #> #> $hdf #> NULL #> #> $geometrical_sets #> NULL #> #> $xpath #> [1] \"time_loop/output\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"fixed_output_times\" #> #> attr(,\"class\") #> [1] \"prj_output\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_parameter.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_parameter — prj_parameter","title":"prj_parameter — prj_parameter","text":"tag: parameter","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_parameter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_parameter — prj_parameter","text":"","code":"prj_parameter( name, type, value = NULL, values = NULL, curve = NULL, parameter = NULL, group_id_property = NULL, field_name = NULL, mesh = NULL, time_series = NULL, use_local_coordinate_system = NULL, range = NULL, seed = NULL, ... )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_parameter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_parameter — prj_parameter","text":"name string: type string: value Optional: string | double: Parameter value values Optional: string | double: Parameter values curve Optional: string: parameter Optional: string: group_id_property Optional: string: field_name Optional: string: mesh Optional: string: time_series Optional: list: use_local_coordinate_system Optional: string, \"true\" | \"false\": range Optional: list seed Optional: number ... Optional: index_values expression tags (since can multiple)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_parameter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_parameter — prj_parameter","text":"","code":"prj_parameter(name = \"zero\", type = \"Constant\", value = 0) #> $name #> [1] \"zero\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 0 #> #> $values #> NULL #> #> $curve #> NULL #> #> $parameter #> NULL #> #> $group_id_property #> NULL #> #> $index_values #> list() #> #> $field_name #> NULL #> #> $mesh #> NULL #> #> $expression #> list() #> #> $time_series #> NULL #> #> $use_local_coordinate_system #> NULL #> #> $range #> NULL #> #> $seed #> NULL #> #> $xpath #> [1] \"parameters/parameter\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"values\" \"range\" #> #> $unwrap_on_exp #> [1] \"index_values\" \"expression\" #> #> attr(,\"class\") #> [1] \"prj_parameter\" prj_parameter(name = \"flux_in\", type = \"Constant\", value = 1e-04) #> $name #> [1] \"flux_in\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 1e-04 #> #> $values #> NULL #> #> $curve #> NULL #> #> $parameter #> NULL #> #> $group_id_property #> NULL #> #> $index_values #> list() #> #> $field_name #> NULL #> #> $mesh #> NULL #> #> $expression #> list() #> #> $time_series #> NULL #> #> $use_local_coordinate_system #> NULL #> #> $range #> NULL #> #> $seed #> NULL #> #> $xpath #> [1] \"parameters/parameter\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"values\" \"range\" #> #> $unwrap_on_exp #> [1] \"index_values\" \"expression\" #> #> attr(,\"class\") #> [1] \"prj_parameter\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_ph_property.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_ph_property — prj_ph_property","title":"prj_ph_property — prj_ph_property","text":"tag: property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_ph_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_ph_property — prj_ph_property","text":"","code":"prj_ph_property( name, type, value = NULL, reference_value = NULL, offset = NULL, exponent = NULL, parameter_name = NULL, swelling_pressures = NULL, exponents = NULL, lower_saturation_limit = NULL, upper_saturation_limit = NULL, tortuosity = NULL, curve = NULL, ... )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_ph_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_ph_property — prj_ph_property","text":"name string: type string: value Optional: reference_value Optional: offset Optional: exponent Optional: parameter_name Optional: swelling_pressures Optional: exponents Optional: lower_saturation_limit Optional: upper_saturation_limit Optional: tortuosity Optional: curve Optional: ... independent_variable, dvalue","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_ph_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_ph_property — prj_ph_property","text":"","code":"prj_ph_property(name = \"porosity\", type = \"Constant\", value = 0.3) #> $name #> [1] \"porosity\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 0.3 #> #> $dvalue #> list() #> #> $reference_value #> NULL #> #> $independent_variable #> list() #> #> $offset #> NULL #> #> $exponent #> NULL #> #> $parameter_name #> NULL #> #> $swelling_pressures #> NULL #> #> $exponents #> NULL #> #> $lower_saturation_limit #> NULL #> #> $upper_saturation_limit #> NULL #> #> $tortuosity #> NULL #> #> $curve #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" \"exponents\" \"swelling_pressures\" #> #> $unwrap_on_exp #> [1] \"independent_variable\" \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_ph_property\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_phase — prj_phase","title":"prj_phase — prj_phase","text":"tag: phase, coherent material homogeneous properties","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_phase — prj_phase","text":"","code":"prj_phase(type, properties = NULL, components = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_phase — prj_phase","text":"type string: Phase type (get valid types get_valid_phase_types()) properties list, prj_pr_property: Properties components list, components","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_phase — prj_phase","text":"","code":"prj_phase( type = \"Solid\", properties = list( property = prj_ph_property(name = \"porosity\", type = \"Constant\", value = 0.3) ) ) #> $type #> [1] \"Solid\" #> #> $properties #> $properties$property #> $name #> [1] \"porosity\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 0.3 #> #> $dvalue #> list() #> #> $reference_value #> NULL #> #> $independent_variable #> list() #> #> $offset #> NULL #> #> $exponent #> NULL #> #> $parameter_name #> NULL #> #> $swelling_pressures #> NULL #> #> $exponents #> NULL #> #> $lower_saturation_limit #> NULL #> #> $upper_saturation_limit #> NULL #> #> $tortuosity #> NULL #> #> $curve #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" \"exponents\" \"swelling_pressures\" #> #> $unwrap_on_exp #> [1] \"independent_variable\" \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_ph_property\" #> #> #> $components #> NULL #> #> $xpath #> [1] \"media/medium/phases/phase\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase_component.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_phase_component — prj_phase_component","title":"prj_phase_component — prj_phase_component","text":"S3 class describing .prj phase_component","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase_component.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_phase_component — prj_phase_component","text":"","code":"prj_phase_component(name, saturation_index, initial_amount = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase_component.