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Add bonds, angles, dihedrals and impropers information to Python wrapper

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This commit is contained in:
Richard Berger
2016-07-14 14:57:13 -04:00
parent 8187989929
commit 85d7e571e3
2 changed files with 936 additions and 0 deletions
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898
python/examples/ipython/interface_usage_bonds.ipynb Normal file
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38
python/lammps.py
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@ -274,7 +274,14 @@ class lammps:
self.lib.lammps_scatter_atoms(self.lmp, name, type, count, data)
####################################################################################
# Alternative Python Wrapper
# Written by Richard Berger <richard.berger@temple.edu>
####################################################################################
class OutputCapture(object):
""" Utility class to capture LAMMPS library output """
def __init__(self):
self.stdout_pipe_read, self.stdout_pipe_write = os.pipe()
self.stdout_fd = 1
@ -377,6 +384,10 @@ class Atom(object):
class LammpsWrapper(object):
"""
More Python-like wrapper for LAMMPS (e.g., for iPython)
See examples/ipython for usage
"""
def __init__(self, lmp):
self.lmp = lmp
@ -474,6 +485,29 @@ class LammpsWrapper(object):
keys, values = [self._split_values(x) for x in self._get_pair(line)]
for key, value in zip(keys, values):
system[key] = float(value)
elif line.startswith("Molecule type"):
system['molecule_type'] = self._get_pair(line)[1]
elif line.startswith("Bonds"):
parts = self._split_values(line)
system['nbonds'] = int(self._get_pair(parts[0])[1])
system['nbondtypes'] = int(self._get_pair(parts[1])[1])
system['bond_style'] = self._get_pair(parts[2])[1]
elif line.startswith("Angles"):
parts = self._split_values(line)
system['nangles'] = int(self._get_pair(parts[0])[1])
system['nangletypes'] = int(self._get_pair(parts[1])[1])
system['angle_style'] = self._get_pair(parts[2])[1]
elif line.startswith("Dihedrals"):
parts = self._split_values(line)
system['ndihedrals'] = int(self._get_pair(parts[0])[1])
system['nangletypes'] = int(self._get_pair(parts[1])[1])
system['dihedral_style'] = self._get_pair(parts[2])[1]
elif line.startswith("Impropers"):
parts = self._split_values(line)
system['nimpropers'] = int(self._get_pair(parts[0])[1])
system['nimpropertypes'] = int(self._get_pair(parts[1])[1])
system['improper_style'] = self._get_pair(parts[2])[1]
return system
def _parse_info_communication(self, output):
@ -539,6 +573,10 @@ class LammpsWrapper(object):
class LammpsIPythonWrapper(LammpsWrapper):
"""
iPython wrapper for LAMMPS which adds embedded graphics capabilities
"""
def __init__(self, lmp):
super(LammpsIPythonWrapper, self).__init__(lmp)