Changeset 923ce2

Timestamp:

May 19, 2021, 7:06:29 PM (4 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

1e490ec

Parents:

ecc050

git-author:

Frederik Heber <frederik.heber@…> (06/21/20 21:29:52)

git-committer:

Frederik Heber <frederik.heber@…> (05/19/21 19:06:29)

Message:

Added get_masses to python functionality.

File:

• src/Python/export_numpy.cpp (modified) (8 diffs)

src/Python/export_numpy.cpp

@@ -37 +37 @@
 #include<boost/bind.hpp>
 #include<boost/function.hpp>
-#include<boost/python/def.hpp>
+#include<boost/python.hpp>
 #include<boost/python/numpy.hpp>
 
@@ -55 +55 @@
 {
   p::tuple shape = p::make_tuple(num_atoms, 3);
-  np::dtype dtype = np::dtype::get_builtin<float>();
+  np::dtype dtype = np::dtype::get_builtin<double>();
   np::ndarray array = np::zeros(shape, dtype);
   return array;
@@ -63 +63 @@
 {
   unsigned int num_atoms = get_num_atoms();
-  std::cout << num_atoms << std::endl;
+  //std::cout << num_atoms << std::endl;
   np::ndarray positions = allocate_ndarray(num_atoms);
 
@@ -74 +74 @@
       positions[ia][i] = _get_function(current)[i];
     ++ia;
-    ASSERT(ia <= num_atoms, "get_positions() - more atoms selected than expected.");
+    ASSERT(ia <= num_atoms, "get_ndarray() - more atoms selected than expected.");
   }
 
@@ -101 +101 @@
 }
 
+np::ndarray get_masses()
+{
+  unsigned int num_atoms = get_num_atoms();
+  //std::cout << num_atoms << std::endl;
+  p::tuple shape = p::make_tuple(num_atoms);
+  np::dtype dtype = np::dtype::get_builtin<double>();
+  np::ndarray masses = np::zeros(shape, dtype);
+
+  unsigned int ia=0;
+  for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+      iter != World::getInstance().endAtomSelection();
+      ++iter) {
+    const atom & current = *iter->second;
+    masses[ia] = current.getMass();
+    ++ia;
+    ASSERT(ia <= num_atoms, "get_masses() - more atoms selected than expected.");
+  }
+
+  return masses;
+}
+
 void set_ndarray(
-    const np::ndarray &new_positions,
+    const np::ndarray &_positions,
     boost::function<void (atom &, const Vector &)> &_set_function)
 {
@@ -108 +129 @@
   
   // check whether shape of array is correct 
-  ASSERT( new_positions.shape()[0] == num_atoms,
-    "pyMoleCuilder::set_positions() - numpy array has unexpected size.");
+  ASSERT( _positions.shape(0) == num_atoms,
+    "pyMoleCuilder::set_ndarray() - numpy array has unexpected size.");
 
+  np::ndarray new_positions = _positions.copy();
   unsigned int ia=0;
   Vector temp;
@@ -117 +139 @@
       ++iter) {
     atom &current = *iter->second;
-    for (unsigned int i=0;i<NDIM;++i)
+    for (unsigned int i=0;i<NDIM;++i) {
+      //std::cout << p::extract<char const *>(p::str(new_positions[ia][i])) << std::endl;
       temp[i] = p::extract<double>(new_positions[ia][i]);
+    }
     _set_function(current, temp);
     ++ia;
-    ASSERT(ia <= num_atoms, "set_positions() - more atoms selected than expected.");
+    ASSERT(ia <= num_atoms, "set_ndarray() - more atoms selected than expected.");
   }
 }
@@ -151 +175 @@
   p::def("get_velocities", get_velocities);
   p::def("get_forces", get_forces);
+  p::def("get_masses", get_masses);
   p::def("set_positions", set_positions, p::args("position"));
   p::def("set_velocities", set_velocities, p::args("velocity"));