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_phase_component — prj_phase_component","text":"name component name saturation_index saturation index component initial_amount optional: initial amount component","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phase_component.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_phase_component — prj_phase_component","text":"","code":"prj_phase_component( name = \"Calcite\", saturation_index = 0, initial_amount = 0.000207 ) #> $name #> [1] \"Calcite\" #> #> $saturation_index #> [1] 0 #> #> $initial_amount #> [1] 0.000207 #> #> $xpath #> [1] \"chemical_system/equilibrium_reactants/phase_component\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phase_component\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phasefield_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_phasefield_parameters — prj_phasefield_parameters","title":"prj_phasefield_parameters — prj_phasefield_parameters","text":"tag: phasefield_parameters","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phasefield_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_phasefield_parameters — prj_phasefield_parameters","text":"","code":"prj_phasefield_parameters( residual_stiffness, crack_resistance, crack_length_scale, kinetic_coefficient = NULL, history_field = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phasefield_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_phasefield_parameters — prj_phasefield_parameters","text":"residual_stiffness string: crack_resistance string: crack_length_scale string: kinetic_coefficient string: history_field Optional: string:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_phasefield_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_phasefield_parameters — prj_phasefield_parameters","text":"","code":"prj_phasefield_parameters( residual_stiffness = \"k\", crack_resistance = \"gc\", crack_length_scale = \"ls\", kinetic_coefficient = \"M\", history_field = \"H\" ) #> $residual_stiffness #> [1] \"k\" #> #> $crack_resistance #> [1] \"gc\" #> #> $crack_length_scale #> [1] \"ls\" #> #> $kinetic_coefficient #> [1] \"M\" #> #> $history_field #> [1] \"H\" #> #> $xpath #> [1] \"processes/process/phasefield_parameters\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_phasefield_parameters\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pipes.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_pipes — prj_pipes","title":"prj_pipes — prj_pipes","text":"tag: pipes","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pipes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_pipes — prj_pipes","text":"","code":"prj_pipes( longitudinal_dispersion_length, inlet = NULL, outlet = NULL, distance_between_pipes = NULL, outer = NULL, inner = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pipes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_pipes — prj_pipes","text":"longitudinal_dispersion_length string | double: inlet Optional: list: outlet Optional: list: distance_between_pipes Optional: string | double: outer Optional: list: inner Optional: list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pipes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_pipes — prj_pipes","text":"","code":"prj_pipes( longitudinal_dispersion_length = 0.001, inlet = list( diameter = \" 0.013665\", wall_thickness = \"0.003035\", wall_thermal_conductivity = \"0.39\" ), outlet = list( diameter = \"0.013665\", wall_thickness = \"0.003035\", wall_thermal_conductivity = \"0.39\" ), distance_between_pipes = 0.053 ) #> $longitudinal_dispersion_length #> [1] 0.001 #> #> $inlet #> $inlet$diameter #> [1] \" 0.013665\" #> #> $inlet$wall_thickness #> [1] \"0.003035\" #> #> $inlet$wall_thermal_conductivity #> [1] \"0.39\" #> #> #> $outlet #> $outlet$diameter #> [1] \"0.013665\" #> #> $outlet$wall_thickness #> [1] \"0.003035\" #> #> $outlet$wall_thermal_conductivity #> [1] \"0.39\" #> #> #> $distance_between_pipes #> [1] 0.053 #> #> $outer #> NULL #> #> $inner #> NULL #> #> $xpath #> [1] \"processes/process/borehole_heat_exchangers/borehole_heat_exchanger/pipes\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_pipes\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_porous_medium.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_porous_medium — prj_porous_medium","title":"prj_porous_medium — prj_porous_medium","text":"tag: porous_medium","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_porous_medium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_porous_medium — prj_porous_medium","text":"","code":"prj_porous_medium( id, permeability, porosity, storage, capillary_pressure, relative_permeability )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_porous_medium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_porous_medium — prj_porous_medium","text":"id string | double: permeability list: porosity list: storage list: capillary_pressure prj_capillary_pressure: relative_permeability list:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_porous_medium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_porous_medium — prj_porous_medium","text":"","code":"prj_porous_medium( id = 0, permeability = list(permeability_tensor_entries = \"kappa1\", type = \"Constant\"), porosity = list(type = \"Constant\", porosity_parameter = \"constant_porosity_parameter\"), storage = list(type = \"Constant\", value = \" 0.0 \"), capillary_pressure = prj_capillary_pressure( type = \"vanGenuchten\", pd = 2e+06, sr = 0.4, smax = 1, m = 0.3288590604, pc_max = 2e+07, has_regularized = \"true\" ), relative_permeability = list( relative_permeability = prj_relative_permeability( type = \"NonWettingPhaseVanGenuchten\", sr = 0, smax = 0.6, m = 0.3288590604, krel_min = 0, id = \"0\" ) ) ) #> $id #> [1] 0 #> #> $permeability #> $permeability$permeability_tensor_entries #> [1] \"kappa1\" #> #> $permeability$type #> [1] \"Constant\" #> #> #> $porosity #> $porosity$type #> [1] \"Constant\" #> #> $porosity$porosity_parameter #> [1] \"constant_porosity_parameter\" #> #> #> $storage #> $storage$type #> [1] \"Constant\" #> #> $storage$value #> [1] \" 0.0 \" #> #> #> $capillary_pressure #> $type #> [1] \"vanGenuchten\" #> #> $pd #> [1] 2e+06 #> #> $sr #> [1] 0.4 #> #> $smax #> [1] 1 #> #> $m #> [1] 0.3288591 #> #> $pc_max #> [1] 2e+07 #> #> $has_regularized #> [1] \"true\" #> #> $curve #> NULL #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/capillary_pressure\" #> [2] \"processes/process/porous_medium/porous_medium/capillary_pressure\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_capillary_pressure\" #> #> $relative_permeability #> $relative_permeability$relative_permeability #> $type #> [1] \"NonWettingPhaseVanGenuchten\" #> #> $sr #> [1] 0 #> #> $smax #> [1] 0.6 #> #> $m #> [1] 0.3288591 #> #> $krel_min #> [1] 0 #> #> $id #> [1] \"0\" #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/relative_permeability/relative_permeability\" #> [2] \"processes/process/porous_medium/porous_medium/relative_permeability\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_relative_permeability\" #> #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium\" #> [2] \"processes/process/porous_medium/porous_medium\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_porous_medium\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pr_property.