From 5b55640fd9013bd46b012fc16a600c427e7f2fb4 Mon Sep 17 00:00:00 2001 From: Shyue Ping Ong Date: Sun, 13 Feb 2022 07:10:55 -0800 Subject: [PATCH] Update dev docs --- custodian/__init__.py | 2 +- docs/_modules/custodian/ansible/actions.html | 4 +- .../custodian/ansible/interpreter.html | 4 +- docs/_modules/custodian/cli/cstdn.html | 4 +- docs/_modules/custodian/custodian.html | 4 +- docs/_modules/custodian/feff/jobs.html | 4 +- docs/_modules/custodian/lobster/jobs.html | 15 +- docs/_modules/custodian/nwchem/jobs.html | 4 +- docs/_modules/custodian/qchem/utils.html | 6 +- docs/_modules/custodian/utils.html | 4 +- docs/_modules/index.html | 16 +- docs/_static/documentation_options.js | 2 +- docs/_themes/README.html | 4 +- docs/changelog.html | 12 +- docs/custodian.ansible.html | 4 +- docs/custodian.cli.html | 99 +- docs/custodian.feff.html | 95 +- docs/custodian.html | 28 +- docs/custodian.lobster.html | 69 +- docs/custodian.nwchem.html | 42 +- docs/custodian.qchem.html | 4 +- docs/custodian.vasp.html | 1291 +---------------- docs/genindex.html | 427 +----- docs/index.html | 8 +- docs/modules.html | 28 +- docs/objects.inv | Bin 2017 -> 1136 bytes docs/py-modindex.html | 64 +- docs/search.html | 4 +- docs/searchindex.js | 2 +- setup.py | 2 +- 30 files changed, 146 insertions(+), 2106 deletions(-) diff --git a/custodian/__init__.py b/custodian/__init__.py index ab4276ee..c9515cce 100644 --- a/custodian/__init__.py +++ b/custodian/__init__.py @@ -4,6 +4,6 @@ """ __author__ = "Shyue Ping Ong, William Davidson Richards, Stephen Dacek, Xiaohui Qu, Matthew Horton, Samuel M. Blau" -__version__ = "2022.1.17" +__version__ = "2022.2.13" from .custodian import Custodian diff --git a/docs/_modules/custodian/ansible/actions.html b/docs/_modules/custodian/ansible/actions.html index 139d915b..ee01ad58 100644 --- a/docs/_modules/custodian/ansible/actions.html +++ b/docs/_modules/custodian/ansible/actions.html @@ -5,7 +5,7 @@ - custodian.ansible.actions — custodian 2022.1.17 documentation + custodian.ansible.actions — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

Navigation

  • modules |
    • -
  • custodian 2022.1.17 documentation »
    • +
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  • custodian.ansible.actions
    • diff --git a/docs/_modules/custodian/ansible/interpreter.html b/docs/_modules/custodian/ansible/interpreter.html index ea526c9e..0fc7d034 100644 --- a/docs/_modules/custodian/ansible/interpreter.html +++ b/docs/_modules/custodian/ansible/interpreter.html @@ -5,7 +5,7 @@ - custodian.ansible.interpreter — custodian 2022.1.17 documentation + custodian.ansible.interpreter — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

    Navigation

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    • diff --git a/docs/_modules/custodian/cli/cstdn.html b/docs/_modules/custodian/cli/cstdn.html index 2f57d5de..4cf25413 100644 --- a/docs/_modules/custodian/cli/cstdn.html +++ b/docs/_modules/custodian/cli/cstdn.html @@ -5,7 +5,7 @@ - custodian.cli.cstdn — custodian 2022.1.17 documentation + custodian.cli.cstdn — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

    Navigation

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  • custodian.cli.cstdn
    • diff --git a/docs/_modules/custodian/custodian.html b/docs/_modules/custodian/custodian.html index 38a88503..d86412bf 100644 --- a/docs/_modules/custodian/custodian.html +++ b/docs/_modules/custodian/custodian.html @@ -5,7 +5,7 @@ - custodian.custodian — custodian 2022.1.17 documentation + custodian.custodian — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

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  • custodian 2022.1.17 documentation »
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  • custodian.custodian
    • diff --git a/docs/_modules/custodian/feff/jobs.html b/docs/_modules/custodian/feff/jobs.html index 10097b87..7de65df0 100644 --- a/docs/_modules/custodian/feff/jobs.html +++ b/docs/_modules/custodian/feff/jobs.html @@ -5,7 +5,7 @@ - custodian.feff.jobs — custodian 2022.1.17 documentation + custodian.feff.jobs — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

    Navigation

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    • diff --git a/docs/_modules/custodian/lobster/jobs.html b/docs/_modules/custodian/lobster/jobs.html index f0b07bf7..6fd19051 100644 --- a/docs/_modules/custodian/lobster/jobs.html +++ b/docs/_modules/custodian/lobster/jobs.html @@ -5,7 +5,7 @@ - custodian.lobster.jobs — custodian 2022.1.17 documentation + custodian.lobster.jobs — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

    Navigation

  • modules |
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  • custodian.lobster.jobs
    • @@ -60,7 +60,7 @@

    Source code for custodian.lobster.jobs

     
 from custodian.custodian import Job
 
-__author__ = "Janine George, Guido Petretto"
+__author__ = "Janine George, Guido Petretto,Aakash Naik"
 __copyright__ = "Copyright 2020, The Materials Project"
 __version__ = "0.1"
 __maintainer__ = "Janine George"
@@ -79,7 +79,13 @@ 
    Source code for custodian.lobster.jobs
         "ICOOPLIST.lobster",
     "lobster.out",
     "projectionData.lobster",
+    "MadelungEnergies.lobster",
+    "SitePotentials.lobster",
+    "bandOverlaps.lobster",
+    "ICOBILIST.lobster",
+    "COBICAR.lobster",
 ]
+FW_FILES = ["custodian.json", "FW.json", "FW_submit.script"]
 
 logger = logging.getLogger(__name__)
 
@@ -149,6 +155,9 @@ 
    Source code for custodian.lobster.jobs
                 if self.backup:
                 if os.path.exists("lobsterin.orig"):
                     compress_file("lobsterin.orig", compression="gz")
+            for file in FW_FILES:
+                if os.path.exists(file):
+                    compress_file(file, compression="gz")
             for file in self.add_files_to_gzip:
                 compress_file(file, compression="gz")
    diff --git a/docs/_modules/custodian/nwchem/jobs.html b/docs/_modules/custodian/nwchem/jobs.html index 3f612c8f..cdbd9ef2 100644 --- a/docs/_modules/custodian/nwchem/jobs.html +++ b/docs/_modules/custodian/nwchem/jobs.html @@ -5,7 +5,7 @@ - custodian.nwchem.jobs — custodian 2022.1.17 documentation + custodian.nwchem.jobs — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

    Navigation

  • modules |
    • -
  • custodian 2022.1.17 documentation »
    • +
  • custodian 2022.2.13 documentation »
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  • custodian.nwchem.jobs
    • diff --git a/docs/_modules/custodian/qchem/utils.html b/docs/_modules/custodian/qchem/utils.html index d2956152..c2178b15 100644 --- a/docs/_modules/custodian/qchem/utils.html +++ b/docs/_modules/custodian/qchem/utils.html @@ -5,7 +5,7 @@ - custodian.qchem.utils — custodian 2022.1.17 documentation + custodian.qchem.utils — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

    Navigation

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  • custodian.qchem.utils
    • @@ -69,7 +69,7 @@

    Source code for custodian.qchem.utils

         reversed_direction (bool): If True, then perturb in direction opposite of frequency modes.
 
