2.8

PrincetonUniversity · Jun 16, 2024 · 1e50f43 · 1e50f43
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diff --git a/.gitignore b/.gitignore
@@ -17,6 +17,7 @@
 !CITATION
 !LICENSE
 .vscode/*.log
+CMakeLists.txt
 __pycache__
 
 *.pyc

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2022, Anatoly Spitkovsky & Hayk Hakobyan
+Copyright (c) 2024, Tristan v2 Dev. Team
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Tristan v2.7
+# Tristan v2.8
 
 [![DOI](https://zenodo.org/badge/234551890.svg)](https://zenodo.org/badge/latestdoi/234551890)
 
@@ -27,6 +27,8 @@ sudo apt libhdf5-openmpi-dev hdf5-tools
 
 ### Usage
 
+#### `configure.py` + GNU Make
+
 ```shell
 # to view all configuration options
 python3 configure.py --help
@@ -38,6 +40,15 @@ make all -j
 mpirun -np <NCORES> ./bin/tristan-mp2d -input ../inputs/input.2d_rec
 ```
 
+#### `CMake` (experimental support)
+
+```shell
+# preconfigure the code using
+cmake -B build -D user=<USERFILE> -D dim=3 ...
+# compile
+cmake --build build -j $(nproc)
+```
+
 ### Docker
 
 Another way to avoid the tedium of installing libraries (especially for local development) is to use [Docker containers](https://docs.docker.com/get-started/). This approach allows to quickly create an isolated linux environment with all the necessary packages already preinstalled (similar to a VM, but much lighter). The best thing is that VSCode can natively attach to a running container, and all the development can be done there (make sure to install the [appropriate extension](https://code.visualstudio.com/docs/remote/containers)).
@@ -103,23 +114,25 @@ or in the VSCode environment (see the extension list in the `.vscode/settings.js
 
 ## Contributors (alphabetical order)
 
-* Fabio Bacchini (University of Colorado Boulder)
-* Alexander Chernoglazov (University of Maryland)
-* Daniel Groselj (Columbia)
-* Hayk Hakobyan (PPPL/Columbia)
-* Jens Mahlmann (Princeton)
-* Arno Vanthieghem (Princeton)
+* Fabio Bacchini (KU Leuven)
+* Alexander Chernoglazov (Univ. of Maryland)
+* Daniel Groselj (KU Leuven)
+* Hayk Hakobyan (Columbia/PPPL)
+* Jens Mahlmann (Columbia)
+* Arno Vanthieghem (Univ. of Paris)
 
 ## Board of trustees
 
 * Prof. Anatoly Spitkovsky (Princeton)
-* Prof. Sasha Philippov (University of Maryland)
+* Prof. Sasha Philippov (Univ. of Maryland)
 
 ## Publications
 
 __@TODO__
 
 ## Latest Releases
+* `v2.8` __Jun 2024__
+  * `CMake` support (experimental)
 * `v2.6.1` __Aug 2023__
   * Fixed a buggy ordering of synchrotron cooling term and particle coordinate update (very minor correction)
 * `v2.6` __Jan 2023__

diff --git a/src/tools/auxiliary.F90 b/src/tools/auxiliary.F90
@@ -1,4 +1,12 @@
 module m_aux
+#ifdef MPI08
+  use mpi_f08
+#else
+  include "mpif.h"
+#endif
+#ifdef HDF5
+  use hdf5
+#endif
   use m_globalnamespace
   implicit none
   real(dprec) :: dseed
@@ -11,7 +19,7 @@ function spatialDistribution(x_glob, y_glob, z_glob, &
       real, intent(in), optional :: dummy1, dummy2, dummy3
     end function spatialDistribution
     function spatialCloudDistribution(x_glob, y_glob, z_glob, &
-        dummy1, dummy2, dummy3)
+                                      dummy1, dummy2, dummy3)
       real :: spatialCloudDistribution
       real, intent(in), optional :: x_glob, y_glob, z_glob
       real, intent(in), optional :: dummy1, dummy2, dummy3
@@ -44,24 +52,24 @@ end function spatialCloudDistribution
   end type simulation_params
 
   abstract interface
-  function getFMT(value, w) result(FMT)
-    implicit none
-    real, intent(in) :: value
-    character(len=STR_MAX) :: FMT
-    integer, intent(in), optional :: w
-  end function getFMT
-end interface
+    function getFMT(value, w) result(FMT)
+      implicit none
+      real, intent(in) :: value
+      character(len=STR_MAX) :: FMT
+      integer, intent(in), optional :: w
+    end function getFMT
+  end interface
 
-type :: warning
-  character(len=STR_MAX) :: description
-  integer :: counter = 0
-end type warning
+  type :: warning
+    character(len=STR_MAX) :: description
+    integer :: counter = 0
+  end type warning
 
