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Merge branch 'develop' into errors-more-cleanup

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This commit is contained in:
Axel Kohlmeyer
2025-03-23 16:01:00 -04:00
parent c65c8819e3 adaa313990
commit 3d5430bfe4
18 changed files with 201 additions and 341 deletions
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47
.github/release_steps.md vendored
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@ -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.

7
doc/src/Build_cmake.rst
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@ -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

26
doc/src/Build_settings.rst
View File

@ -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

31
doc/src/Howto_python.rst
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@ -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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

13
doc/src/Python_install.rst
View File

@ -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
but not attempt to install it.
* the optional ``-n`` instructs the script to only build a wheel file but not attempt
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

2
doc/src/Tools.rst
View File

@ -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

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10
doc/utils/sphinx-config/_themes/lammps_theme/layout.html
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@ -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">

2
doc/utils/sphinx-config/conf.py.in
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@ -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

12
python/install.py
View File

@ -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)

4
src/BPM/bond_bpm_spring_plastic.cpp
View File

@ -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;

6
src/EXTRA-COMPUTE/compute_stress_mop.cpp
View File

@ -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;

1
src/fix_halt.cpp
View File

@ -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);
}
}

6
src/utils.cpp
View File

@ -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));
} catch (fmt::format_error &) {
; // do nothing
}
print(fp, fmt::vformat(format, args));
}
std::string utils::errorurl(int errorcode)

6
tools/lammps-gui/CMakeLists.txt
View File

@ -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_MD5 "f56751ac71a8d1c485b9ebd4ccff8dbe" CACHE STRING "MD5 checksum of 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 "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()

1
tools/lammps-gui/lammps-gui.appdata.xml
View File

@ -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>

366
tools/lammps-gui/update-wham-2.0.11.patch → tools/lammps-gui/update-wham-2.1.0.patch
View File

@ -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 0000000..b4f0fe6
--- /dev/null
index b4f0fe6..a61cec8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -0,0 +1,38 @@
+# Custom minimal -*- CMake -*- file for wham
+
+cmake_minimum_required(VERSION 3.16)
+project(wham VERSION 2.0.11
+ DESCRIPTION "WHAM: a fast, memory efficient implementation of the Weighted Histogram Analysis Method"
+ LANGUAGES C
+ HOMEPAGE_URL http://membrane.urmc.rochester.edu/content/wham/)
+
+include(GNUInstallDirs)
+
+add_executable(wham
+ nr/ran2.c
+ nr/locate.c
+ wham/wham.c
+ wham/file_read.c
+ wham/histogram.c
+ wham/bootstrap.c
+)
+target_include_directories(wham PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/wham)
+target_link_libraries(wham PRIVATE m)
+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;
@@ -1,7 +1,7 @@
# Custom minimal -*- CMake -*- file for wham
cmake_minimum_required(VERSION 3.16)
-project(wham VERSION 2.0.11
+project(wham VERSION 2.1.0
DESCRIPTION "WHAM: a fast, memory efficient implementation of the Weighted Histogram Analysis Method"
LANGUAGES C
HOMEPAGE_URL http://membrane.urmc.rochester.edu/content/wham/)
diff --git a/doc/doc.tex b/doc/doc.tex
index cf36616..84ee891 100644
--- a/doc/doc.tex
+++ b/doc/doc.tex
@@ -53,7 +53,7 @@ Suggestions and patches are welcome.
\subsection{New in release 2.1.0}
-Two changes, both contributed by Alex Kohlmeyer. First, we switched from old
+Two changes, both contributed by Axel Kohlmeyer. First, we switched from old
make to CMake for the build. Second, we changed how energy units are set; where
it used to be a compile-time option, now it is set on the command line.
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 @@
#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)
@@ -417,8 +417,8 @@ 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 @@
#include "wham.h"
-#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"
+#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;
@@ -39,10 +39,9 @@ double kT; // temperature
int i,j;
int len;
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++)
}
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)
@@ -179,7 +178,7 @@ 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

2
unittest/force-styles/tests/mol-pair-tip4p_table.yaml
View File

@ -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