Changeset 802a9d

Timestamp:

Dec 21, 2025, 9:50:27 PM (5 days ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.1, stable

Children:

2e7888

Parents:

e4b9d5

git-author:

Frederik Heber <frederik.heber@…> (11/18/25 19:34:57)

git-committer:

Frederik Heber <frederik.heber@…> (12/21/25 21:50:27)

Message:

Adds scripts to generate a bond table.

• one python script for the computation and a bash script to call it. With this split, we can easily parallelize the computations to make use of JobMarket's multiple workers.

Files:

• configure.ac (modified) (1 diff)
• src/Python/export_numpy.cpp (modified) (3 diffs)
• utils/Python/HOWTO-generate_bondtable (added)
• utils/Python/Makefile.am (modified) (2 diffs)
• utils/Python/compute_pair_bondlength.py.in (added)
• utils/Python/generate_bondtable.sh.in (added)

configure.ac

@@ -631 +631 @@
 AM_COND_IF([CONDPYTHON],[
         AC_CONFIG_FILES([utils/Python/boxmaker.py:utils/Python/boxmaker.py.in], [chmod +x utils/Python/boxmaker.py])
+        AC_CONFIG_FILES([utils/Python/generate_bondtable.sh:utils/Python/generate_bondtable.sh.in], [chmod +x utils/Python/generate_bondtable.sh])
+        AC_CONFIG_FILES([utils/Python/compute_pair_bondlength.py:utils/Python/compute_pair_bondlength.py.in], [chmod +x utils/Python/compute_pair_bondlength.py])
         AC_CONFIG_FILES([utils/Python/python_wrapper:utils/Python/python_wrapper.in], [chmod +x utils/Python/python_wrapper])
         AC_CONFIG_FILES([tests/Python/run], [chmod +x tests/Python/run])

src/Python/export_numpy.cpp

@@ -41 +41 @@
 
 #include "CodePatterns/Assert.hpp"
-
+#include "CodePatterns/Log.hpp"
+
+#include "Geometry/GeometryRegistry.hpp"
 #include "World.hpp"
 
@@ -78 +80 @@
 
   return positions;
+}
+
+np::ndarray get_geometryobject(const std::string &name)
+{
+  LOG(1, "Getting GeometryObject of name " << name);
+  const GeometryObject *object = GeometryRegistry::getInstance().getByName(name);
+  p::tuple shape = p::make_tuple(3);
+  np::dtype dtype = np::dtype::get_builtin<double>();
+  np::ndarray distance = np::zeros(shape, dtype);
+  if (object != NULL) {
+    for (unsigned int i=0;i<NDIM;++i)
+      distance[i] = object->getVector()[i];
+  }
+  return distance;
 }
 
@@ -173 +189 @@
 void export_numpy()
 {
+  p::def("get_geometryobject", get_geometryobject, p::args("name"));
   p::def("get_positions", get_positions);
   p::def("get_velocities", get_velocities);

utils/Python/Makefile.am

@@ -1 +1 @@
 if CONDPYTHON
 PYTHON_TOOLS = \
-        Python/boxmaker
+        Python/boxmaker \
+        Python/generate_bondtable \
+        Python/compute_pair_bondlength
 endif
 
@@ -13 +15 @@
 BUILT_SOURCES += ${PYTHON_TOOLS}
 CLEANFILES += ${PYTHON_TOOLS}
-pyexec_SCRIPTS += Python/boxmaker.py
+pyexec_SCRIPTS += \
+        Python/boxmaker.py \
+        Python/compute_pair_bondlength.py
 endif