     """
-    max_dis = max(math.sqrt(sum(x ** 2 for x in vec)) for vec in negative_freq_vecs)
+    max_dis = max(math.sqrt(sum(x**2 for x in vec)) for vec in negative_freq_vecs)
     scale = molecule_perturb_scale / max_dis
     normalized_vecs = [[x * scale for x in vec] for vec in negative_freq_vecs]
     direction = 1.0
diff --git a/docs/_modules/custodian/utils.html b/docs/_modules/custodian/utils.html
index 1418741d..54b482ad 100644
--- a/docs/_modules/custodian/utils.html
+++ b/docs/_modules/custodian/utils.html
@@ -5,7 +5,7 @@
   
     
     
-    custodian.utils — custodian 2022.1.17 documentation
+    custodian.utils — custodian 2022.2.13 documentation
     
     
     
@@ -36,7 +36,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • custodian 2022.1.17 documentation »
    • 
+        
  • custodian 2022.2.13 documentation »
    • 
           
  • Module code »
    • 
         
  • custodian.utils
    •  
       
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index 2aad0951..4995cc93 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -5,7 +5,7 @@
   
     
     
-    Overview: module code — custodian 2022.1.17 documentation
+    Overview: module code — custodian 2022.2.13 documentation
     
     
     
@@ -36,7 +36,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • custodian 2022.1.17 documentation »
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+        
  • custodian 2022.2.13 documentation »
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  • Overview: module code
    •
    @@ -49,25 +49,13 @@

    Navigation

    All modules for which code is available

    diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index e95ca3d9..c8afe1ac 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '2022.1.17', + VERSION: '2022.2.13', LANGUAGE: 'None', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_themes/README.html b/docs/_themes/README.html index 57277f32..8fd83600 100644 --- a/docs/_themes/README.html +++ b/docs/_themes/README.html @@ -6,7 +6,7 @@ - krTheme Sphinx Style — custodian 2022.1.17 documentation + krTheme Sphinx Style — custodian 2022.2.13 documentation @@ -37,7 +37,7 @@

    Navigation

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    • diff --git a/docs/changelog.html b/docs/changelog.html index dbec837b..73190644 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -6,7 +6,7 @@ - Change Log — custodian 2022.1.17 documentation + Change Log — custodian 2022.2.13 documentation @@ -37,7 +37,7 @@

    Navigation

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  • custodian 2022.1.17 documentation »
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  • Change Log
    • @@ -49,6 +49,13 @@

    Navigation

    Change Log

    +
    +

    v2022.2.13

    +
      +

    • Support for new Lobster versions (@naik-aakash)

      • +

    • Bug fix for termination of gamma VASP runs.

      • +
    +

    v2022.1.17

    -
    -

    custodian.cli.converge_geometry module

    -

    This is a script to converge the geometry of a system

    -
    -
    -do_run(args)[source]
    -

    Perform the run.

    -
    - -
    -
    -get_runs(args)[source]
    -

    Get the runs.

    -
    - +
    +

    custodian.cli.converge_geometry module

    -
    -

    custodian.cli.converge_kpoints module

    -

    This is a master vasp running script to converging kpoints for a calculation

    -
    -
    -do_run(args)[source]
    -

    Perform the run.

    -
    - -
    -
    -get_runs(vasp_command, target=0.001, max_steps=10, mode='linear')[source]
    -

    Generate the runs using a generator until convergence is achieved.

    -
    - -
    -
    -main()[source]
    -

    Main method

    -
    - +
    +

    custodian.cli.converge_kpoints module

    custodian.cli.cstdn module

    @@ -112,50 +80,11 @@

    Submodules -

    custodian.cli.run_nwchem module

    -

    Basic script to run nwchem job.

    -
    -
    -do_run(args)[source]
    -

    Do the run.

    -
    - -
    -
    -main()[source]
    -

    Main method

    -
    - +
    +

    custodian.cli.run_nwchem module

    -
    -

    custodian.cli.run_vasp module

    -

    This is a master vasp running script to perform various combinations of VASP -runs.

    -
    -
    -do_run(args)[source]
    -

    Do the run.

    -
    - -
    -
    -get_jobs(args)[source]
    -

    Returns a generator of jobs. Allows of “infinite” jobs.

    -
    - -
    -
    -load_class(mod, name)[source]
    -

    Load the class from mod and name specification.

    -
    - -
    -
    -main()[source]
    -

    Main method

    -
    - +
    +

    custodian.cli.run_vasp module

    Module contents

    @@ -175,11 +104,11 @@

    Table of Contents

    @@ -57,90 +57,11 @@

    Subpackages

    Submodules

    -
    -

    custodian.feff.handlers module

    -

    This module implements specific error handler for FEFF runs.

    -
    -
    -class UnconvergedErrorHandler(output_filename='log1.dat')[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Correct the unconverged error of FEFF’s SCF calculation.

    -

    Initializes the handler with the output file to check

    -
    -
    Parameters
    -

    output_filename (str) – Filename for the log1.dat file. log1.dat file -contains the SCF calculation convergence information. Change this only -if it is different from the default (unlikely).

    -
    -
    -
    -
    -check()[source]
    -

    If the FEFF run does not converge, the check will return -“TRUE”

    -
    - -
    -
    -correct()[source]
    -

    Perform the corrections.

    -
    - -
    -
    -is_monitor = False
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

    -
    - -
    - +
    +

    custodian.feff.handlers module

    -
    -

    custodian.feff.interpreter module

    -

    Implements various interpreters and modders for FEFF calculations.

    -
    -
    -class FeffModder(actions=None, strict=True, feffinp=None)[source]
    -

    Bases: custodian.ansible.interpreter.Modder

    -

    A Modder for FeffInput sets

    -
    -
    Parameters
    -
      -

    • actions ([Action]) – A sequence of supported actions. See

      • -

    • actions – A sequence of supported actions. See -custodian.ansible.actions. Default is None, -which means DictActions and FileActions are supported.

      • -

    • strict (bool) – Indicating whether to use strict mode. In non-strict -mode, unsupported actions are simply ignored without any -errors raised. In strict mode, if an unsupported action is -supplied, a ValueError is raised. Defaults to True.

      • -

    • feffinp (FEFFInput) – A FeffInput object from the current directory. -Initialized automatically if not passed (but passing it will -avoid having to reparse the directory).

      • -
    -
    -
    -
    -
    -apply_actions(actions)[source]
    -

    Applies a list of actions to the FEFF Input Set and rewrites modified -files.