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_pr_property — prj_pr_property","title":"prj_pr_property — prj_pr_property","text":"tag: property","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pr_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_pr_property — prj_pr_property","text":"","code":"prj_pr_property( name, type, value = NULL, parameter_name = NULL, exponent = NULL, residual_liquid_saturation = NULL, residual_gas_saturation = NULL, initial_porosity = NULL, minimal_porosity = NULL, maximal_porosity = NULL, p_b = NULL, independent_variable = NULL, curve = NULL, minimum_relative_permeability_liquid = NULL, cutoff_value = NULL, lambda = NULL, min_relative_permeability = NULL, initial_permeability = NULL, maximum_permeability = NULL, intrinsic_permeability = NULL, initial_aperture = NULL, mean_frac_distance = NULL, mean_frac_distances = NULL, threshold_strain = NULL, threshold_strains = NULL, fracture_normal = NULL, fracture_normals = NULL, fracture_rotation_xy = NULL, fracture_rotation_yz = NULL, reference_permeability = NULL, fitting_factor = NULL, cohesion = NULL, friction_angle = NULL, tensile_strength_parameter = NULL, b1 = NULL, b2 = NULL, b3 = NULL, minimum_permeability = NULL, entry_pressure = NULL, intrinsic_permeabilities = NULL, exponents = NULL, jacobian_factor = NULL, dry_thermal_conductivity = NULL, wet_thermal_conductivity = NULL, mean_type = NULL, ... )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pr_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_pr_property — prj_pr_property","text":"name string: type string: value Optional: parameter_name Optional: exponent Optional: residual_liquid_saturation Optional: residual_gas_saturation Optional: initial_porosity Optional: minimal_porosity Optional: maximal_porosity Optional: p_b Optional: independent_variable Optional: curve Optional: minimum_relative_permeability_liquid Optional: cutoff_value Optional: lambda Optional: min_relative_permeability Optional: initial_permeability Optional: maximum_permeability Optional: intrinsic_permeability Optional: initial_aperture Optional: mean_frac_distance Optional: mean_frac_distances Optional: numeric vector threshold_strain Optional: threshold_strains Optional: numeric vector fracture_normal Optional: fracture_normals Optional: numeric vector fracture_rotation_xy Optional: fracture_rotation_yz Optional: reference_permeability Optional: fitting_factor Optional: cohesion Optional: friction_angle Optional: tensile_strength_parameter Optional: b1 Optional: b2 Optional: b3 Optional: minimum_permeability Optional: entry_pressure Optional: intrinsic_permeabilities Optional: exponents Optional: jacobian_factor Optional: dry_thermal_conductivity Optional: wet_thermal_conductivity Optional: mean_type Optional: string ... dvalue","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_pr_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_pr_property — prj_pr_property","text":"","code":"prj_pr_property(name = \"reference_temperature\", type = \"Constant\", value = 293.15) #> $name #> [1] \"reference_temperature\" #> #> $type #> [1] \"Constant\" #> #> $value #> [1] 293.15 #> #> $parameter_name #> NULL #> #> $exponent #> NULL #> #> $residual_liquid_saturation #> NULL #> #> $residual_gas_saturation #> NULL #> #> $initial_porosity #> NULL #> #> $minimal_porosity #> NULL #> #> $maximal_porosity #> NULL #> #> $p_b #> NULL #> #> $independent_variable #> NULL #> #> $curve #> NULL #> #> $minimum_relative_permeability_liquid #> NULL #> #> $cutoff_value #> NULL #> #> $lambda #> NULL #> #> $min_relative_permeability #> NULL #> #> $initial_permeability #> NULL #> #> $maximum_permeability #> NULL #> #> $intrinsic_permeability #> NULL #> #> $initial_aperture #> NULL #> #> $mean_frac_distance #> NULL #> #> $mean_frac_distances #> NULL #> #> $threshold_strain #> NULL #> #> $threshold_strains #> NULL #> #> $fracture_normal #> NULL #> #> $fracture_normals #> NULL #> #> $fracture_rotation_xy #> NULL #> #> $fracture_rotation_yz #> NULL #> #> $reference_permeability #> NULL #> #> $fitting_factor #> NULL #> #> $cohesion #> NULL #> #> $friction_angle #> NULL #> #> $tensile_strength_parameter #> NULL #> #> $b1 #> NULL #> #> $b2 #> NULL #> #> $b3 #> NULL #> #> $minimum_permeability #> NULL #> #> $entry_pressure #> NULL #> #> $intrinsic_permeabilities #> NULL #> #> $exponents #> NULL #> #> $jacobian_factor #> NULL #> #> $dry_thermal_conductivity #> NULL #> #> $wet_thermal_conductivity #> NULL #> #> $mean_type #> NULL #> #> $dvalue #> list() #> #> $xpath #> [1] \"media/medium/properties/property\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"value\" #> #> $unwrap_on_exp #> [1] \"dvalue\" #> #> attr(,\"class\") #> [1] \"prj_pr_property\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_process — prj_process","title":"prj_process — prj_process","text":"tag: process (parent tag: processes)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_process — prj_process","text":"","code":"prj_process( name, type, integration_order, process_variables, secondary_variables = NULL, specific_body_force = NULL, solid_density = NULL, dimension = NULL, coupling_scheme = NULL, darcy_gravity = NULL, reference_temperature = NULL, fracture_model = NULL, jacobian_assembler = NULL, internal_length = NULL, mass_lumping = NULL, porosity = NULL, calculatesurfaceflux = NULL, intrinsic_permeability = NULL, specific_storage = NULL, fluid_viscosity = NULL, biot_coefficient = NULL, fluid_density = NULL, initial_effective_stress = NULL, initial_fracture_effective_stress = NULL, phasefield_parameters = NULL, deactivate_matrix_in_flow = NULL, borehole_heat_exchangers = NULL, temperature = NULL, reactive_system = NULL, fluid_specific_heat_source = NULL, fluid_specific_isobaric_heat_capacity = NULL, solid_hydraulic_permeability = NULL, solid_specific_heat_source = NULL, solid_heat_conductivity = NULL, solid_specific_isobaric_heat_capacity = NULL, tortuosity = NULL, diffusion_coefficient = NULL, solid_density_dry = NULL, solid_density_initial = NULL, characteristic_pressure = NULL, characteristic_temperature = NULL, characteristic_vapour_mass_fraction = NULL, output_element_matrices = NULL, material_property = NULL, diffusion_coeff_component_b = NULL, diffusion_coeff_component_a = NULL, hydro_crack_scheme = NULL, at_num = NULL, initial_stress = NULL, split_method = NULL, reg_param = NULL, thermal_parameters = NULL, non_advective_form = NULL, fluid = NULL, porous_medium = NULL, decay_rate = NULL, fluid_reference_density = NULL, retardation_factor = NULL, solute_dispersivity_longitudinal = NULL, solute_dispersivity_transverse = NULL, molecular_diffusion_coefficient = NULL, pf_irrv = NULL, micro_porosity = NULL, explicit_hm_coupling_in_unsaturated_zone = NULL, simplified_elasticity = NULL, chemically_induced_porosity_change = NULL, use_server_communication = NULL, phasefield_model = NULL, irreversible_threshold = NULL, tabular_file = NULL, temperature_field = NULL, use_stokes_brinkman_form = NULL, energy_split_model = NULL, softening_curve = NULL, characteristic_length = NULL, coupling_scheme_parameter = NULL, numerical_stabilization = NULL, aperture_size = NULL, linear = NULL, pressurized_crack_scheme = NULL, subtype = NULL, apply_body_force_for_deformation = NULL, ... )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_process — prj_process","text":"name string: type string: integration_order string | double: process_variables list, character: secondary_variables Optional: specific_body_force Optional: solid_density Optional: dimension Optional: coupling_scheme Optional: darcy_gravity Optional: reference_temperature Optional: fracture_model Optional: jacobian_assembler Optional: internal_length Optional: mass_lumping Optional: porosity Optional: calculatesurfaceflux Optional: intrinsic_permeability Optional: specific_storage Optional: fluid_viscosity Optional: biot_coefficient Optional: fluid_density Optional: initial_effective_stress Optional: initial_fracture_effective_stress Optional: phasefield_parameters Optional: deactivate_matrix_in_flow Optional: borehole_heat_exchangers Optional: temperature Optional: reactive_system Optional: fluid_specific_heat_source Optional: fluid_specific_isobaric_heat_capacity Optional: solid_hydraulic_permeability Optional: solid_specific_heat_source Optional: solid_heat_conductivity Optional: solid_specific_isobaric_heat_capacity Optional: tortuosity Optional: diffusion_coefficient Optional: solid_density_dry Optional: solid_density_initial Optional: characteristic_pressure Optional: characteristic_temperature Optional: characteristic_vapour_mass_fraction Optional: output_element_matrices Optional: material_property Optional: diffusion_coeff_component_b Optional: diffusion_coeff_component_a Optional: hydro_crack_scheme Optional: at_num Optional: initial_stress Optional: split_method Optional: reg_param Optional: thermal_parameters Optional: non_advective_form Optional: fluid Optional: porous_medium Optional: decay_rate Optional: fluid_reference_density Optional: retardation_factor Optional: solute_dispersivity_longitudinal Optional: solute_dispersivity_transverse Optional: molecular_diffusion_coefficient Optional: pf_irrv Optional: micro_porosity Optional: explicit_hm_coupling_in_unsaturated_zone Optional: simplified_elasticity Optional: character chemically_induced_porosity_change Optional: character use_server_communication Optional: phasefield_model Optional: irreversible_threshold Optional: numeric tabular_file Optional: character temperature_field Optional: character use_stokes_brinkman_form Optional: character energy_split_model Optional: string softening_curve Optional: string characteristic_length Optional: double coupling_scheme_parameter Optional: double numerical_stabilization Optional: list aperture_size Optional: list linear Optional: pressurized_crack_scheme Optional: subtype Optional: apply_body_force_for_deformation Optional: ... Optional: fracture_properties, constitutive_relation","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_process — prj_process","text":"","code":"prj_process( name = \"HM\", type = \"HYDRO_MECHANICS\", integration_order = 3, process_variables = list(displacement = \"displacement\", pressure = \"pressure\"), secondary_variables = list( secondary_variable = c(internal_name = \"sigma_xx\", output_name = \"sigma_xx\"), secondary_variable = c(internal_name = \"sigma_yy\", output_name = \"sigma_yy\") ), specific_body_force = c(0, 0, 0), dimension = 3, constitutive_relation = prj_constitutive_relation( type = \"LinearElasticIsotropic\", youngs_modulus = \"E\", poissons_ratio = \"nu\" ) ) #> $name #> [1] \"HM\" #> #> $type #> [1] \"HYDRO_MECHANICS\" #> #> $integration_order #> [1] 3 #> #> $process_variables #> $process_variables$displacement #> [1] \"displacement\" #> #> $process_variables$pressure #> [1] \"pressure\" #> #> #> $secondary_variables #> $secondary_variables$secondary_variable #> internal_name output_name #> \"sigma_xx\" \"sigma_xx\" #> #> $secondary_variables$secondary_variable #> internal_name output_name #> \"sigma_yy\" \"sigma_yy\" #> #> #> $specific_body_force #> [1] 0 0 0 #> #> $constitutive_relation #> $constitutive_relation$constitutive_relation #> $type #> [1] \"LinearElasticIsotropic\" #> #> $id #> NULL #> #> $youngs_modulus #> [1] \"E\" #> #> $poissons_ratio #> [1] \"nu\" #> #> $nonlinear_solver #> NULL #> #> $behaviour #> NULL #> #> $material_properties #> NULL #> #> $shear_modulus #> NULL #> #> $bulk_modulus #> NULL #> #> $kappa #> NULL #> #> $beta #> NULL #> #> $gamma #> NULL #> #> $hardening_modulus #> NULL #> #> $alpha #> NULL #> #> $delta #> NULL #> #> $eps #> NULL #> #> $m #> NULL #> #> $alphap #> NULL #> #> $deltap #> NULL #> #> $epsp #> NULL #> #> $mp #> NULL #> #> $betap #> NULL #> #> $gammap #> NULL #> #> $tangent_type #> NULL #> #> $damage_properties #> NULL #> #> $youngs_moduli #> NULL #> #> $shear_moduli #> NULL #> #> $poissons_ratios #> NULL #> #> $a #> NULL #> #> $n #> NULL #> #> $sigma0 #> NULL #> #> $q #> NULL #> #> $kelvin_shear_modulus #> NULL #> #> $kelvin_viscosity #> NULL #> #> $maxwell_shear_modulus #> NULL #> #> $maxwell_bulk_modulus #> NULL #> #> $maxwell_viscosity #> NULL #> #> $dependency_parameter_mk #> NULL #> #> $dependency_parameter_mvk #> NULL #> #> $dependency_parameter_mvm #> NULL #> #> $xpath #> [1] \"processes/process/constitutive_relation\" #> #> $attr_names #> [1] \"id\" \"material_property\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_constitutive_relation\" #> #> #> $solid_density #> NULL #> #> $dimension #> [1] 3 #> #> $coupling_scheme #> NULL #> #> $darcy_gravity #> NULL #> #> $reference_temperature #> NULL #> #> $fracture_model #> NULL #> #> $fracture_properties #> named list() #> #> $jacobian_assembler #> NULL #> #> $internal_length #> NULL #> #> $mass_lumping #> NULL #> #> $porosity #> NULL #> #> $calculatesurfaceflux #> NULL #> #> $intrinsic_permeability #> NULL #> #> $specific_storage #> NULL #> #> $fluid_viscosity #> NULL #> #> $biot_coefficient #> NULL #> #> $fluid_density #> NULL #> #> $initial_effective_stress #> NULL #> #> $initial_fracture_effective_stress #> NULL #> #> $phasefield_parameters #> NULL #> #> $deactivate_matrix_in_flow #> NULL #> #> $borehole_heat_exchangers #> NULL #> #> $temperature #> NULL #> #> $reactive_system #> NULL #> #> $fluid_specific_heat_source #> NULL #> #> $fluid_specific_isobaric_heat_capacity #> NULL #> #> $solid_hydraulic_permeability #> NULL #> #> $solid_specific_heat_source #> NULL #> #> $solid_heat_conductivity #> NULL #> #> $solid_specific_isobaric_heat_capacity #> NULL #> #> $tortuosity #> NULL #> #> $diffusion_coefficient #> NULL #> #> $solid_density_dry #> NULL #> #> $solid_density_initial #> NULL #> #> $characteristic_pressure #> NULL #> #> $characteristic_temperature #> NULL #> #> $characteristic_vapour_mass_fraction #> NULL #> #> $output_element_matrices #> NULL #> #> $material_property #> NULL #> #> $diffusion_coeff_component_b #> NULL #> #> $diffusion_coeff_component_a #> NULL #> #> $hydro_crack_scheme #> NULL #> #> $at_num #> NULL #> #> $initial_stress #> NULL #> #> $split_method #> NULL #> #> $reg_param #> NULL #> #> $thermal_parameters #> NULL #> #> $non_advective_form #> NULL #> #> $fluid #> NULL #> #> $porous_medium #> NULL #> #> $decay_rate #> NULL #> #> $fluid_reference_density #> NULL #> #> $retardation_factor #> NULL #> #> $solute_dispersivity_longitudinal #> NULL #> #> $solute_dispersivity_transverse #> NULL #> #> $molecular_diffusion_coefficient #> NULL #> #> $pf_irrv #> NULL #> #> $micro_porosity #> NULL #> #> $explicit_hm_coupling_in_unsaturated_zone #> NULL #> #> $simplified_elasticity #> NULL #> #> $chemically_induced_porosity_change #> NULL #> #> $use_server_communication #> NULL #> #> $phasefield_model #> NULL #> #> $irreversible_threshold #> NULL #> #> $tabular_file #> NULL #> #> $temperature_field #> NULL #> #> $use_stokes_brinkman_form #> NULL #> #> $energy_split_model #> NULL #> #> $softening_curve #> NULL #> #> $characteristic_length #> NULL #> #> $coupling_scheme_parameter #> NULL #> #> $numerical_stabilization #> NULL #> #> $aperture_size #> NULL #> #> $linear #> NULL #> #> $pressurized_crack_scheme #> NULL #> #> $subtype #> NULL #> #> $apply_body_force_for_deformation #> NULL #> #> $xpath #> [1] \"processes/process\" #> #> $attr_names #> [1] \"secondary_variable\" #> #> $flatten_on_exp #> [1] \"specific_body_force\" #> #> $unwrap_on_exp #> [1] \"fracture_properties\" \"constitutive_relation\" #> #> attr(,\"class\") #> [1] \"prj_process\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process_variable.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_process_variable — prj_process_variable","title":"prj_process_variable — prj_process_variable","text":"tag: process_variable","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process_variable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_process_variable — prj_process_variable","text":"","code":"prj_process_variable( name, components, order, initial_condition, boundary_conditions = NULL, source_terms = NULL, mesh = NULL, deactivated_subdomains = NULL, compensate_non_equilibrium_initial_residuum = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process_variable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_process_variable — prj_process_variable","text":"name string: name process variable components string | double: order string | double: initial_condition string: boundary_conditions list, prj_boundary_condition: source_terms Optional: list, prj_source_term: mesh Optional: string: list: deactivated_subdomains Optional: list, prj_deactivated_subdomain: compensate_non_equilibrium_initial_residuum Optional: string","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_process_variable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_process_variable — prj_process_variable","text":"","code":"prj_process_variable( name = \"pressure\", components = 1, order = 1, initial_condition = \"pressure0\", boundary_conditions = list( boundary_condition = prj_boundary_condition( type = \"Neumann\", parameter = \"flux_in\", geometrical_set = \"cube_1x1x1_geometry\", geometry = \"left\", component = 0 ) ) ) #> $name #> [1] \"pressure\" #> #> $components #> [1] 1 #> #> $order #> [1] 1 #> #> $initial_condition #> [1] \"pressure0\" #> #> $boundary_conditions #> $boundary_conditions$boundary_condition #> $type #> [1] \"Neumann\" #> #> $parameter #> [1] \"flux_in\" #> #> $geometrical_set #> [1] \"cube_1x1x1_geometry\" #> #> $geometry #> [1] \"left\" #> #> $component #> [1] 0 #> #> $mesh #> NULL #> #> $alpha #> NULL #> #> $u_0 #> NULL #> #> $constraint_type #> NULL #> #> $constraining_process_variable #> NULL #> #> $constraint_threshold #> NULL #> #> $constraint_direction #> NULL #> #> $area_parameter #> NULL #> #> $bc_object #> NULL #> #> $flush_stdout #> NULL #> #> $property_name #> NULL #> #> $initial_value_parameter #> NULL #> #> $constant_name #> NULL #> #> $coefficient_current_variable_name #> NULL #> #> $coefficient_other_variable_name #> NULL #> #> $coefficient_mixed_variables_name #> NULL #> #> $threshold_parameter #> NULL #> #> $comparison_operator #> NULL #> #> $time_interval #> NULL #> #> $xpath #> [1] \"process_variables/process_variable/boundary_conditions/boundary_condition\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_boundary_condition\" #> #> #> $source_terms #> NULL #> #> $mesh #> NULL #> #> $deactivated_subdomains #> NULL #> #> $compensate_non_equilibrium_initial_residuum #> NULL #> #> $xpath #> [1] \"process_variables/process_variable\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_process_variable\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_python_script.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_python_script — prj_python_script","title":"prj_python_script — prj_python_script","text":"tag: python_script","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_python_script.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_python_script — prj_python_script","text":"","code":"prj_python_script(file_path)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_python_script.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_python_script — prj_python_script","text":"file_path string: Path name python script file (*.py).","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_python_script.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_python_script — prj_python_script","text":"","code":"prj_python_script(file_path = \"bcs_laplace_eq.py\") #> [[1]] #> [1] \"bcs_laplace_eq.py\" #> #> $xpath #> [1] \"python_script\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_python_script\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_rate — prj_rate","title":"prj_rate — prj_rate","text":"S3 class describing .prj rate","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_rate — prj_rate","text":"","code":"prj_rate(kinetic_reactant, expression)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_rate — prj_rate","text":"kinetic_reactant string: References kinetic_reactant object expression character: Statements","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_rate — prj_rate","text":"","code":"prj_rate( kinetic_reactant = \"Productc\", expression = list( statement = \"Km = 10\", statement = \"U = 1e-3\", statement = \"rate = U * TOT(\\\"Synthetica\\\") / (Km + TOT(\\\"Syntheticb\\\"))\", statement = \"moles = - rate * TIME\", statement = \"save moles\" ) ) #> $kinetic_reactant #> [1] \"Productc\" #> #> $expression #> $expression$statement #> [1] \"Km = 10\" #> #> $expression$statement #> [1] \"U = 1e-3\" #> #> $expression$statement #> [1] \"rate = U * TOT(\\\"Synthetica\\\") / (Km + TOT(\\\"Syntheticb\\\"))\" #> #> $expression$statement #> [1] \"moles = - rate * TIME\" #> #> $expression$statement #> [1] \"save moles\" #> #> #> $xpath #> [1] \"chemical_system/rates/rate\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_rate\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_relative_permeability.