Merge branch 'develop' into errors-more-cleanup

.github/release_steps.md

@@ -216,7 +216,7 @@ and using the CMake settings:
 
 ``` sh
 -D CMAKE_OSX_ARCHITECTURES=arm64;x86_64
--D CMAKE_OSX_DEPLOYMENT_TARGER=11.0
+-D CMAKE_OSX_DEPLOYMENT_TARGET=11.0
 ```
 
 This will add the compiler flags `-arch arm64 -arch x86_64
@@ -324,6 +324,47 @@ At this point it should be possible to do a fast-forward merge of
 
 ### Push branches and tags
 
-
-
 ## LAMMPS Stable Update Release
+
+After making a stable release, bugfixes from the 'develop' branch
+are selectively backported to the 'maintenance' branch.  This is
+done with "git cherry-pick \<commit hash\>' wherever possible.
+The LAMMPS\_UPDATE define in "src/version.h" is set to "Maintenance".
+
+### Prerequesites
+
+When a sufficient number of bugfixes has accumulated or an urgent
+or important bugfix needs to be distributed a new stable update
+release is made.  To make this publicly visible a pull request
+is submitted that will merge 'maintenance' into 'stable'.  Before
+merging, set LAMMPS\_UPDATE in "src/version.h" to "Update #" with
+"#" indicating the update count (1, 2, and so on).
+Also draft suitable release notes under https://github.com/lammps/lammps/releases
+
+### Fast-forward merge of 'maintenance' into 'stable', apply tag, and publish
+
+Do a fast-forward merge of 'maintenance' to 'stable' and then
+apply the stable\_DMmmYYYY\_update# tag and push branch and tag
+to GitHub. The corresponding pull request will be automatically
+closed.   Example:
+
+```
+git checkout maintenance
+git pull
+git checkout stable
+git pull
+git merge --ff-only maintenance
+git tag -s -m 'Update 2 for Stable LAMMPS version 29 August 2024' stable_29Aug2024_update2
+git push git@github.com:lammps/lammps.git --tags maintenance stable
+```
+
+Associate draft release notes with new tag and publish as "latest release".
+
+On https://ci.lammps.org/ go to "dev", "stable" and manually execute
+the "update\_release" task. This will update https://docs.lammps.org/stable
+and prepare a stable tarball.
+
+### Build and upload binary packages and source tarball to GitHub
+
+The build procedure is the same as for the feature releases, only
+that packages are built from the 'stable' branch.

doc/src/Build_cmake.rst

@@ -119,6 +119,13 @@ configured) and additional files like LAMMPS API headers, manpages,
 potential and force field files.  The location of the installation tree
 defaults to ``${HOME}/.local``.
 
+.. note::
+
+   If you have set `-D CMAKE_INSTALL_PREFIX` to install LAMMPS into a
+   system location on a Linux machine , you may also have to run (as
+   root) the `ldconfig` program to update the cache file for fast lookup
+   of system shared libraries.
+
 .. _cmake_options:
 
 Configuration and build options

doc/src/Build_settings.rst

@@ -13,7 +13,8 @@ explains how to do this for building both with CMake and make.
 * `Size of LAMMPS integer types and size limits`_
 * `Read or write compressed files`_
 * `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
-* `Support for downloading files`_
+* `Support for downloading files from the input`_
+* `Prevent download of large potential files`_
 * `Memory allocation alignment`_
 * `Workaround for long long integers`_
 * `Exception handling when using LAMMPS as a library`_ to capture errors
@@ -509,8 +510,8 @@ during a run.
 
 .. _libcurl:
 
-Support for downloading files
+Support for downloading files from the input
------------------------------
+--------------------------------------------
 
 .. versionadded:: 29Aug2024
 
@@ -553,6 +554,25 @@ LAMMPS is compiled accordingly which needs the following settings:
 
 ----------
 
+.. _download_pot:
+
+Prevent download of large potential files
+-----------------------------------------
+
+.. versionadded:: 8Feb2023
+
+LAMMPS bundles a selection of potential files in the ``potentials``
+folder as examples of how those kinds of potential files look like and
+for use with the provided input examples in the ``examples`` tree.  To
+keep the size of the distributed LAMMPS source package small, very large
+potential files (> 5 MBytes) are not bundled, but only downloaded on
+demand when the :doc:`corresponding package <Packages_list>` is
+installed.  This automatic download can be prevented when :doc:`building
+LAMMPS with CMake <Build_cmake>` by adding the setting `-D
+DOWNLOAD_POTENTIALS=off` when configuring.
+
+----------
+
 .. _align:
 
 Memory allocation alignment

doc/src/Howto_python.rst

@@ -62,17 +62,17 @@ with :ref:`PNG, JPEG and FFMPEG output support <graphics>` enabled.
 
          cd $LAMMPS_DIR/src
 
-         # add packages if necessary
+         # add LAMMPS packages if necessary
          make yes-MOLECULE
          make yes-PYTHON
 
          # compile shared library using Makefile
          make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
 
-Step 2: Installing the LAMMPS Python package
+Step 2: Installing the LAMMPS Python module
-""""""""""""""""""""""""""""""""""""""""""""
+"""""""""""""""""""""""""""""""""""""""""""
 
-Next install the LAMMPS Python package into your current Python installation with:
+Next install the LAMMPS Python module into your current Python installation with:
 
 .. code-block:: bash
 
@@ -89,6 +89,29 @@ privileges) or into your personal Python module folder.
    Recompiling the shared library requires re-installing the Python
    package.
 