    -
    -
    Parameters
    -

    [dict] (actions) – A list of actions of the form {‘file’: filename, -‘action’: moddermodification} or {‘dict’: feffinput_key, -‘action’: moddermodification}

    -
    -
    -
    - -
    - +
    +

    custodian.feff.interpreter module

    custodian.feff.jobs module

    @@ -211,8 +132,8 @@

    Table of Contents

  • custodian.feff package diff --git a/docs/custodian.html b/docs/custodian.html index 13d92d43..c52f1d4a 100644 --- a/docs/custodian.html +++ b/docs/custodian.html @@ -6,7 +6,7 @@ - custodian package — custodian 2022.1.17 documentation + custodian package — custodian 2022.2.13 documentation @@ -37,7 +37,7 @@

    Navigation

  • modules |
    • -
  • custodian 2022.1.17 documentation »
    • +
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  • custodian package
    • @@ -65,11 +65,11 @@

    Subpackagescustodian.cli package @@ -78,8 +78,8 @@

    SubpackagesSubmodules -
  • custodian.feff.handlers module
    • -
  • custodian.feff.interpreter module
    • +
  • custodian.feff.handlers module
    • +
  • custodian.feff.interpreter module
  • custodian.feff.jobs module
  • Module contents
    • @@ -89,7 +89,7 @@

    SubpackagesSubmodules -
  • custodian.lobster.handlers module
    • +
  • custodian.lobster.handlers module
  • custodian.lobster.jobs module
  • Module contents
    • @@ -99,7 +99,7 @@

    SubpackagesSubmodules -
  • custodian.nwchem.handlers module
    • +
  • custodian.nwchem.handlers module
  • custodian.nwchem.jobs module
  • Module contents
    • @@ -120,10 +120,10 @@

    SubpackagesSubmodules -
  • custodian.vasp.handlers module
    • -
  • custodian.vasp.interpreter module
    • -
  • custodian.vasp.jobs module
    • -
  • custodian.vasp.validators module
    • +
  • custodian.vasp.handlers module
    • +
  • custodian.vasp.interpreter module
    • +
  • custodian.vasp.jobs module
    • +
  • custodian.vasp.validators module
  • Module contents
    • diff --git a/docs/custodian.lobster.html b/docs/custodian.lobster.html index 91947160..aecc16b7 100644 --- a/docs/custodian.lobster.html +++ b/docs/custodian.lobster.html @@ -6,7 +6,7 @@ - custodian.lobster package — custodian 2022.1.17 documentation + custodian.lobster package — custodian 2022.2.13 documentation @@ -37,7 +37,7 @@

    Navigation

  • modules |
    • -
  • custodian 2022.1.17 documentation »
    • +
  • custodian 2022.2.13 documentation »
  • custodian.lobster package
    • @@ -57,67 +57,8 @@

    Subpackages

    Submodules

    -
    -

    custodian.lobster.handlers module

    -

    This module implements specific error handler for Lobster runs.

    -
    -
    -class ChargeSpillingValidator(output_filename: str = 'lobsterout', charge_spilling_limit: float = 0.05)[source]
    -

    Bases: custodian.custodian.Validator

    -

    Check if spilling is below certain threshold!

    -
    -
    Parameters
    -
      -

    • output_filename – filename of the output file of lobter, usually lobsterout

      • -

    • charge_spilling_limit – limit of the charge spilling that will be considered okay

      • -
    -
    -
    -
    -
    -check() → bool[source]
    -

    open lobsterout and find charge spilling

    -
    - -
    - -
    -
    -class EnoughBandsValidator(output_filename: str = 'lobsterout')[source]
    -

    Bases: custodian.custodian.Validator

    -

    validates if enough bands for COHP calculation are available

    -
    -
    Parameters
    -

    output_filename – filename of output file, usually lobsterout

    -
    -
    -
    -
    -check() → bool[source]
    -

    checks if the VASP calculation had enough bands -:returns: (bool) if True, too few bands have been applied

    -
    - -
    - -
    -
    -class LobsterFilesValidator[source]
    -

    Bases: custodian.custodian.Validator

    -
    -
    Check for existence of some of the files that lobster

    normally create upon running.

    -
    -
    -

    Check if lobster terminated normally by looking for finished

    -

    Dummy init

    -
    -
    -check() → bool[source]
    -

    Check for errors.

    -
    - -
    - +
    +

    custodian.lobster.handlers module

    custodian.lobster.jobs module

    @@ -179,7 +120,7 @@

    Table of Contents

  • custodian.lobster package diff --git a/docs/custodian.nwchem.html b/docs/custodian.nwchem.html index 11b622b3..7e4cac14 100644 --- a/docs/custodian.nwchem.html +++ b/docs/custodian.nwchem.html @@ -6,7 +6,7 @@ - custodian.nwchem package — custodian 2022.1.17 documentation + custodian.nwchem package — custodian 2022.2.13 documentation @@ -37,7 +37,7 @@

    Navigation

  • modules |
    • -
  • custodian 2022.1.17 documentation »
    • +
  • custodian 2022.2.13 documentation »
  • custodian.nwchem package
    • @@ -57,40 +57,8 @@

    Subpackages

    Submodules

    -
    -

    custodian.nwchem.handlers module

    -

    This module implements error handlers for Nwchem runs. Currently tested only -for B3LYP DFT jobs.

    -
    -
    -class NwchemErrorHandler(output_filename='mol.nwout')[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Error handler for Nwchem Jobs. Currently tested only for B3LYP DFT jobs -generated by pymatgen.

    -

    Initializes with an output file name.

    -
    -
    Parameters
    -

    output_filename (str) – This is the file where the stdout for nwchem -is being redirected. The error messages that are checked are -present in the stdout. Defaults to “mol.nwout”, which is the -default redirect used by custodian.nwchem.jobs -.NwchemJob.

    -
    -
    -
    -
    -check()[source]
    -

    Check for errors.

    -
    - -
    -
    -correct()[source]
    -

    Correct errors

    -
    - -
    - +
    +

    custodian.nwchem.handlers module

    custodian.nwchem.jobs module

    @@ -159,7 +127,7 @@

    Table of Contents

  • custodian.nwchem package diff --git a/docs/custodian.qchem.html b/docs/custodian.qchem.html index 4070e92a..fbc87268 100644 --- a/docs/custodian.qchem.html +++ b/docs/custodian.qchem.html @@ -6,7 +6,7 @@ - custodian.qchem package — custodian 2022.1.17 documentation + custodian.qchem package — custodian 2022.2.13 documentation @@ -37,7 +37,7 @@

    Navigation

  • modules |
    • -
  • custodian 2022.1.17 documentation »
    • +
  • custodian 2022.2.13 documentation »
  • custodian.qchem package
    • diff --git a/docs/custodian.vasp.html b/docs/custodian.vasp.html index 8d6979cb..32e04816 100644 --- a/docs/custodian.vasp.html +++ b/docs/custodian.vasp.html @@ -6,7 +6,7 @@ - custodian.vasp package — custodian 2022.1.17 documentation + custodian.vasp package — custodian 2022.2.13 documentation @@ -37,7 +37,7 @@

    Navigation

  • modules |
    • -
  • custodian 2022.1.17 documentation »
    • +
  • custodian 2022.2.13 documentation »
  • custodian.vasp package
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    Subpackages

    Submodules

    -
    -

    custodian.vasp.handlers module

    -

    This module implements specific error handlers for VASP runs. These handlers -try to detect common errors in vasp runs and attempt to fix them on the fly -by modifying the input files.

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    -class AliasingErrorHandler(output_filename='vasp.out')[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Master VaspErrorHandler class that handles a number of common errors -that occur during VASP runs.

    -

    Initializes the handler with the output file to check.