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_relative_permeability — prj_relative_permeability","title":"prj_relative_permeability — prj_relative_permeability","text":"tag: relative_permeability","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_relative_permeability.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_relative_permeability — prj_relative_permeability","text":"","code":"prj_relative_permeability(type, sr, smax, m, krel_min, id = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_relative_permeability.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_relative_permeability — prj_relative_permeability","text":"type string: sr string | number: smax string | number: m string | number: krel_min string | number: id string: Optional:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_relative_permeability.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_relative_permeability — prj_relative_permeability","text":"","code":"prj_relative_permeability( type = \"NonWettingPhaseVanGenuchten\", sr = 0, smax = 0.6, m = 0.3288590604, krel_min = 0, id = \"0\" ) #> $type #> [1] \"NonWettingPhaseVanGenuchten\" #> #> $sr #> [1] 0 #> #> $smax #> [1] 0.6 #> #> $m #> [1] 0.3288591 #> #> $krel_min #> [1] 0 #> #> $id #> [1] \"0\" #> #> $xpath #> [1] \"processes/process/material_property/porous_medium/porous_medium/relative_permeability/relative_permeability\" #> [2] \"processes/process/porous_medium/porous_medium/relative_permeability\" #> #> $attr_names #> [1] \"id\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_relative_permeability\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_search_length_algorithm.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_search_length_algorithm — prj_search_length_algorithm","title":"prj_search_length_algorithm — prj_search_length_algorithm","text":"tag: search_length_algorithm","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_search_length_algorithm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_search_length_algorithm — prj_search_length_algorithm","text":"","code":"prj_search_length_algorithm(type, value = NULL)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_search_length_algorithm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_search_length_algorithm — prj_search_length_algorithm","text":"type string: type value string | double: value","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_search_length_algorithm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_search_length_algorithm — prj_search_length_algorithm","text":"","code":"prj_search_length_algorithm(type = \"fixed\", value = 1e-06) #> $type #> [1] \"fixed\" #> #> $value #> [1] 1e-06 #> #> $xpath #> [1] \"search_length_algorithm\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_search_length_algorithm\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_solution.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_solution — prj_solution","title":"prj_solution — prj_solution","text":"tag: solution","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_solution — prj_solution","text":"","code":"prj_solution( temperature, pressure, pe, components, charge_balance = NULL, fixing_pe = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_solution — prj_solution","text":"temperature string | double: Temperature pressure string | double: Pressure pe string | double: pe components list: Components charge_balance Optional: string: Charge balance fixing_pe Optional: string","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_solution — prj_solution","text":"","code":"prj_solution( temperature = 25, pressure = 1, pe = 4, components = list( component = \"C(4)\", component = \"Ca\" ), charge_balance = \"pH\" ) #> $temperature #> [1] 25 #> #> $pressure #> [1] 1 #> #> $pe #> [1] 4 #> #> $components #> $components$component #> [1] \"C(4)\" #> #> $components$component #> [1] \"Ca\" #> #> #> $charge_balance #> [1] \"pH\" #> #> $fixing_pe #> NULL #> #> $xpath #> [1] \"chemical_system/solution\" #> #> $attr_names #> [1] \"fixing_pe\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_solution\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_source_term.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_source_term — prj_source_term","title":"prj_source_term — prj_source_term","text":"tag: source_term","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_source_term.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_source_term — prj_source_term","text":"","code":"prj_source_term( type, parameter = NULL, geometrical_set = NULL, geometry = NULL, mesh = NULL, source_term_object = NULL, flush_stdout = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_source_term.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_source_term — prj_source_term","text":"type string: parameter Optional: string: geometrical_set Optional: string: geometry Optional: string: mesh Optional: string: source_term_object Optional: string: flush_stdout Optional: string:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_source_term.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_source_term — prj_source_term","text":"","code":"prj_source_term( type = \"Nodal\", parameter = \"sourceterm_heat_transfer_coefficient\", geometrical_set = \"geometry\", geometry = \"po0\" ) #> $type #> [1] \"Nodal\" #> #> $parameter #> [1] \"sourceterm_heat_transfer_coefficient\" #> #> $geometrical_set #> [1] \"geometry\" #> #> $geometry #> [1] \"po0\" #> #> $mesh #> NULL #> #> $source_term_object #> NULL #> #> $flush_stdout #> NULL #> #> $xpath #> [1] \"process_variables/process_variable/source_terms/source_term\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_source_term\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_submesh_residuum_output.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_submesh_residuum_output — prj_submesh_residuum_output","title":"prj_submesh_residuum_output — prj_submesh_residuum_output","text":"tag: submesh_residuum_output","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_submesh_residuum_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_submesh_residuum_output — prj_submesh_residuum_output","text":"","code":"prj_submesh_residuum_output( type, prefix, variables, suffix = NULL, timesteps = NULL, compress_output = NULL, data_mode = NULL, output_iteration_results = NULL, meshes = NULL, fixed_output_times = NULL, hdf = NULL, geometrical_sets = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_submesh_residuum_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_submesh_residuum_output — prj_submesh_residuum_output","text":"type string: prefix string: variables vector: suffix Optional: string: timesteps Optional: compress_output Optional: string: output compressed? Either \"true\" \"false\" data_mode Optional: string: output_iteration_results Optional: string: Either \"true\" \"false\" meshes Optional: list: list meshes fixed_output_times Optional: string | numeric: hdf Optional: numeric geometrical_sets Optional: list, prj_geometrical_set","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_surface.