+.. _externally_managed:
+
+.. admonition:: Handling an "externally-managed-environment" Error
+   :class: Hint
+
+   Some Python installations made through Linux distributions
+   (e.g. Ubuntu 24.04LTS or later) will prevent installing the LAMMPS
+   Python module into a system folder or a corresponding folder of the
+   individual user as attempted by ``make install-python`` with an error
+   stating that an *externally managed* python installation must be only
+   managed by the same package package management tool.  This is an
+   optional setting, so not all Linux distributions follow it currently
+   (Spring 2025).  The reasoning and explanations for this error can be
+   found in the `Python Packaging User Guide
+   <https://packaging.python.org/en/latest/specifications/externally-managed-environments/>`_
+
+   These guidelines suggest to create a virtual environment and install
+   the LAMMPS Python module there (see below).  This is generally a good
+   idea and the LAMMPS developers recommend this, too.  If, however, you
+   want to proceed and install the LAMMPS Python module regardless, you
+   can install the "wheel" file (see above) manually with the ``pip``
+   command by adding the ``--break-system-packages`` flag.
+
 Installation inside of a virtual environment
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Python_install.rst

@@ -110,13 +110,16 @@ folder that the dynamic loader searches or inside of the installed
 
       .. code-block:: bash
 
-         python install.py -p <python package> -l <shared library> -v <version.h file> [-n]
+         python install.py -p <python package> -l <shared library> -v <version.h file> [-n] [-f]
 
       * The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
       * the ``-l`` flag points to the LAMMPS shared library file to be installed,
       * the ``-v`` flag points to the LAMMPS version header file to extract the version date,
-      * and the optional ``-n`` instructs the script to only build a wheel file
+      * the optional ``-n`` instructs the script to only build a wheel file but not attempt
-        but not attempt to install it.
+        to install it,
+      * and the optional ``-f`` argument instructs the script to force installation even if
+        pip would otherwise refuse installation with an
+        :ref:`error about externally managed environments <externally_managed>`.
 
    .. tab:: Virtual environment
 
@@ -198,6 +201,10 @@ folder that the dynamic loader searches or inside of the installed
 
          The ``PYTHONPATH`` needs to point to the parent folder that contains the ``lammps`` package!
 
+In case you run into an "externally-managed-environment" error when
+trying to install the LAMMPS Python module, please refer to
+:ref:`corresponding paragraph <externally_managed>` in the Python HOWTO
+page to learn about options for handling this error.
 
 To verify if LAMMPS can be successfully started from Python, start the
 Python interpreter, load the ``lammps`` Python module and create a

doc/src/Tools.rst

@@ -930,7 +930,7 @@ dependencies and redirects the download to the local cache.
 
    mkdir build
    cd build
-   cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
+   cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake -D DOWNLOAD_POTENTIALS=off ../cmake
    make -j 8
 
    deactivate_caches

doc/utils/sphinx-config/_themes/lammps_theme/layout.html

@@ -137,6 +137,7 @@
           {# the master_doc variable was renamed to root_doc in Sphinx 4 (master_doc still exists in later Sphinx versions) #}
           {%- set _logo_url = logo_url|default(pathto('_static/' + (logo or ""), 1)) %}
           {%- set _root_doc = root_doc|default(master_doc) %}
+          <div id="sidebar-top-target"></div>
           <a href="{{ pathto(_root_doc) }}"{% if not theme_logo_only %} class="icon icon-home"{% endif %}>
             {% if not theme_logo_only %}{{ project }}{% endif %}
             {%- if logo or logo_url %}
@@ -172,6 +173,15 @@
         </div>
         {%- endblock %}
       </div>
+<!--      <div style="padding: 4px;">
+        <center>
+          <a href="#sidebar-top-target"><img src="_static/up.png" alt="(Up)"/> Go to top</a>
+        </center>
+      </div>
+-->
+    <div style="position: fixed; bottom: 0px; width: 300px; height: 64px; padding: 4px; background-color: #272525; text-align: center">
+      <a href="#sidebar-top-target" class="fa fa-caret-up" style="color: white"> Go to top</a>
+    </div>
     </nav>
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">

doc/utils/sphinx-config/conf.py.in

@@ -288,7 +288,7 @@ rst_prolog = r"""
 