    -
    -
    Parameters
    -

    output_filename (str) – This is the file where the stdout for vasp -is being redirected. The error messages that are checked are -present in the stdout. Defaults to “vasp.out”, which is the -default redirect used by custodian.vasp.jobs.VaspJob.

    -
    -
    -
    -
    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

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    - -
    -
    -error_msgs = {'aliasing': ['WARNING: small aliasing (wrap around) errors must be expected'], 'aliasing_incar': ['Your FFT grids (NGX,NGY,NGZ) are not sufficient for an accurate']}
    -
    - -
    -
    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

    -
    - -
    - -
    -
    -class CheckpointHandler(interval=3600)[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    This is not an error handler per se, but rather a checkpointer. What this -does is that every X seconds, a STOPCAR and CHKPT will be written. This -forces VASP to stop at the end of the next ionic step. The files are then -copied into a subdir, and then the job is restarted. To use this proper, -max_errors in Custodian must be set to a very high value, and you -probably wouldn’t want to use any standard VASP error handlers. The -checkpoint will be stored in subdirs chk_#. This should be used in -combination with the StoppedRunHandler.

    -

    Initializes the handler with an interval.

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    Parameters
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    • interval (int) – Interval at which to checkpoint in seconds.

      • -

    • 3600 (Defaults to) –

      • -
    -
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    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

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    - -
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    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    - -
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    -is_terminating = False
    -

    Whether this handler terminates a job upon error detection. By -default, this is True, which means that the current Job will be -terminated upon error detection, corrections applied, -and restarted. In some instances, some errors may not need the job to be -terminated or may need to wait for some other event to terminate a job. -For example, a particular error may require a flag to be set to request -a job to terminate gracefully once it finishes its current task. The -handler to set the flag should be classified as is_terminating = False to -not terminate the job.

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    - -
    - -
    -
    -class DriftErrorHandler(max_drift=None, to_average=3, enaug_multiply=2)[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Corrects for total drift exceeding the force convergence criteria.

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    Initializes the handler with max drift -:param max_drift: This defines the max drift. Leaving this at the default of None gets the max_drift from

    -
    -

    EDFIFFG

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    -
    -
    -
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    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

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    - -
    - -
    -
    -class FrozenJobErrorHandler(output_filename='vasp.out', timeout=21600)[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Detects an error when the output file has not been updated -in timeout seconds. Changes ALGO to Normal from Fast

    -

    Initializes the handler with the output file to check.

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    Parameters
    -
      -

    • output_filename (str) – This is the file where the stdout for vasp -is being redirected. The error messages that are checked are -present in the stdout. Defaults to “vasp.out”, which is the -default redirect used by custodian.vasp.jobs.VaspJob.

      • -

    • timeout (int) – The time in seconds between checks where if there -is no activity on the output file, the run is considered -frozen. Defaults to 3600 seconds, i.e., 1 hour.

      • -
    -
    -
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    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

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    - -
    -
    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

    -
    - -
    - -
    -
    -class IncorrectSmearingHandler(output_filename='vasprun.xml')[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Check if a calculation is a metal (zero bandgap), has been run with -ISMEAR=-5, and is not a static calculation, which is only appropriate for -semiconductors. If this occurs, this handler will rerun the calculation -using the smearing settings appropriate for metals (ISMEAR=2, SIGMA=0.2).

    -

    Initializes the handler with the output file to check.

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    -
    Parameters
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    output_filename (str) – Filename for the vasprun.xml file. Change -this only if it is different from the default (unlikely).

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    -
    -
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    -check()[source]
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    Check for error.

    -
    - -
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    -correct()[source]
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    Perform corrections.

    -
    - -
    -
    -is_monitor = False
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    - -
    - -
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    -class LargeSigmaHandler[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    When ISMEAR > 0 (Methfessel-Paxton), monitor the magnitude of the entropy -term T*S in the OUTCAR file. If the entropy term is larger than 1 meV/atom, reduce the -value of SIGMA. See VASP documentation for ISMEAR.

    -

    Initializes the handler with a buffer time.

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    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

    -
    - -
    -
    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    - -
    - -
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    -class LrfCommutatorHandler(output_filename='std_err.txt')[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Corrects LRF_COMMUTATOR errors by setting LPEAD=True if not already set. -Note that switching LPEAD=T can slightly change results versus the -default due to numerical evaluation of derivatives.

    -

    Initializes the handler with the output file to check.

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    -
    Parameters
    -

    output_filename (str) – This is the file where the stderr for vasp -is being redirected. The error messages that are checked are -present in the stderr. Defaults to “std_err.txt”, which is the -default redirect used by custodian.vasp.jobs.VaspJob.

    -
    -
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    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

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    - -
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    -error_msgs = {'lrf_comm': ['LRF_COMMUTATOR internal error']}
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    - -
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    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

    -
    - -
    - -
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    -class MeshSymmetryErrorHandler(output_filename='vasp.out', output_vasprun='vasprun.xml')[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Corrects the mesh symmetry error in VASP. This error is sometimes -non-fatal. So this error handler only checks at the end of the run, -and if the run has converged, no error is recorded.

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    Initializes the handler with the output files to check.

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    Parameters
    -
      -

    • output_filename (str) – This is the file where the stdout for vasp -is being redirected. The error messages that are checked are -present in the stdout. Defaults to “vasp.out”, which is the -default redirect used by custodian.vasp.jobs.VaspJob.

      • -

    • output_vasprun (str) – Filename for the vasprun.xml file. Change -this only if it is different from the default (unlikely).

      • -
    -
    -
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    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

    -
    - -
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    -is_monitor = False
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

    -
    - -
    - -
    -
    -class NonConvergingErrorHandler(output_filename='OSZICAR', nionic_steps=10)[source]
    -

    Bases: custodian.custodian.ErrorHandler

    -

    Check if a run is hitting the maximum number of electronic steps at the -last nionic_steps ionic steps (default=10). If so, change ALGO using a -multi-step ladder scheme or kill the job.

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    Initializes the handler with the output file to check.

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    Parameters
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    • output_filename (str) – This is the OSZICAR file. Change -this only if it is different from the default (unlikely).

      • -

    • nionic_steps (int) – The threshold number of ionic steps that -needs to hit the maximum number of electronic steps for the -run to be considered non-converging.

      • -
    -
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    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

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    - -
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    -classmethod from_dict(d)[source]
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    Custom from_dict method to preserve backwards compatibility with -older versions of Custodian.

    -
    - -
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    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    - -
    - -
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    -class PositiveEnergyErrorHandler(output_filename='OSZICAR')[source]
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    Bases: custodian.custodian.ErrorHandler

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    Check if a run has positive absolute energy. -If so, change ALGO from Fast to Normal or kill the job.

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    Initializes the handler with the output file to check.

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    Parameters
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    output_filename (str) – This is the OSZICAR file. Change -this only if it is different from the default (unlikely).

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    -check()[source]
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    Check for error.

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    - -
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    -correct()[source]
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    Perform corrections.

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    - -
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    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

    -
    - -
    - -
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    -class PotimErrorHandler(input_filename='POSCAR', output_filename='OSZICAR', dE_threshold=1)[source]
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    Bases: custodian.custodian.ErrorHandler

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    Check if a run has excessively large positive energy changes. -This is typically caused by too large a POTIM. Runs typically -end up crashing with some other error (e.g. BRMIX) as the geometry -gets progressively worse.