-type(warning) :: warnings(100)
-type(simulation_params) :: sim_params
+  type(warning) :: warnings(100)
+  type(simulation_params) :: sim_params
 
 !--- PRIVATE functions -----------------------------------------!
-private :: intToStr, realToStr, int8ToStr, real8ToStr
+  private :: intToStr, realToStr, int8ToStr, real8ToStr
 !...............................................................!
 contains
   subroutine initializeSimulationParameters()
@@ -93,7 +101,7 @@ subroutine printDiag(msg, level)
       if (present(level)) then
         sz = sz + level * 3
         do i = 1, level * 3
-        dummy(i:i) = '.'
+          dummy(i:i) = '.'
         end do
       end if
       dummy = trim(dummy)//trim(msg)
@@ -115,8 +123,8 @@ subroutine printWarnings(timestep)
     integer :: warnings_global(100)
 
     do w = 1, 100
-    call MPI_REDUCE(warnings(w) % counter, warnings_global(w), 1, MPI_INTEGER, &
-      MPI_SUM, root_rnk, MPI_COMM_WORLD, ierr)
+      call MPI_REDUCE(warnings(w) % counter, warnings_global(w), 1, MPI_INTEGER, &
+                      MPI_SUM, root_rnk, MPI_COMM_WORLD, ierr)
     end do
 
     if (mpi_rank .eq. root_rnk) then
@@ -133,7 +141,7 @@ subroutine printWarnings(timestep)
     end if
 
     do w = 1, 100
-    warnings(w) % counter = 0
+      warnings(w) % counter = 0
     end do
   end subroutine printWarnings
 
@@ -162,18 +170,18 @@ end function getFMTForReal
 
   function getFMTForRealScientific(value, w) result(FMT)
     implicit none
-    real, intent(in)              :: value
-    character(len=STR_MAX)        :: FMT
+    real, intent(in) :: value
+    character(len=STR_MAX) :: FMT
     integer, intent(in), optional :: w
-    integer                       :: w_
-    character(len=10)             :: dummy
+    integer :: w_
+    character(len=10) :: dummy
     if (.not. present(w)) then
       w_ = 10
     else
       w_ = w
     end if
-    write(dummy, '(I10)') w_
-    FMT = 'ES' // trim(dummy) // '.3'
+    write (dummy, '(I10)') w_
+    FMT = 'ES'//trim(dummy)//'.3'
   end function getFMTForRealScientific
 
   subroutine printTimeHeader(tstep)
@@ -193,7 +201,7 @@ subroutine printTimeHeader(tstep)
 
     write (*, "(1X,A10,I9)", advance='no') "Timestep: ", tstep
     do i = 1, 48
-    write (*, "(A)", advance='no') '.'
+      write (*, "(A)", advance='no') '.'
     end do
     print "(A4)", "[OK]"
     print "(1X,A71)", "[ROUTINE]          [TIME, ms]      [MIN  /  MAX, ms]      [FRACTION, %]"
@@ -332,8 +340,8 @@ logical function arraysAreEqual(array1, array2)
     arraysAreEqual = (size(array1) .eq. size(array2))
     if (arraysAreEqual) then
       do i = 1, size(array1)
-      arraysAreEqual = (array1(i) .eq. array2(i))
-      if (.not. arraysAreEqual) exit
+        arraysAreEqual = (array1(i) .eq. array2(i))
+        if (.not. arraysAreEqual) exit
       end do
     end if
   end function arraysAreEqual
@@ -356,7 +364,7 @@ real function random(DSEED)
     real :: rnd
     rnd = 1.0
     do while (rnd .ge. 1.0)
-    rnd = REAL(randomNum(DSEED))
+      rnd = REAL(randomNum(DSEED))
     end do
     random = rnd
     return
@@ -379,9 +387,9 @@ real function poisson(num)
     kps = 0
     pps = 1
     do while (pps .ge. Lps)
-    kps = kps + 1
-    ups = random(dseed)
-    pps = pps * ups
+      kps = kps + 1
+      ups = random(dseed)
+      pps = pps * ups
     end do
     poisson = kps - 1
     return
@@ -405,19 +413,19 @@ subroutine log_normal(n_bins, lognorm)
     allocate (lognorm(n_bins))
     sum = 0.0
     do i = 1, n_bins
-    x = random(dseed)
-    y = random(dseed)
-    z = sqrt(-2.0 * log(x)) * cos(2.0 * M_PI * y) ! now z has standard normal distribution
-    z = exp(0.0 + 1.0 * z) ! now z has lognormal distribution with certain sigma=1 and mu=0
-    lognorm(i) = z
-    sum = sum + z
+      x = random(dseed)
+      y = random(dseed)
+      z = sqrt(-2.0 * log(x)) * cos(2.0 * M_PI * y) ! now z has standard normal distribution
+      z = exp(0.0 + 1.0 * z) ! now z has lognormal distribution with certain sigma=1 and mu=0
+      lognorm(i) = z
+      sum = sum + z
     end do
 