 .. only:: html
 
-   :math:`\renewcommand{\AA}{\textup{\r{A}}`
+   :math:`\renewcommand{\AA}{\text{Å}}`
 
 .. role:: lammps(code)
     :language: LAMMPS

python/install.py

@@ -27,6 +27,8 @@ parser.add_argument("-w", "--wheeldir", required=False,
                     help="path to a directory where the created wheel will be stored")
 parser.add_argument("-v", "--versionfile", required=True,
                     help="path to the LAMMPS version.h source file")
+parser.add_argument("-f", "--force", action="store_true", required=False, default=False,
+                    help="force installation of LAMMPS Python package")
 
 args = parser.parse_args()
 
@@ -145,7 +147,10 @@ else:
   py_exe = sys.executable
 
 try:
-  txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
+  if args.force:
+    txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', '--break-system-packages', wheel], stderr=subprocess.STDOUT, shell=False)
+  else:
+    txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
   print(txt.decode('UTF-8'))
   sys.exit(0)
 except subprocess.CalledProcessError as err:
@@ -154,7 +159,10 @@ except subprocess.CalledProcessError as err:
     sys.exit(errmsg + "You need to uninstall the LAMMPS python module manually first.\n")
 try:
   print('Installing wheel into system site-packages folder failed. Trying user folder now')
-  txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--user', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
+  if args.force:
+    txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--user', '--force-reinstall', '--break-system-packages', wheel], stderr=subprocess.STDOUT, shell=False)
+  else:
+    txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--user', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
   print(txt.decode('UTF-8'))
 except:
   sys.exit('Failed to install wheel ' + wheel)

src/BPM/bond_bpm_spring_plastic.cpp

@@ -440,7 +440,7 @@ double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double &
 
   double r = sqrt(rsq);
   double rinv = 1.0 / r;
-  double e = (r - r0) / r0;
+  double e = (r0 != 0.0) ? (r - r0) / r0 : 0.0;
 
   if (normalize_flag)
     fforce = -k[type] * (e - ep);
@@ -460,7 +460,7 @@ double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double &
   fforce *= rinv;
 
   if (smooth_flag) {
-    double smooth = (r - r0) / (r0 * ecrit[type]);
+    double smooth = (r0 != 0.0) ? (r - r0) / (r0 * ecrit[type]) : 0.0;
     smooth *= smooth;
     smooth *= smooth;
     smooth *= smooth;

src/EXTRA-COMPUTE/compute_stress_mop.cpp

@@ -882,7 +882,7 @@ void ComputeStressMop::compute_dihedrals()
   double x_atom_4[3] = {0.0, 0.0, 0.0};
 
   // initialization
-  for (int i = 0; i < nvalues; i++) { dihedral_local[i] = 0.0; }
+  for (int i = 0; i < nvalues; i++) dihedral_local[i] = 0.0;
   double local_contribution[3] = {0.0, 0.0, 0.0};
 
   for (atom2 = 0; atom2 < nlocal; atom2++) {
@@ -1118,10 +1118,6 @@ void ComputeStressMop::compute_dihedrals()
         df[2] = sgn * (f1[2] + f3[2]);
       }
 
-      // no if matches
-      else {
-       df[0] = df[1] = df[2] = 0.0;
-      }
       local_contribution[0] += df[0] / area * nktv2p;
       local_contribution[1] += df[1] / area * nktv2p;
       local_contribution[2] += df[2] / area * nktv2p;

src/fix_halt.cpp

@@ -294,6 +294,7 @@ void FixHalt::end_of_step()
     for (int i = 0; i < universe->nworlds; ++i) {
       if (universe->me == universe->root_proc[i]) continue;
       MPI_Wait(req + i, MPI_STATUS_IGNORE);
+      MPI_Request_free(req + i);
     }
   }
 

src/utils.cpp

@@ -272,11 +272,7 @@ void utils::print(FILE *fp, const std::string &mesg)
 
 void utils::fmtargs_print(FILE *fp, fmt::string_view format, fmt::format_args args)
 {
-  try {
+  print(fp, fmt::vformat(format, args));
-    print(fp, fmt::vformat(format, args));
-  } catch (fmt::format_error &) {
-    ; // do nothing
-  }
 }
 
 std::string utils::errorurl(int errorcode)

tools/lammps-gui/CMakeLists.txt

@@ -94,8 +94,8 @@ endif()
 
 option(BUILD_WHAM "Download and compile WHAM executable from Grossfield Lab" YES)
 if(BUILD_WHAM)
-  set(WHAM_URL "http://membrane.urmc.rochester.edu/sites/default/files/wham/wham-release-2.0.11.tgz" CACHE STRING "URL for WHAM tarball")
+  set(WHAM_URL "http://membrane.urmc.rochester.edu/sites/default/files/wham/wham-release-2.1.0.tgz" CACHE STRING "URL for WHAM tarball")
-  set(WHAM_MD5 "f56751ac71a8d1c485b9ebd4ccff8dbe" CACHE STRING "MD5 checksum of WHAM tarball")
+  set(WHAM_MD5 "4ed6e24254925ec124f44bb381c3b87f" CACHE STRING "MD5 checksum of WHAM tarball")
   mark_as_advanced(WHAM_URL)
   mark_as_advanced(WHAM_MD5)
 