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    Initializes the handler with the input and output files to check.

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    Parameters
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    • input_filename (str) – This is the POSCAR file that the run -started from. Defaults to “POSCAR”. Change -this only if it is different from the default (unlikely).

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    • output_filename (str) – This is the OSZICAR file. Change -this only if it is different from the default (unlikely).

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    • dE_threshold (float) – The threshold energy change. Defaults to 1eV.

      • -
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    -check()[source]
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    Check for error.

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    -correct()[source]
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    Perform corrections.

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    - -
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    -is_monitor = True
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    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    - -
    - -
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    -class ScanMetalHandler(output_filename='vasprun.xml')[source]
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    Bases: custodian.custodian.ErrorHandler

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    Check if a SCAN calculation is a metal (zero bandgap) but has been run with -a KSPACING value appropriate for semiconductors. If this occurs, this handler -will rerun the calculation using the KSPACING setting appropriate for metals -(KSPACING=0.22). Note that this handler depends on values set in MPScanRelaxSet.

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    Initializes the handler with the output file to check.

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    Parameters
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    output_filename (str) – Filename for the vasprun.xml file. Change -this only if it is different from the default (unlikely).

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    -check()[source]
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    Check for error.

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    -correct()[source]
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    Perform corrections.

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    -is_monitor = False
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    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    - -
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    -class StdErrHandler(output_filename='std_err.txt')[source]
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    Bases: custodian.custodian.ErrorHandler

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    Master StdErr class that handles a number of common errors -that occur during VASP runs with error messages only in -the standard error.

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    Initializes the handler with the output file to check.

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    Parameters
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    output_filename (str) – This is the file where the stderr for vasp -is being redirected. The error messages that are checked are -present in the stderr. Defaults to “std_err.txt”, which is the -default redirect used by custodian.vasp.jobs.VaspJob.

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    -check()[source]
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    Check for error.

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    -correct()[source]
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    Perform corrections.

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    -error_msgs = {'kpoints_trans': ['internal error in GENERATE_KPOINTS_TRANS: number of G-vector changed in star'], 'out_of_memory': ['Allocation would exceed memory limit']}
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    -is_monitor = True
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    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    -class StoppedRunHandler[source]
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    Bases: custodian.custodian.ErrorHandler

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    This is not an error handler per se, but rather a checkpointer. What this -does is that every X seconds, a STOPCAR will be written. This forces VASP to -stop at the end of the next ionic step. The files are then copied into a -subdir, and then the job is restarted. To use this proper, max_errors in -Custodian must be set to a very high value, and you probably wouldn’t -want to use any standard VASP error handlers. The checkpoint will be -stored in subdirs chk_#. This should be used in combination with the -StoppedRunHandler.

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    Dummy init.

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    -check()[source]
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    Check for error.

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    -correct()[source]
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    Perform corrections.

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    -is_monitor = False
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    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    -is_terminating = False
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    Whether this handler terminates a job upon error detection. By -default, this is True, which means that the current Job will be -terminated upon error detection, corrections applied, -and restarted. In some instances, some errors may not need the job to be -terminated or may need to wait for some other event to terminate a job. -For example, a particular error may require a flag to be set to request -a job to terminate gracefully once it finishes its current task. The -handler to set the flag should be classified as is_terminating = False to -not terminate the job.

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    -class UnconvergedErrorHandler(output_filename='vasprun.xml')[source]
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    Bases: custodian.custodian.ErrorHandler

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    Check if a run is converged.

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    Initializes the handler with the output file to check.

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    Parameters
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    output_vasprun (str) – Filename for the vasprun.xml file. Change -this only if it is different from the default (unlikely).

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    -check()[source]
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    Check for error.

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    -correct()[source]
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    Perform corrections.

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    -is_monitor = False
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    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    - -
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    -class VaspErrorHandler(output_filename='vasp.out', natoms_large_cell=None, errors_subset_to_catch=None, vtst_fixes=False)[source]
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    Bases: custodian.custodian.ErrorHandler

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    Master VaspErrorHandler class that handles a number of common errors -that occur during VASP runs.

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    Initializes the handler with the output file to check.

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    Parameters
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    • output_filename (str) – This is the file where the stdout for vasp -is being redirected. The error messages that are checked are -present in the stdout. Defaults to “vasp.out”, which is the -default redirect used by custodian.vasp.jobs.VaspJob.

      • -

    • natoms_large_cell (int) – Number of atoms threshold to treat cell -as large. Affects the correction of certain errors. Defaults to -None (not used). Deprecated.

      • -

    • errors_subset_to_detect (list) – A subset of errors to catch. The -default is None, which means all supported errors are detected. -Use this to only catch only a subset of supported errors. -E.g., [“eddrrm”, “zheev”] will only catch the eddrmm and zheev -errors, and not others. If you wish to only excluded one or -two of the errors, you can create this list by the following -lines:

      • -

    • vtst_fixes (bool) –

      Whether to consider VTST optimizers. Defaults to -False for compatibility purposes.

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      ``` -subset = list(VaspErrorHandler.error_msgs.keys()) -subset.pop(“eddrrm”)

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      handler = VaspErrorHandler(errors_subset_to_catch=subset) -```

      -

      • -
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    -check()[source]
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    Check for error.

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    -correct()[source]
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    Perform corrections.

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    - -
    -
    -error_msgs = {'algo_tet': ['ALGO=A and IALGO=5X tend to fail'], 'amin': ['One of the lattice vectors is very long (>50 A), but AMIN'], 'bravais': ['Inconsistent Bravais lattice'], 'brions': ['BRIONS problems: POTIM should be increased'], 'brmix': ['BRMIX: very serious problems'], 'dentet': ['DENTET'], 'dfpt_ncore': ['PEAD routines do not work for NCORE', 'remove the tag NPAR from the INCAR file'], 'edddav': ['Error EDDDAV: Call to ZHEGV failed'], 'eddrmm': ['WARNING in EDDRMM: call to ZHEGV failed'], 'elf_kpar': ['ELF: KPAR>1 not implemented'], 'elf_ncl': ['WARNING: ELF not implemented for non collinear case'], 'grad_not_orth': ['EDWAV: internal error, the gradient is not orthogonal'], 'hnform': ['HNFORM: k-point generating'], 'incorrect_shift': ['Could not get correct shifts'], 'inv_rot_mat': ['rotation matrix was not found (increase SYMPREC)'], 'nbands_not_sufficient': ['number of bands is not sufficient'], 'nicht_konv': ['ERROR: SBESSELITER : nicht konvergent'], 'point_group': ['group operation missing'], 'posmap': ['POSMAP'], 'pricel': ['internal error in subroutine PRICEL'], 'pssyevx': ['ERROR in subspace rotation PSSYEVX'], 'real_optlay': ['REAL_OPTLAY: internal error', 'REAL_OPT: internal ERROR'], 'rhosyg': ['RHOSYG'], 'rot_matrix': ['Found some non-integer element in rotation matrix', 'SGRCON'], 'rspher': ['ERROR RSPHER'], 'subspacematrix': ['WARNING: Sub-Space-Matrix is not hermitian in DAV'], 'symprec_noise': ['determination of the symmetry of your systems shows a strong'], 'tet': ['Tetrahedron method fails', 'tetrahedron method fails', 'Fatal error detecting k-mesh', 'Fatal error: unable to match k-point', 'Routine TETIRR needs special values', 'Tetrahedron method fails (number of k-points < 4)', 'BZINTS'], 'tetirr': ['Routine TETIRR needs special values'], 'too_few_bands': ['TOO FEW BANDS'], 'triple_product': ['ERROR: the triple product of the basis vectors'], 'zbrent': ['ZBRENT: fatal internal in', 'ZBRENT: fatal error in bracketing'], 'zheev': ['ERROR EDDIAG: Call to routine ZHEEV failed!'], 'zpotrf': ['LAPACK: Routine ZPOTRF failed']}
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    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

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    -class WalltimeHandler(wall_time=None, buffer_time=300, electronic_step_stop=False)[source]
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    Bases: custodian.custodian.ErrorHandler

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    Check if a run is nearing the walltime. If so, write a STOPCAR with -LSTOP or LABORT = .True.. You can specify the walltime either in the init ( -which is unfortunately necessary for SGE and SLURM systems. If you happen -to be running on a PBS system and the PBS_WALLTIME variable is in the run -environment, the wall time will be automatically determined if not set.