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_surface — prj_surface","title":"prj_surface — prj_surface","text":"tag: surface","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_surface.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_surface — prj_surface","text":"","code":"prj_surface(site_unit = NULL, ...)"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_surface.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_surface — prj_surface","text":"site_unit Optional: string ... site","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_loop.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_time_loop — prj_time_loop","title":"prj_time_loop — prj_time_loop","text":"tag: time_loop","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_loop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_time_loop — prj_time_loop","text":"","code":"prj_time_loop( processes, output, global_process_coupling = NULL, submesh_residuum_output = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_loop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_time_loop — prj_time_loop","text":"processes list, prj_tl_process: output prj_output: global_process_coupling Optional: prj_global_process_coupling: submesh_residuum_output Optional: prj_submesh_residuum_output:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_loop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_time_loop — prj_time_loop","text":"","code":"prj_time_loop( processes = list( process = prj_tl_process( ref = \"HM\", nonlinear_solver = \"basic_newton\", convergence_criterion = prj_convergence_criterion( type = \"DeltaX\", norm_type = \"NORM2\", reltol = 1e-08 ), time_discretization = list(type = \"BackwardEuler\"), time_stepping = prj_time_stepping( type = \"FixedTimeStepping\", t_initial = 0, t_end = 10000, timesteps = list(pair = list(1000, delta_t = 10)) ) ) ), output = prj_output( type = \"VTK\", prefix = \"flow_free_expansion\", variables = list( variable = \"displacement\", variable = \"pressure\" ), suffix = \"_ts_{:timestep}_t_{:time}\", timesteps = list(pair = list(1, each_steps = 1000)) ) ) #> $processes #> $processes$process #> $ref #> [1] \"HM\" #> #> $nonlinear_solver #> [1] \"basic_newton\" #> #> $convergence_criterion #> $type #> [1] \"DeltaX\" #> #> $norm_type #> [1] \"NORM2\" #> #> $abstol #> NULL #> #> $reltol #> [1] 1e-08 #> #> $abstols #> NULL #> #> $reltols #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/convergence_criterion\" #> [2] \"time_loop/global_process_coupling/convergence_criteria/convergence_criterion\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"abstols\" \"reltols\" #> #> attr(,\"class\") #> [1] \"prj_convergence_criterion\" #> #> $time_discretization #> $time_discretization$type #> [1] \"BackwardEuler\" #> #> #> $time_stepping #> $type #> [1] \"FixedTimeStepping\" #> #> $t_initial #> [1] 0 #> #> $t_end #> [1] 10000 #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1000 #> #> $timesteps$pair$delta_t #> [1] 10 #> #> #> #> $initial_dt #> NULL #> #> $minimum_dt #> NULL #> #> $maximum_dt #> NULL #> #> $number_iterations #> NULL #> #> $multiplier #> NULL #> #> $dt_guess #> NULL #> #> $dt_min #> NULL #> #> $dt_max #> NULL #> #> $rel_dt_min #> NULL #> #> $rel_dt_max #> NULL #> #> $tol #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/time_stepping\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"number_iterations\" \"multiplier\" #> #> attr(,\"class\") #> [1] \"prj_time_stepping\" #> #> $compensate_non_equilibrium_initial_residuum #> NULL #> #> $xpath #> [1] \"time_loop/processes/process\" #> #> $attr_names #> [1] \"ref\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_tl_process\" #> #> #> $output #> $type #> [1] \"VTK\" #> #> $prefix #> [1] \"flow_free_expansion\" #> #> $variables #> $variables$variable #> [1] \"displacement\" #> #> $variables$variable #> [1] \"pressure\" #> #> #> $suffix #> [1] \"_ts_{:timestep}_t_{:time}\" #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1 #> #> $timesteps$pair$each_steps #> [1] 1000 #> #> #> #> $compress_output #> NULL #> #> $data_mode #> NULL #> #> $output_iteration_results #> NULL #> #> $meshes #> NULL #> #> $fixed_output_times #> NULL #> #> $hdf #> NULL #> #> $geometrical_sets #> NULL #> #> $xpath #> [1] \"time_loop/output\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"fixed_output_times\" #> #> attr(,\"class\") #> [1] \"prj_output\" #> #> $global_process_coupling #> NULL #> #> $submesh_residuum_output #> NULL #> #> $xpath #> [1] \"time_loop\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_time_loop\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_stepping.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_time_stepping — prj_time_stepping","title":"prj_time_stepping — prj_time_stepping","text":"tag: time_stepping","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_stepping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_time_stepping — prj_time_stepping","text":"","code":"prj_time_stepping( type, t_initial = NULL, t_end = NULL, timesteps = NULL, initial_dt = NULL, minimum_dt = NULL, maximum_dt = NULL, number_iterations = NULL, multiplier = NULL, dt_guess = NULL, dt_min = NULL, dt_max = NULL, rel_dt_min = NULL, rel_dt_max = NULL, tol = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_stepping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_time_stepping — prj_time_stepping","text":"type string: t_initial Optional: string | double: t_end Optional: string | double: timesteps Optional: list: initial_dt Optional: string | double: minimum_dt Optional: string | double: maximum_dt Optional: string | double: number_iterations Optional: string | numeric: multiplier Optional: string | numeric: dt_guess Optional: string | double: dt_min Optional: string | double: dt_max Optional: string | double: rel_dt_min Optional: string | double: rel_dt_max Optional: string | double: tol Optional: string | double:","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_time_stepping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_time_stepping — prj_time_stepping","text":"","code":"prj_time_stepping( type = \"FixedTimeStepping\", t_initial = 0, t_end = 10000, timesteps = list(pair = list(1000, delta_t = 10)) ) #> $type #> [1] \"FixedTimeStepping\" #> #> $t_initial #> [1] 0 #> #> $t_end #> [1] 10000 #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1000 #> #> $timesteps$pair$delta_t #> [1] 10 #> #> #> #> $initial_dt #> NULL #> #> $minimum_dt #> NULL #> #> $maximum_dt #> NULL #> #> $number_iterations #> NULL #> #> $multiplier #> NULL #> #> $dt_guess #> NULL #> #> $dt_min #> NULL #> #> $dt_max #> NULL #> #> $rel_dt_min #> NULL #> #> $rel_dt_max #> NULL #> #> $tol #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/time_stepping\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"number_iterations\" \"multiplier\" #> #> attr(,\"class\") #> [1] \"prj_time_stepping\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_tl_process.