@@ -122,7 +122,7 @@ if(BUILD_WHAM)
   if(PATCH_FOUND)
     message(STATUS "Apply patch to customize WHAM using ${Patch_EXECUTABLE}")
     execute_process(
-      COMMAND ${Patch_EXECUTABLE} -p1 -i ${CMAKE_CURRENT_SOURCE_DIR}/update-wham-2.0.11.patch
+      COMMAND ${Patch_EXECUTABLE} -p1 -i ${CMAKE_CURRENT_SOURCE_DIR}/update-wham-2.1.0.patch
       WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src/wham/
     )
   endif()

tools/lammps-gui/lammps-gui.appdata.xml

@@ -61,7 +61,6 @@
         Highlight warnings and error messages in Output window
         Make Tutorial wizards more compact
         Include download and compilation of WHAM software from Alan Grossfield
-        Add dialog to run WHAM directly from LAMMPS-GUI
         Add entry to Run menu to restart the LAMMPS instance
         Use mutex to avoid corruption of thermo data
       </description>

tools/lammps-gui/update-wham-2.1.0.patch

@@ -1,73 +1,29 @@
-diff --git a/.gitignore b/.gitignore
-index 28ac6ef..a401160 100644
---- a/.gitignore
-+++ b/.gitignore
-@@ -6,6 +6,8 @@ doc.toc
- wham-dist.tar.gz
- 
- *.o
-+*~
- 
- wham/wham
- wham-2d/wham-2d
-+/build
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-new file mode 100644
+index b4f0fe6..a61cec8 100644
-index 0000000..b4f0fe6
+--- a/CMakeLists.txt
---- /dev/null
 +++ b/CMakeLists.txt
-@@ -0,0 +1,38 @@
+@@ -1,7 +1,7 @@
-+# Custom minimal -*- CMake -*- file for wham
+ # Custom minimal -*- CMake -*- file for wham
-+
+ 
-+cmake_minimum_required(VERSION 3.16)
+ cmake_minimum_required(VERSION 3.16)
-+project(wham VERSION 2.0.11
+-project(wham VERSION 2.0.11
-+  DESCRIPTION "WHAM: a fast, memory efficient implementation of the Weighted Histogram Analysis Method"
++project(wham VERSION 2.1.0
-+  LANGUAGES C
+   DESCRIPTION "WHAM: a fast, memory efficient implementation of the Weighted Histogram Analysis Method"
-+  HOMEPAGE_URL http://membrane.urmc.rochester.edu/content/wham/)
+   LANGUAGES C
-+
+   HOMEPAGE_URL http://membrane.urmc.rochester.edu/content/wham/)
-+include(GNUInstallDirs)
+diff --git a/doc/doc.tex b/doc/doc.tex
-+
+index cf36616..84ee891 100644
-+add_executable(wham
+--- a/doc/doc.tex
-+  nr/ran2.c
++++ b/doc/doc.tex
-+  nr/locate.c
+@@ -53,7 +53,7 @@ Suggestions and patches are welcome.
-+  wham/wham.c
+ 
-+  wham/file_read.c
+ 
-+  wham/histogram.c
+ \subsection{New in release 2.1.0}
-+  wham/bootstrap.c
+-Two changes, both contributed by Alex Kohlmeyer. First, we switched from old
-+)
++Two changes, both contributed by Axel Kohlmeyer. First, we switched from old
-+target_include_directories(wham PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/wham)
+ make to CMake for the build. Second, we changed how energy units are set; where
-+target_link_libraries(wham PRIVATE m)
+ it used to be a compile-time option, now it is set on the command line.
-+install(TARGETS wham DESTINATION ${CMAKE_INSTALL_BINDIR})
+ 
-+
-+add_executable(wham-2d
-+  nr/ran2.c
-+  nr/locate.c
-+  wham-2d/wham-2d.c
-+  wham-2d/file_read.c
-+  wham-2d/histogram.c
-+  wham/bootstrap.c
-+)
-+target_include_directories(wham-2d PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/wham)
-+target_link_libraries(wham-2d PRIVATE m)
-+install(TARGETS wham-2d DESTINATION ${CMAKE_INSTALL_BINDIR})
-+
-+install(FILES doc/doc.pdf
-+  TYPE DOC
-+  PERMISSIONS OWNER_READ GROUP_READ WORLD_READ
-+)
-diff --git a/nr/locate.c b/nr/locate.c
-index 9f92dc0..f3bf294 100644
---- a/nr/locate.c
