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add python interface with optional numpy support for lammps_gather_bonds()

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unit tests are included
This commit is contained in:
Axel Kohlmeyer
2021-07-26 22:36:00 -04:00
parent cc87e7eee3
commit 458253b452
9 changed files with 447 additions and 2 deletions
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29
python/lammps/core.py
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@ -201,6 +201,9 @@ class lammps(object):
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_scatter_atoms_subset.restype = None
self.lib.lammps_gather_bonds.argtypes = [c_void_p,c_void_p]
self.lib.lammps_gather_bonds.restype = None
self.lib.lammps_gather.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather.restype = None
@ -1206,6 +1209,32 @@ class lammps(object):
with ExceptionCheck(self):
self.lib.lammps_scatter_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data)
# -------------------------------------------------------------------------
def gather_bonds(self):
"""Retrieve global list of bonds
This is a wrapper around the :cpp:func:`lammps_gather_bonds`
function of the C-library interface.
This function returns a tuple with the number of bonds and a
flat list of ctypes integer values with the bond type, bond atom1,
bond atom2 for each bond.
.. versionadded:: 28Jul2021
:return: a tuple with the number of bonds and a list of c_int or c_long
:rtype: (int, 3*nbonds*c_tagint)
"""
nbonds = self.extract_global("nbonds")
with ExceptionCheck(self):
data = ((3*nbonds)*self.c_tagint)()
self.lib.lammps_gather_bonds(self.lmp,data)
return nbonds,data
# -------------------------------------------------------------------------
# return vector of atom/compute/fix properties gathered across procs
# 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()