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    Initializes the handler with a buffer time.

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    Parameters
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    • wall_time (int) – Total walltime in seconds. If this is None and -the job is running on a PBS system, the handler will attempt to -determine the walltime from the PBS_WALLTIME environment -variable. If the wall time cannot be determined or is not -set, this handler will have no effect.

      • -

    • buffer_time (int) – The min amount of buffer time in secs at the -end that the STOPCAR will be written. The STOPCAR is written -when the time remaining is < the higher of 3 x the average -time for each ionic step and the buffer time. Defaults to -300 secs, which is the default polling time of Custodian. -This is typically sufficient for the current ionic step to -complete. But if other operations are being performed after -the run has stopped, the buffer time may need to be increased -accordingly.

      • -

    • electronic_step_stop (bool) – Whether to check for electronic steps -instead of ionic steps (e.g. for static runs on large systems or -static HSE runs, …). Be careful that results such as density -or wavefunctions might not be converged at the electronic level. -Should be used with LWAVE = .True. to be useful. If this is -True, the STOPCAR is written with LABORT = .TRUE. instead of -LSTOP = .TRUE.

      • -
    -
    -
    -
    -
    -check()[source]
    -

    Check for error.

    -
    - -
    -
    -correct()[source]
    -

    Perform corrections.

    -
    - -
    -
    -is_monitor = True
    -

    This class property indicates whether the error handler is a monitor, -i.e., a handler that monitors a job as it is running. If a -monitor-type handler notices an error, the job will be sent a -termination signal, the error is then corrected, -and then the job is restarted. This is useful for catching errors -that occur early in the run but do not cause immediate failure.

    -
    - -
    -
    -is_terminating = False
    -

    Whether this handler terminates a job upon error detection. By -default, this is True, which means that the current Job will be -terminated upon error detection, corrections applied, -and restarted. In some instances, some errors may not need the job to be -terminated or may need to wait for some other event to terminate a job. -For example, a particular error may require a flag to be set to request -a job to terminate gracefully once it finishes its current task. The -handler to set the flag should be classified as is_terminating = False to -not terminate the job.

    -
    - -
    -
    -raises_runtime_error = False
    -

    Whether this handler causes custodian to raise a runtime error if it cannot -handle the error (i.e. if correct returns a dict with “actions”:None, or -“actions”:[])

    -
    - -
    - +
    +

    custodian.vasp.handlers module

    -
    -

    custodian.vasp.interpreter module

    -

    Implements various interpreters and modders for VASP.

    -
    -
    -class VaspModder(actions=None, strict=True, vi=None)[source]
    -

    Bases: custodian.ansible.interpreter.Modder

    -

    A Modder for VaspInputSets.

    -

    Initializes a Modder for VaspInput sets

    -
    -
    Parameters
    -
      -

    • actions ([Action]) – A sequence of supported actions. See -custodian.ansible.actions. Default is None, -which means DictActions and FileActions are supported.

      • -

    • strict (bool) – Indicating whether to use strict mode. In non-strict -mode, unsupported actions are simply ignored without any -errors raised. In strict mode, if an unsupported action is -supplied, a ValueError is raised. Defaults to True.

      • -

    • vi (VaspInput) – A VaspInput object from the current directory. -Initialized automatically if not passed (but passing it will -avoid having to reparse the directory).

      • -
    -
    -
    -
    -
    -apply_actions(actions)[source]
    -

    Applies a list of actions to the Vasp Input Set and rewrites modified -files. -:param actions [dict]: A list of actions of the form {‘file’: filename,

    -
    -

    ‘action’: moddermodification} or {‘dict’: vaspinput_key, -‘action’: moddermodification}

    -
    -
    - -
    - +
    +

    custodian.vasp.interpreter module

    -
    -

    custodian.vasp.jobs module

    -

    This module implements basic kinds of jobs for VASP runs.

    -
    -
    -class GenerateVaspInputJob(input_set, contcar_only=True, **kwargs)[source]
    -

    Bases: custodian.custodian.Job

    -

    Generates a VASP input based on an existing directory. This is typically -used to modify the VASP input files before the next VaspJob.

    -
    -
    Parameters
    -
      -

    • input_set (str) – Full path to the input set. E.g., -“pymatgen.io.vasp.sets.MPNonSCFSet”.

      • -

    • contcar_only (bool) – If True (default), only CONTCAR structures -are used as input to the input set.

      • -
    -
    -
    -
    -
    -postprocess()[source]
    -

    Dummy postprocess.

    -
    - -
    -
    -run()[source]
    -

    Run the calculation.

    -
    - -
    -
    -setup()[source]
    -

    Dummy setup

    -
    - -
    - -
    -
    -class VaspJob(vasp_cmd, output_file='vasp.out', stderr_file='std_err.txt', suffix='', final=True, backup=True, auto_npar=False, auto_gamma=True, settings_override=None, gamma_vasp_cmd=None, copy_magmom=False, auto_continue=False)[source]
    -

    Bases: custodian.custodian.Job

    -

    A basic vasp job. Just runs whatever is in the directory. But conceivably -can be a complex processing of inputs etc. with initialization.

    -

    This constructor is necessarily complex due to the need for -flexibility. For standard kinds of runs, it’s often better to use one -of the static constructors. The defaults are usually fine too.

    -
    -
    Parameters
    -
      -

    • vasp_cmd (str) – Command to run vasp as a list of args. For example, -if you are using mpirun, it can be something like -[“mpirun”, “pvasp.5.2.11”]

      • -

    • output_file (str) – Name of file to direct standard out to. -Defaults to “vasp.out”.

      • -

    • stderr_file (str) – Name of file to direct standard error to. -Defaults to “std_err.txt”.

      • -

    • suffix (str) – A suffix to be appended to the final output. E.g., -to rename all VASP output from say vasp.out to -vasp.out.relax1, provide “.relax1” as the suffix.

      • -

    • final (bool) – Indicating whether this is the final vasp job in a -series. Defaults to True.

      • -

    • backup (bool) – Whether to backup the initial input files. If True, -the INCAR, KPOINTS, POSCAR and POTCAR will be copied with a -“.orig” appended. Defaults to True.