-+++ b/nr/locate.c
-@@ -11,7 +11,7 @@ void locate(double xx[], int n, double x, int *j)
- 	ascnd=(xx[n] > xx[0]);  // I think this makes it zero based
- 	while (ju-jl > 1) {
- 		jm=(ju+jl) >> 1;
--		if (x > xx[jm] == ascnd)
-+		if ((x > xx[jm]) == ascnd)
- 			jl=jm;
- 		else
- 			ju=jm;
 diff --git a/wham-2d/histogram.c b/wham-2d/histogram.c
 index 1bd1329..b5d1c01 100644
 --- a/wham-2d/histogram.c
@@ -127,99 +83,10 @@ index 1bd1329..b5d1c01 100644
 -
 -
 diff --git a/wham-2d/wham-2d.c b/wham-2d/wham-2d.c
-index fb6e059..a6b8483 100644
+index 76389ac..05fe7cf 100644
 --- a/wham-2d/wham-2d.c
 +++ b/wham-2d/wham-2d.c
-@@ -25,7 +25,7 @@
+@@ -417,8 +417,8 @@ while ( ! iConverged || first)
- #include <time.h>
- #include "wham-2d.h"
- 
--#define COMMAND_LINE "Command line:  wham-2d Px[=0|pi|val] hist_min_x hist_max_x num_bins_x Py[=0|pi|val] hist_min_y hist_max_y num_bins_y tol temperature numpad metadatafile freefile use_mask\n"
-+#define COMMAND_LINE "Command line:  wham-2d [units <real|metal|lj|...>] Px[=0|pi|val] hist_min_x hist_max_x num_bins_x Py[=0|pi|val] hist_min_y hist_max_y num_bins_y tol temperature numpad metadatafile freefile use_mask\n"
- double HIST_MAXx,HIST_MINx,BIN_WIDTHx;
- double HIST_MAXy,HIST_MINy,BIN_WIDTHy;
- double TOL;
-@@ -35,7 +35,7 @@ int  NUM_BINSx, NUM_BINSy;
- int PERIODICx, PERIODICy;
- double PERIODx, PERIODy;
- double *data1,**num,***bias;
--
-+double k_B = k_B_DEFAULT;
- 
- int main(int argc, char *argv[])
- {
-@@ -57,7 +57,7 @@ double sum;
- int iteration;
- int max_iteration = 100000;
- int numpad;
--int **mask;
-+int **mask = NULL;
- int use_mask;
- 
- cpu1 = ((double) clock())/CLOCKS_PER_SEC;
-@@ -76,6 +76,61 @@ for (i=0; i<argc; i++)
-     }
- printf("\n");
- 
-+// set k_B according to LAMMPS units settings
-+if (strcmp(argv[1],"units") == 0)
-+    {
-+        if (argc < 3)
-+        {
-+            printf( COMMAND_LINE );
-+            exit(-1);
-+        }
-+
-+        if (strcmp(argv[2], "lj") == 0)
-+        {
-+            k_B = 1.0;
-+        }
-+        else if (strcmp(argv[2], "real") == 0)
-+        {
-+            k_B = 0.0019872067;
-+        }
-+        else if (strcmp(argv[2], "metal") == 0)
-+        {
-+            k_B = 8.617343e-5;
-+        }
-+        else if (strcmp(argv[2], "si") == 0)
-+        {
-+            k_B = 1.3806504e-23;
-+        }
-+        else if (strcmp(argv[2], "cgs") == 0)
-+        {
-+            k_B = 1.3806504e-16;
-+        }
-+        else if (strcmp(argv[2], "electron") == 0)
-+        {
-+            k_B = 3.16681534e-6;
-+        }
-+        else if (strcmp(argv[2], "micro") == 0)
-+        {
-+            k_B = 1.3806504e-8;
-+        }
-+        else if (strcmp(argv[2], "nano") == 0)
-+        {
-+            k_B = 0.013806504;
-+        }
-+        else if (strcmp(argv[2], "default") == 0)
-+        {
-+            k_B = k_B_DEFAULT;
-+        }
-+        else
-+        {
-+            printf("Unknown unit style: %s\n%s", argv[2], COMMAND_LINE);
-+            exit(-1);
-+        }
-+        printf("# Setting value of k_B to = %.15g\n", k_B);
-+        argc -= 2;
-+        argv += 2;
-+    }
-+
- PERIODICx = parse_periodic(argv[1], &PERIODx);
- if (PERIODICx)
-     {
-@@ -360,8 +415,8 @@ while ( ! iConverged || first)
              for (j=0; j< NUM_BINSy; j++)
                  {
                  calc_coor(i,j,coor);
@@ -230,7 +97,7 @@ index fb6e059..a6b8483 100644
                  }
              }
  
