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add patch for customization of wham to support LAMMPS units

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This commit is contained in:
Axel Kohlmeyer
2025-01-02 19:39:02 -05:00
parent f7cea5e428
commit 1fcf1a7c56
2 changed files with 173 additions and 2 deletions
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11
tools/lammps-gui/CMakeLists.txt
View File

@ -118,9 +118,16 @@ if(BUILD_WHAM)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf ${CMAKE_BINARY_DIR}/_deps/${archive}
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
file(GLOB TARGET_SOURCE "${CMAKE_BINARY_DIR}/_deps/src/wham")
find_package(Patch)
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
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src/wham/
)
endif()
file(REMOVE_RECURSE ${CMAKE_BINARY_DIR}/_deps/wham-src)
file(RENAME ${TARGET_SOURCE} ${CMAKE_BINARY_DIR}/_deps/wham-src)
file(RENAME "${CMAKE_BINARY_DIR}/_deps/src/wham" ${CMAKE_BINARY_DIR}/_deps/wham-src)
file(COPY CMakeLists.wham DESTINATION ${CMAKE_BINARY_DIR}/_deps/wham-src/)
file(RENAME "${CMAKE_BINARY_DIR}/_deps/wham-src/CMakeLists.wham"
"${CMAKE_BINARY_DIR}/_deps/wham-src/CMakeLists.txt")

164
tools/lammps-gui/update-wham-2.0.11.patch Normal file
View File

@ -0,0 +1,164 @@
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
+++ 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/wham/wham.c b/wham/wham.c
index 487871b..526908e 100644
--- a/wham/wham.c
+++ b/wham/wham.c
@@ -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 [P|Ppi|Pval] [units <real|metal|lj|...>] 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[])
{
@@ -117,6 +118,61 @@ else
PERIODIC = 0;
}
+// 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;
+ }
+
// Parse command line arguments
if (argc != 9 && argc !=11)
{
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