      • -

    • auto_npar (bool) – Whether to automatically tune NPAR to be sqrt( -number of cores) as recommended by VASP for DFT calculations. -Generally, this results in significant speedups. Defaults to -False. Set to False for HF, GW and RPA calculations.

      • -

    • auto_gamma (bool) – Whether to automatically check if run is a -Gamma 1x1x1 run, and whether a Gamma optimized version of -VASP exists with “.gamma” appended to the name of the VASP -executable (typical setup in many systems). If so, run the -gamma optimized version of VASP instead of regular VASP. You -can also specify the gamma vasp command using the -gamma_vasp_cmd argument if the command is named differently.

      • -

    • settings_override ([dict]) –

      An ansible style list of dict to -override changes. For example, to set ISTART=1 for subsequent -runs and to copy the CONTCAR to the POSCAR, you will provide:

      -
      [{"dict": "INCAR", "action": {"_set": {"ISTART": 1}}},
- {"file": "CONTCAR",
-  "action": {"_file_copy": {"dest": "POSCAR"}}}]
-
      -
      -

      • -

    • gamma_vasp_cmd (str) – Command for gamma vasp version when -auto_gamma is True. Should follow the list style of -subprocess. Defaults to None, which means “.gamma” is added -to the last argument of the standard vasp_cmd.

      • -

    • copy_magmom (bool) – Whether to copy the final magmom from the -OUTCAR to the next INCAR. Useful for multi-relaxation runs -where the CHGCAR and WAVECAR are sometimes deleted (due to -changes in fft grid, etc.). Only applies to non-final runs.

      • -

    • auto_continue (bool) – Whether to automatically continue a run -if a STOPCAR is present. This is very useful if using the -wall-time handler which will write a read-only STOPCAR to -prevent VASP from deleting it once it finishes

      • -
    -
    -
    -
    -
    -classmethod constrained_opt_run(vasp_cmd, lattice_direction, initial_strain, atom_relax=True, max_steps=20, algo='bfgs', **vasp_job_kwargs)[source]
    -

    Returns a generator of jobs for a constrained optimization run. Typical -use case is when you want to approximate a biaxial strain situation, -e.g., you apply a defined strain to a and b directions of the lattice, -but allows the c-direction to relax.

    -

    Some guidelines on the use of this method: -i. It is recommended you do not use the Auto kpoint generation. The

    -
    -

    grid generated via Auto may fluctuate with changes in lattice -param, resulting in numerical noise.

    -
    -
      -

    1. Make sure your EDIFF/EDIFFG is properly set in your INCAR. The -optimization relies on these values to determine convergence.

      2. -
    -
    -
    Parameters
    -
      -

    • vasp_cmd (str) – Command to run vasp as a list of args. For example, -if you are using mpirun, it can be something like -[“mpirun”, “pvasp.5.2.11”]

      • -

    • lattice_direction (str) – Which direction to relax. Valid values are -“a”, “b” or “c”.

      • -

    • initial_strain (float) – An initial strain to be applied to the -lattice_direction. This can usually be estimated as the -negative of the strain applied in the other two directions. -E.g., if you apply a tensile strain of 0.05 to the a and b -directions, you can use -0.05 as a reasonable first guess for -initial strain.

      • -

    • atom_relax (bool) – Whether to relax atomic positions.

      • -

    • max_steps (int) – The maximum number of runs. Defaults to 20 ( -highly unlikely that this limit is ever reached).

      • -

    • algo (str) – Algorithm to use to find minimum. Default is “bfgs”, -which is fast, but can be sensitive to numerical noise -in energy calculations. The alternative is “bisection”, -which is more robust but can be a bit slow. The code does fall -back on the bisection when bfgs gives a non-sensical result, -e.g., negative lattice params.

      • -

    • **vasp_job_kwargs – Passthrough kwargs to VaspJob. See -custodian.vasp.jobs.VaspJob.

      • -
    -
    -
    Returns
    -

    Generator of jobs. At the end of the run, an “EOS.txt” is written -which provides a quick look at the E vs lattice parameter.

    -
    -
    -
    - -
    -
    -classmethod double_relaxation_run(vasp_cmd, auto_npar=True, ediffg=- 0.05, half_kpts_first_relax=False, auto_continue=False)[source]
    -

    Returns a list of two jobs corresponding to an AFLOW style double -relaxation run.

    -
    -
    Parameters
    -
      -

    • vasp_cmd (str) – Command to run vasp as a list of args. For example, -if you are using mpirun, it can be something like -[“mpirun”, “pvasp.5.2.11”]

      • -

    • auto_npar (bool) – Whether to automatically tune NPAR to be sqrt( -number of cores) as recommended by VASP for DFT calculations. -Generally, this results in significant speedups. Defaults to -True. Set to False for HF, GW and RPA calculations.

      • -

    • ediffg (float) – Force convergence criteria for subsequent runs ( -ignored for the initial run.)

      • -

    • half_kpts_first_relax (bool) – Whether to halve the kpoint grid -for the first relaxation. Speeds up difficult convergence -considerably. Defaults to False.

      • -
    -
    -
    Returns
    -

    List of two jobs corresponding to an AFLOW style run.

    -
    -
    -
    - -
    -
    -classmethod full_opt_run(vasp_cmd, vol_change_tol=0.02, max_steps=10, ediffg=- 0.05, half_kpts_first_relax=False, **vasp_job_kwargs)[source]
    -

    Returns a generator of jobs for a full optimization run. Basically, -this runs an infinite series of geometry optimization jobs until the -% vol change in a particular optimization is less than vol_change_tol.

    -
    -
    Parameters
    -
      -

    • vasp_cmd (str) – Command to run vasp as a list of args. For example, -if you are using mpirun, it can be something like -[“mpirun”, “pvasp.5.2.11”]

      • -

    • vol_change_tol (float) – The tolerance at which to stop a run. -Defaults to 0.05, i.e., 5%.

      • -

    • max_steps (int) – The maximum number of runs. Defaults to 10 ( -highly unlikely that this limit is ever reached).

      • -

    • ediffg (float) – Force convergence criteria for subsequent runs ( -ignored for the initial run.)

      • -

    • half_kpts_first_relax (bool) – Whether to halve the kpoint grid -for the first relaxation. Speeds up difficult convergence -considerably. Defaults to False.

      • -

    • **vasp_job_kwargs – Passthrough kwargs to VaspJob. See -custodian.vasp.jobs.VaspJob.

      • -
    -
    -
    Returns
    -

    Generator of jobs.

    -
    -
    -
    - -
    -
    -classmethod metagga_opt_run(vasp_cmd, auto_npar=True, ediffg=- 0.05, half_kpts_first_relax=False, auto_continue=False)[source]
    -

    Returns a list of thres jobs to perform an optimization for any -metaGGA functional. There is an initial calculation of the -GGA wavefunction which is fed into the initial metaGGA optimization -to precondition the electronic structure optimizer. The metaGGA -optimization is performed using the double relaxation scheme

    -
    - -
    -
    -postprocess()[source]
    -

    Postprocessing includes renaming and gzipping where necessary. -Also copies the magmom to the incar if necessary

    -
    - -
    -
    -run()[source]
    -

    Perform the actual VASP run.

    -
    -
    Returns
    -

    (subprocess.Popen) Used for monitoring.

    -
    -
    -
    - -
    -
    -setup()[source]
    -

    Performs initial setup for VaspJob, including overriding any settings -and backing up.