-@@ -444,8 +499,9 @@ if (!FREEFILE)
+@@ -501,8 +501,9 @@ if (!FREEFILE)
          for (j=0; j< NUM_BINSy; j++)
              {
              calc_coor(i,j,coor);
@@ -242,7 +109,7 @@ index fb6e059..a6b8483 100644
              }
          }
      exit(errno);
-@@ -461,25 +517,28 @@ else
+@@ -518,25 +519,28 @@ else
          for (j=-numpad; j<0; j++)
              {
              calc_coor(i,j,coor);
@@ -280,7 +147,7 @@ index fb6e059..a6b8483 100644
              }
          fprintf(FREEFILE, "\n");
          }
-@@ -490,25 +549,28 @@ else
+@@ -547,25 +551,28 @@ else
          for (j=-numpad; j<0; j++)
              {
              calc_coor(i,j,coor);
@@ -318,7 +185,7 @@ index fb6e059..a6b8483 100644
              }
          fprintf(FREEFILE, "\n");
          }
-@@ -519,25 +581,28 @@ else
+@@ -576,25 +583,28 @@ else
          for (j=-numpad; j<0; j++)
              {
              calc_coor(NUM_BINSx+i,j,coor);
@@ -356,30 +223,6 @@ index fb6e059..a6b8483 100644
              }
          fprintf(FREEFILE, "\n");
          }
-diff --git a/wham-2d/wham-2d.h b/wham-2d/wham-2d.h
-index b17e4bd..5fc17ff 100644
---- a/wham-2d/wham-2d.h
-+++ b/wham-2d/wham-2d.h
-@@ -20,15 +20,15 @@ extern int    NUM_BINSy;
- 
- extern int    PERIODICx,PERIODICy;  // flags to turn on periodicity
- extern double PERIODx, PERIODy;     // flags to control periodic interval
-+extern double k_B;
- 
- // A couple of predefined periodic units
- #define DEGREES   360.0
- #define RADIANS   6.28318530717959
- 
--#define k_B 0.001982923700 // Boltzmann's constant in kcal/mol K
--//#define k_B  0.0083144621 // Boltzmann's constant kJ/mol-K
--//#define k_B 1.0  // Boltzmann's constant in reduced units
--
-+#define k_B_DEFAULT 0.001982923700 // Boltzmann's constant in kcal/mol K
-+//#define k_B_DEFAULT 0.0083144621 // Boltzmann's constant kJ/mol-K
-+//#define k_B_DEFAULT 1.0  // Boltzmann's constant in reduced units
- 
- 
- // Value inserted for the free energy of masked values
 diff --git a/wham/histogram.c b/wham/histogram.c
 index bc52d74..635b39f 100644
 --- a/wham/histogram.c
@@ -432,7 +275,7 @@ index bc52d74..635b39f 100644
 +return HIST_MIN + BIN_WIDTH*((double)i+0.5);
  }
 diff --git a/wham/wham.c b/wham/wham.c
-index 487871b..edb8125 100644
+index 19cf695..7bdbce1 100644
 --- a/wham/wham.c
 +++ b/wham/wham.c
 @@ -1,4 +1,4 @@
@@ -441,25 +284,11 @@ index 487871b..edb8125 100644
   * WHAM -- Weighted Histogram Analysis Method
   *
   * Reference 1: Computer Physics Communications, 91(1995) 275-282, Benoit Roux
-@@ -21,7 +21,7 @@
+@@ -39,10 +39,9 @@ double kT; // temperature
- #include "wham.h"
+ int i,j;
- 
+ int len;
- 
+ int first;
--#define COMMAND_LINE "Command line: wham [P|Ppi|Pval] hist_min hist_max num_bins tol temperature numpad metadatafile freefile [num_MC_trials randSeed]\n"
+-int bin_min;
-+#define COMMAND_LINE "Command line: wham [units <real|metal|lj|...>] [P|Ppi|Pval] hist_min hist_max num_bins tol temperature numpad metadatafile freefile [num_MC_trials randSeed]\n"
- 
- double HIST_MAX,HIST_MIN,BIN_WIDTH,TOL;
- double *HISTOGRAM;
-@@ -29,6 +29,7 @@ double kT;
- int  NUM_BINS;
- int PERIODIC;
- double PERIOD;
-+double k_B = k_B_DEFAULT;
- 
- int main(int argc, char *argv[])
- {
-@@ -41,7 +42,7 @@ int first;
- int bin_min;
  int have_energy;
  char *freefile;
 -FILE *METAFILE, *FREEFILE; 
@@ -467,69 +296,7 @@ index 487871b..edb8125 100644
  struct hist_group *hist_group;
  struct histogram  *hp;
  double coor;
-@@ -82,6 +83,61 @@ for (i=0; i<argc; i++)
+@@ -179,7 +178,7 @@ if (argc != 9 && argc !=11)
-     }
- printf("\n");
- 
-+// set k_B according to LAMMPS units settings
-+if (strcmp(argv[1],"units") == 0)
-+    {
-+        if (argc < 3)
-+        {
-+            printf( COMMAND_LINE );
-+            exit(-1);
-+        }
-+
-+        if (strcmp(argv[2], "lj") == 0)
-+        {
-+            k_B = 1.0;
-+        }
-+        else if (strcmp(argv[2], "real") == 0)
-+        {
-+            k_B = 0.0019872067;
-+        }
-+        else if (strcmp(argv[2], "metal") == 0)
-+        {
-+            k_B = 8.617343e-5;
-+        }
-+        else if (strcmp(argv[2], "si") == 0)
-+        {
-+            k_B = 1.3806504e-23;
-+        }
-+        else if (strcmp(argv[2], "cgs") == 0)
-+        {
-+            k_B = 1.3806504e-16;
-+        }
-+        else if (strcmp(argv[2], "electron") == 0)
-+        {
-+            k_B = 3.16681534e-6;
-+        }
-+        else if (strcmp(argv[2], "micro") == 0)
-+        {
-+            k_B = 1.3806504e-8;
-+        }
-+        else if (strcmp(argv[2], "nano") == 0)
-+        {
-+            k_B = 0.013806504;
-+        }
-+        else if (strcmp(argv[2], "default") == 0)
-+        {
-+            k_B = k_B_DEFAULT;
-+        }
-+        else
-+        {
-+            printf("Unknown unit style: %s\n%s", argv[2], COMMAND_LINE);
-+            exit(-1);
-+        }
-+        printf("# Setting value of k_B to = %.15g\n", k_B);
-+        argc -= 2;
-+        argv += 2;
-+    }
-+
- if (toupper(argv[1][0]) == 'P')
-     {
-     PERIODIC = 1;
-@@ -123,7 +179,7 @@ if (argc != 9 && argc !=11)
      printf( COMMAND_LINE );
      exit(-1);
      }
@@ -538,7 +305,7 @@ index 487871b..edb8125 100644
  HIST_MIN = atof(argv[1]);
  HIST_MAX = atof(argv[2]);
  NUM_BINS = atoi(argv[3]);
-@@ -213,13 +269,13 @@ if (!ave_pdf2)
+@@ -269,13 +268,13 @@ if (!ave_pdf2)
      printf("couldn't allocate space for ave_pdf2: %s\n", strerror(errno));
      exit(errno);
      }
@@ -554,7 +321,7 @@ index 487871b..edb8125 100644
  