     ! this allows having lognorm(max) != 1/
     !   in this case bins are not fixed in upper limit
     lognorm(1) = lognorm(1) / (n_bins + 1.)
     do i = 2, n_bins
-    lognorm(i) = lognorm(i) / (n_bins + 1.) + lognorm(i - 1)
+      lognorm(i) = lognorm(i) / (n_bins + 1.) + lognorm(i - 1)
     end do
     ! /this allows having lognorm(max) != 1
   end subroutine log_normal
@@ -431,20 +439,20 @@ subroutine lin_normal(n_bins, linnorm)
     allocate (linnorm(n_bins))
     sum = 0.0
     do i = 1, n_bins
-    x = random(dseed)
-    linnorm(i) = x
-    sum = sum + x
+      x = random(dseed)
+      linnorm(i) = x
+      sum = sum + x
     end do
 
     ! this allows having linnorm(max) != 1/
     !   in this case bins are not fixed in upper limit
     linnorm(1) = linnorm(1) / (n_bins + 1.0)
     do i = 2, n_bins
-    linnorm(i) = linnorm(i) / (n_bins + 1.0) + linnorm(i - 1)
+      linnorm(i) = linnorm(i) / (n_bins + 1.0) + linnorm(i - 1)
     end do
 
     do i = 1, n_bins
-    linnorm(i) = 2.0 * linnorm(i)
+      linnorm(i) = 2.0 * linnorm(i)
     end do
     ! /this allows having linnorm(max) != 1
   end subroutine lin_normal
@@ -499,16 +507,16 @@ subroutine rotateRandomlyIn3D(rx, ry, rz, rnd1, rnd2, rnd3)
     one_m_cos_phi = (1.0 - cos_phi)
 
     rx = (one_m_cos_phi * ux**2 + cos_phi) * rx_ + &
-      (one_m_cos_phi * ux * uy - sin_phi * uz) * ry_ + &
-      (one_m_cos_phi * ux * uz + sin_phi * uy) * rz_
+         (one_m_cos_phi * ux * uy - sin_phi * uz) * ry_ + &
+         (one_m_cos_phi * ux * uz + sin_phi * uy) * rz_
 
     ry = (one_m_cos_phi * ux * uy + sin_phi * uz) * rx_ + &
-      (one_m_cos_phi * uy**2 + cos_phi) * ry_ + &
-      (one_m_cos_phi * uy * uz - sin_phi * ux) * rz_
+         (one_m_cos_phi * uy**2 + cos_phi) * ry_ + &
+         (one_m_cos_phi * uy * uz - sin_phi * ux) * rz_
 
     rz = (one_m_cos_phi * ux * uz - sin_phi * uy) * rx_ + &
-      (one_m_cos_phi * uy * uz + sin_phi * ux) * ry_ + &
-      (one_m_cos_phi * uz**2 + cos_phi) * rz_
+         (one_m_cos_phi * uy * uz + sin_phi * ux) * ry_ + &
+         (one_m_cos_phi * uz**2 + cos_phi) * rz_
   end subroutine rotateRandomlyIn3D
 
   subroutine rotateIn3D(rx, ry, rz, ax, ay, az, ang)
@@ -530,16 +538,16 @@ subroutine rotateIn3D(rx, ry, rz, ax, ay, az, ang)
     one_m_cos_phi = (1.0 - cos_phi)
 
     rx = (one_m_cos_phi * ux**2 + cos_phi) * rx_ + &
-      (one_m_cos_phi * ux * uy - sin_phi * uz) * ry_ + &
-      (one_m_cos_phi * ux * uz + sin_phi * uy) * rz_
+         (one_m_cos_phi * ux * uy - sin_phi * uz) * ry_ + &
+         (one_m_cos_phi * ux * uz + sin_phi * uy) * rz_
 
     ry = (one_m_cos_phi * ux * uy + sin_phi * uz) * rx_ + &
-      (one_m_cos_phi * uy**2 + cos_phi) * ry_ + &
-      (one_m_cos_phi * uy * uz - sin_phi * ux) * rz_
+         (one_m_cos_phi * uy**2 + cos_phi) * ry_ + &
+         (one_m_cos_phi * uy * uz - sin_phi * ux) * rz_
 
     rz = (one_m_cos_phi * ux * uz - sin_phi * uy) * rx_ + &
-      (one_m_cos_phi * uy * uz + sin_phi * ux) * ry_ + &
-      (one_m_cos_phi * uz**2 + cos_phi) * rz_
+         (one_m_cos_phi * uy * uz + sin_phi * ux) * ry_ + &
+         (one_m_cos_phi * uz**2 + cos_phi) * rz_
   end subroutine rotateIn3D
 
 end module m_aux