    -
    - -
    -
    -terminate()[source]
    -

    Ensure all vasp jobs are killed.

    -
    - -
    - -
    -
    -class VaspNEBJob(vasp_cmd, output_file='neb_vasp.out', stderr_file='neb_std_err.txt', suffix='', final=True, backup=True, auto_npar=True, half_kpts=False, auto_gamma=True, auto_continue=False, gamma_vasp_cmd=None, settings_override=None)[source]
    -

    Bases: custodian.custodian.Job

    -

    A NEB vasp job, especially for CI-NEB running at PBS clusters. -The class is added for the purpose of handling a different folder -arrangement in NEB calculation.

    -

    This constructor is a simplified version of VaspJob, which satisfies -the need for flexibility. For standard kinds of runs, it’s often -better to use one of the static constructors. The defaults are -usually fine too.

    -
    -
    Parameters
    -
      -

    • vasp_cmd (str) – Command to run vasp as a list of args. For example, -if you are using mpirun, it can be something like -[“mpirun”, “pvasp.5.2.11”]

      • -

    • output_file (str) – Name of file to direct standard out to. -Defaults to “vasp.out”.

      • -

    • stderr_file (str) – Name of file to direct standard error to. -Defaults to “std_err.txt”.

      • -

    • suffix (str) – A suffix to be appended to the final output. E.g., -to rename all VASP output from say vasp.out to -vasp.out.relax1, provide “.relax1” as the suffix.

      • -

    • final (bool) – Indicating whether this is the final vasp job in a -series. Defaults to True.

      • -

    • backup (bool) – Whether to backup the initial input files. If True, -the INCAR, KPOINTS, POSCAR and POTCAR will be copied with a -“.orig” appended. Defaults to True.

      • -

    • auto_npar (bool) – Whether to automatically tune NPAR to be sqrt( -number of cores) as recommended by VASP for DFT calculations. -Generally, this results in significant speedups. Defaults to -True. Set to False for HF, GW and RPA calculations.

      • -

    • half_kpts (bool) – Whether to halve the kpoint grid for NEB. -Speeds up convergence considerably. Defaults to False.

      • -

    • auto_gamma (bool) – Whether to automatically check if run is a -Gamma 1x1x1 run, and whether a Gamma optimized version of -VASP exists with “.gamma” appended to the name of the VASP -executable (typical setup in many systems). If so, run the -gamma optimized version of VASP instead of regular VASP. You -can also specify the gamma vasp command using the -gamma_vasp_cmd argument if the command is named differently.

      • -

    • auto_continue (bool) – Whether to automatically continue a run -if a STOPCAR is present. This is very useful if using the -wall-time handler which will write a read-only STOPCAR to -prevent VASP from deleting it once it finishes.

      • -

    • gamma_vasp_cmd (str) – Command for gamma vasp version when -auto_gamma is True. Should follow the list style of -subprocess. Defaults to None, which means “.gamma” is added -to the last argument of the standard vasp_cmd.

      • -

    • settings_override ([dict]) –

      An ansible style list of dict to -override changes. For example, to set ISTART=1 for subsequent -runs and to copy the CONTCAR to the POSCAR, you will provide:

      -
      [{"dict": "INCAR", "action": {"_set": {"ISTART": 1}}},
- {"file": "CONTCAR",
-  "action": {"_file_copy": {"dest": "POSCAR"}}}]
-
      -
      -

      • -
    -
    -
    -
    -
    -postprocess()[source]
    -

    Postprocessing includes renaming and gzipping where necessary.

    -
    - -
    -
    -run()[source]
    -

    Perform the actual VASP run.

    -
    -
    Returns
    -

    (subprocess.Popen) Used for monitoring.

    -
    -
    -
    - -
    -
    -setup()[source]
    -

    Performs initial setup for VaspNEBJob, including overriding any settings -and backing up.

    -
    - -
    - +
    +

    custodian.vasp.jobs module

    -
    -

    custodian.vasp.validators module

    -

    Implements various validatiors, e.g., check if vasprun.xml is valid, for VASP.

    -
    -
    -class VaspAECCARValidator[source]
    -

    Bases: custodian.custodian.Validator

    -

    Check if the data in the AECCAR is corrupted

    -

    Dummy init

    -
    -
    -check()[source]
    -

    Check for error.

    -
    - -
    - -
    -
    -class VaspFilesValidator[source]
    -

    Bases: custodian.custodian.Validator

    -
    -
    Check for existence of some of the files that VASP

    normally create upon running.

    -
    -
    -

    Dummy init

    -
    -
    -check()[source]
    -

    Check for error.

    -
    - -
    - -
    -
    -class VaspNpTMDValidator[source]
    -

    Bases: custodian.custodian.Validator

    -

    Check NpT-AIMD settings is loaded by VASP compiled with -Dtbdyn. -Currently, VASP only have Langevin thermostat (MDALGO = 3) for NpT ensemble.

    -

    Dummy init.

    -
    -
    -check()[source]
    -

    Check for error.

    -
    - -
    - -
    -
    -class VasprunXMLValidator(output_file='vasp.out', stderr_file='std_err.txt')[source]
    -

    Bases: custodian.custodian.Validator

    -

    Checks that a valid vasprun.xml was generated

    -
    -
    Parameters
    -
      -

    • output_file (str) – Name of file VASP standard output is directed to. -Defaults to “vasp.out”.

      • -

    • stderr_file (str) – Name of file VASP standard error is direct to. -Defaults to “std_err.txt”.

      • -
    -
    -
    -
    -
    -check()[source]
    -

    Check for error.

    -
    - -
    - -
    -
    -check_broken_chgcar(chgcar, diff_thresh=None)[source]
    -

    Check if the charge density file is corrupt -:param chgcar: Chgcar-like object. -:type chgcar: Chgcar -:param diff_thresh: Threshold for diagonal difference.

    -
    -

    None means we won’t check for this.

    -
    -
    -
    -
    - +
    +

    custodian.vasp.validators module

    Module contents

    @@ -1351,10 +88,10 @@

    Table of Contents

  • custodian.vasp package
    • diff --git a/docs/genindex.html b/docs/genindex.html index 26cbe5ab..d175fca5 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -5,7 +5,7 @@ - Index — custodian 2022.1.17 documentation + Index — custodian 2022.2.13 documentation @@ -36,7 +36,7 @@

    Navigation

  • modules |
    • -
  • custodian 2022.1.17 documentation »
    • +
  • custodian 2022.2.13 documentation »
  • Index
    • @@ -68,7 +68,6 @@

    Index

    | T | U | V - | W

    A

    @@ -76,16 +75,6 @@

    A

    - @@ -100,110 +89,14 @@

    B

    C

    - +
    -
    • custodian.ansible.actions @@ -241,20 +132,6 @@

      C

      • -
    • - custodian.cli.converge_geometry - -
      • -
    • - custodian.cli.converge_kpoints - -
    • @@ -262,20 +139,6 @@

      C

      • -
    • - custodian.cli.run_nwchem - -
      • -
    • - custodian.cli.run_vasp - -
    • @@ -292,20 +155,8 @@

      C

    • module
    -
  • - custodian.feff.handlers - -
    • -
  • - custodian.feff.interpreter - -
    • +     		diff --git a/docs/searchindex.js b/docs/searchindex.js index 9221047f..53e99cf3 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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