  i = get_numwindows(METAFILE);
  printf("#Number of windows = %d\n", i);
-@@ -248,7 +304,7 @@ assert(i == hist_group->num_windows);
+@@ -304,7 +303,7 @@ assert(i == hist_group->num_windows);
  // Figure out if we have trajectories at different temperatures.
  // Missing temperatures are set to -1 in read_metadata, and
  // since we require that either all trajectories specify a temperature
@@ -563,7 +330,7 @@ index 487871b..edb8125 100644
  // have to check one of them
  if (hist_group->kT[0] > 0)
      {
-@@ -257,7 +313,7 @@ if (hist_group->kT[0] > 0)
+@@ -313,7 +312,7 @@ if (hist_group->kT[0] > 0)
  else
      {
      have_energy = 0;
@@ -572,7 +339,7 @@ index 487871b..edb8125 100644
          {
          hist_group->kT[i] = kT;
          }
-@@ -269,7 +325,7 @@ if (!final_f)
+@@ -325,7 +324,7 @@ if (!final_f)
      {
      printf("couldn't allocate space for final_f: %s\n", strerror(errno));
      exit(errno);
@@ -581,7 +348,7 @@ index 487871b..edb8125 100644
  
  free(HISTOGRAM);
  
-@@ -305,7 +361,8 @@ while (! is_converged(hist_group) || first )
+@@ -361,7 +360,8 @@ while (! is_converged(hist_group) || first )
          for (i=0; i< NUM_BINS; i++)
              {
              coor = calc_coor(i);
@@ -591,7 +358,7 @@ index 487871b..edb8125 100644
              }
          printf("\n");
  