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_tl_process — prj_tl_process","title":"prj_tl_process — prj_tl_process","text":"tag: process (parent: time_loop, processes!)","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_tl_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_tl_process — prj_tl_process","text":"","code":"prj_tl_process( ref, nonlinear_solver, convergence_criterion, time_discretization, time_stepping, compensate_non_equilibrium_initial_residuum = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_tl_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_tl_process — prj_tl_process","text":"ref string: References prj_process object name nonlinear_solver string: convergence_criterion prj_convergence_criterion: time_discretization vector: time_stepping prj_time_stepping: compensate_non_equilibrium_initial_residuum string: Optional: Either \"true\" \"false\"","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_tl_process.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_tl_process — prj_tl_process","text":"","code":"prj_tl_process( ref = \"HM\", nonlinear_solver = \"basic_newton\", convergence_criterion = prj_convergence_criterion( type = \"DeltaX\", norm_type = \"NORM2\", reltol = 1e-08 ), time_discretization = list(type = \"BackwardEuler\"), time_stepping = prj_time_stepping( type = \"FixedTimeStepping\", t_initial = 0, t_end = 10000, timesteps = list(pair = list(1000, delta_t = 10)) ) ) #> $ref #> [1] \"HM\" #> #> $nonlinear_solver #> [1] \"basic_newton\" #> #> $convergence_criterion #> $type #> [1] \"DeltaX\" #> #> $norm_type #> [1] \"NORM2\" #> #> $abstol #> NULL #> #> $reltol #> [1] 1e-08 #> #> $abstols #> NULL #> #> $reltols #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/convergence_criterion\" #> [2] \"time_loop/global_process_coupling/convergence_criteria/convergence_criterion\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"abstols\" \"reltols\" #> #> attr(,\"class\") #> [1] \"prj_convergence_criterion\" #> #> $time_discretization #> $time_discretization$type #> [1] \"BackwardEuler\" #> #> #> $time_stepping #> $type #> [1] \"FixedTimeStepping\" #> #> $t_initial #> [1] 0 #> #> $t_end #> [1] 10000 #> #> $timesteps #> $timesteps$pair #> $timesteps$pair$`repeat` #> [1] 1000 #> #> $timesteps$pair$delta_t #> [1] 10 #> #> #> #> $initial_dt #> NULL #> #> $minimum_dt #> NULL #> #> $maximum_dt #> NULL #> #> $number_iterations #> NULL #> #> $multiplier #> NULL #> #> $dt_guess #> NULL #> #> $dt_min #> NULL #> #> $dt_max #> NULL #> #> $rel_dt_min #> NULL #> #> $rel_dt_max #> NULL #> #> $tol #> NULL #> #> $xpath #> [1] \"time_loop/processes/process/time_stepping\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> [1] \"number_iterations\" \"multiplier\" #> #> attr(,\"class\") #> [1] \"prj_time_stepping\" #> #> $compensate_non_equilibrium_initial_residuum #> NULL #> #> $xpath #> [1] \"time_loop/processes/process\" #> #> $attr_names #> [1] \"ref\" #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_tl_process\""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_vtkdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"prj_vtkdiff — prj_vtkdiff","title":"prj_vtkdiff — prj_vtkdiff","text":"tag: vtkdiff","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_vtkdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prj_vtkdiff — prj_vtkdiff","text":"","code":"prj_vtkdiff( field, absolute_tolerance, relative_tolerance, file = NULL, regex = NULL )"},{"path":"https://joboog.github.io/r2ogs6/reference/prj_vtkdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prj_vtkdiff — prj_vtkdiff","text":"field string: ... absolute_tolerance string | double: Absolute tolerance relative_tolerance string | double: Relative tolerance file string: Optional: File regex string: Optional: regular expression","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/prj_vtkdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prj_vtkdiff — prj_vtkdiff","text":"","code":"prj_vtkdiff(field = \"displacement\", absolute_tolerance = 1e-15, relative_tolerance = 0, regex = \"gravity_pcs_0_ts_.*_t_.*.vtu\") #> $field #> [1] \"displacement\" #> #> $absolute_tolerance #> [1] 1e-15 #> #> $relative_tolerance #> [1] 0 #> #> $file #> NULL #> #> $regex #> [1] \"gravity_pcs_0_ts_.*_t_.*.vtu\" #> #> $xpath #> [1] \"test_definition/vtkdiff\" #> #> $attr_names #> character(0) #> #> $flatten_on_exp #> character(0) #> #> attr(,\"class\") #> [1] \"prj_vtkdiff\""},{"path":"https://joboog.github.io/r2ogs6/reference/read_in_prj.html","id":null,"dir":"Reference","previous_headings":"","what":"read_in_prj — read_in_prj","title":"read_in_prj — read_in_prj","text":"Wrapper function read whole .prj file","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/read_in_prj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read_in_prj — read_in_prj","text":"","code":"read_in_prj( ogs6_obj, prj_path, read_in_gml, read_in_vtu = FALSE, read_includes = FALSE )"},{"path":"https://joboog.github.io/r2ogs6/reference/read_in_prj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_in_prj — read_in_prj","text":"ogs6_obj OGS6: Simulation object prj_path string: Path .prj file read read_in_gml flag: Optional: .gml file just copied read ? parameter missing .gml file contains <= options(\"r2ogs6.max_lines_gml\"), .gml read . Else, geometry reference saved. read_in_vtu flag: .vtu file just copied read read_includes flag: files referenced include tages read ?","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/set_ogs6_bin_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Set default OpenGeoSys 6 binary path — set_ogs6_bin_path","title":"Set default OpenGeoSys 6 binary path — set_ogs6_bin_path","text":"function automatically detects temporarily sets path OpenGeoSys (OGS) binary within active Python virtual environment. typically called installing OGS using `install_ogs()` function. permanent setting OGS binary path, consider define `r2ogs6.default_ogs6_bin_path` `config.yml` file.'","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/set_ogs6_bin_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set default OpenGeoSys 6 binary path — set_ogs6_bin_path","text":"","code":"set_ogs6_bin_path()"},{"path":"https://joboog.github.io/r2ogs6/reference/set_ogs6_bin_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set default OpenGeoSys 6 binary path — set_ogs6_bin_path","text":"None, sets option `r2ogs6.default_ogs6_bin_path` point detected OGS binary path.","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/xpaths_for_classes.html","id":null,"dir":"Reference","previous_headings":"","what":"xpaths_for_classes — xpaths_for_classes","title":"xpaths_for_classes — xpaths_for_classes","text":"Path .xml document containing information .prj file structure","code":""},{"path":"https://joboog.github.io/r2ogs6/reference/xpaths_for_classes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"xpaths_for_classes — xpaths_for_classes","text":"","code":"xpaths_for_classes"},{"path":"https://joboog.github.io/r2ogs6/reference/xpaths_for_classes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"xpaths_for_classes — xpaths_for_classes","text":"list: named list character vectors names r2ogs6 class names values corresponding xpaths","code":""}]