-@@ -319,7 +376,7 @@ while (! is_converged(hist_group) || first )
+@@ -375,7 +375,7 @@ while (! is_converged(hist_group) || first )
              }
          }
      // Cheesy bailout if we're going on too long
@@ -600,7 +367,16 @@ index 487871b..edb8125 100644
          {
          printf("Too many iterations: %d\n", iteration);
          break;
-@@ -383,11 +440,11 @@ for (i=0; i< num_mc_runs; i++)
+@@ -408,7 +408,7 @@ for (i=0; i < NUM_BINS; i++)
+     }
+ 
+ // Compute the free energy from the normalized probability
+-bin_min = calc_free(free_ene, prob,kT);
++   calc_free(free_ene, prob,kT);
+ 
+ // Do the requested number of bootstrap monte carlo error analysis runs.
+ if (num_mc_runs <= 0)
+@@ -439,11 +439,11 @@ for (i=0; i< num_mc_runs; i++)
          //printf("Faking %d: %d  %d\n", i,j,hp->num_points);
          num_used = hp->last - hp->first + 1;
          mk_new_hist(hp->cum, hp->data, num_used, hp->num_mc_samples, &idum);
@@ -614,7 +390,7 @@ index 487871b..edb8125 100644
        // perform WHAM iterations on the fake data sets
        iteration = 0;
        first = 1;
-@@ -403,7 +460,7 @@ for (i=0; i< num_mc_runs; i++)
+@@ -459,7 +459,7 @@ for (i=0; i< num_mc_runs; i++)
            printf("Too many iterations: %d\n", iteration);
            break;
            }
@@ -623,7 +399,7 @@ index 487871b..edb8125 100644
        printf("#MC trial %d: %d iterations\n", i, iteration);
        printf("#PMF values\n");
        // accumulate the average and stdev of the resulting probabilities
-@@ -419,18 +476,19 @@ for (i=0; i< num_mc_runs; i++)
+@@ -475,18 +475,19 @@ for (i=0; i< num_mc_runs; i++)
        for (j=0; j < NUM_BINS; j++)
            {
            pdf = -kT*log(prob[j]);
@@ -647,7 +423,7 @@ index 487871b..edb8125 100644
   for (i=0; i < NUM_BINS; i++)
     {
     ave_p[i] /= (double)num_mc_runs;
-@@ -457,12 +515,12 @@ if (!FREEFILE)
+@@ -513,12 +514,12 @@ if (!FREEFILE)
      for (i=0; i< NUM_BINS; i++)
          {
          coor = calc_coor(i);
@@ -663,7 +439,7 @@ index 487871b..edb8125 100644
          }
  
      exit(errno);
-@@ -470,38 +528,37 @@ if (!FREEFILE)
+@@ -526,38 +527,37 @@ if (!FREEFILE)
  else
      {
      // write out header
@@ -714,7 +490,7 @@ index 487871b..edb8125 100644
          }
      }
  
-@@ -515,7 +572,7 @@ exit(0);
+@@ -571,7 +571,7 @@ exit(0);
  /*
   *  Perform a single WHAM iteration
   */
@@ -723,7 +499,7 @@ index 487871b..edb8125 100644
                     int have_energy)
  {
  int i,j;
-@@ -535,9 +592,9 @@ for (i=0; i<NUM_BINS; i++)
+@@ -591,9 +591,9 @@ for (i=0; i<NUM_BINS; i++)
          num += (double) get_histval( &(hist_group->hists[j]),i);
          bias = calc_bias(hist_group,j,coor);
          bf = exp((hist_group->F_old[j] - bias) / hist_group->kT[j]);
@@ -736,27 +512,3 @@ index 487871b..edb8125 100644
           * number of points.
           */
          if (have_energy)
-diff --git a/wham/wham.h b/wham/wham.h
-index aacc1e8..7d509f2 100644
---- a/wham/wham.h
-+++ b/wham/wham.h
-@@ -15,14 +15,16 @@ extern double kT;
- extern int    NUM_BINS;
- extern int    PERIODIC;
- extern double PERIOD;
-+extern double k_B;
-+
- 
- // Some predefined periodic units
- #define DEGREES   360.0
- #define RADIANS   6.28318530717959
- 
--#define k_B 0.001982923700 // Boltzmann's constant in kcal/mol K
--//#define k_B  0.0083144621 // Boltzmann's constant kJ/mol-K
--//#define k_B 1.0  // Boltzmann's constant in reduced units
-+#define k_B_DEFAULT 0.001982923700 // Boltzmann's constant in kcal/mol K
-+//#define k_B_DEFAULT  0.0083144621 // Boltzmann's constant kJ/mol-K
-+//#define k_B_DEFAULT 1.0  // Boltzmann's constant in reduced units
- 
- 
- // global (untrimmed) histogram, global to prevent reallocation

unittest/force-styles/tests/mol-pair-tip4p_table.yaml

@@ -2,7 +2,7 @@
 lammps_version: 17 Feb 2022
 tags: unstable
 date_generated: Fri Mar 18 22:17:36 2022
-epsilon: 2.5e-13
+epsilon: 1.0e-11
 skip_tests:
 prerequisites: ! |
   atom full