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pylammps: reduce dependency to info command output

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This commit is contained in:
Richard Berger
2023-06-11 18:02:11 -06:00
parent bc87c69d60
commit 2f7c3bf959
1 changed files with 35 additions and 50 deletions
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85
python/lammps/pylammps.py
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@ -707,66 +707,55 @@ class PyLammps(object):
def _parse_info_system(self, output):
system = {}
system['dimensions'] = self.lmp.extract_setting("dimension")
system['xlo'] = self.lmp.extract_global("boxxlo")
system['ylo'] = self.lmp.extract_global("boxylo")
system['zlo'] = self.lmp.extract_global("boxzlo")
system['xhi'] = self.lmp.extract_global("boxxhi")
system['yhi'] = self.lmp.extract_global("boxyhi")
system['zhi'] = self.lmp.extract_global("boxzhi")
xprd = system["xhi"] - system["xlo"]
yprd = system["yhi"] - system["ylo"]
zprd = system["zhi"] - system["zlo"]
if self.lmp.extract_setting("triclinic") == 1:
system['triclinic_box'] = (xprd, yprd, zprd)
else:
system['orthogonal_box'] = (xprd, yprd, zprd)
system['nangles'] = self.lmp.extract_global("nbonds")
system['nangletypes'] = self.lmp.extract_setting("nbondtypes")
system['angle_style'] = self.lmp.extract_global("angle_style")
system['nbonds'] = self.lmp.extract_global("nbonds")
system['nbondtypes'] = self.lmp.extract_setting("nbondtypes")
system['bond_style'] = self.lmp.extract_global("bond_style")
system['ndihedrals'] = self.lmp.extract_global("ndihedrals")
system['ndihedraltypes'] = self.lmp.extract_setting("ndihedraltypes")
system['dihedral_style'] = self.lmp.extract_global("dihedral_style")
system['nimpropers'] = self.lmp.extract_global("nimpropers")
system['nimpropertypes'] = self.lmp.extract_setting("nimpropertypes")
system['improper_style'] = self.lmp.extract_global("improper_style")
system['kspace_style'] = self.lmp.extract_global("kspace_style")
system['natoms'] = self.lmp.extract_global("natoms")
system['ntypes'] = self.lmp.extract_global("ntypes")
system['pair_style'] = self.lmp.extract_global("pair_style")
system['atom_style'] = self.lmp.extract_global("atom_style")
system['units'] = self.lmp.extract_global("units")
for line in output:
if line.startswith("Units"):
system['units'] = self._get_pair(line)[1]
elif line.startswith("Atom style"):
system['atom_style'] = self._get_pair(line)[1]
elif line.startswith("Atom map"):
if line.startswith("Atom map"):
system['atom_map'] = self._get_pair(line)[1]
elif line.startswith("Atoms"):
parts = self._split_values(line)
system['natoms'] = int(self._get_pair(parts[0])[1])
system['ntypes'] = int(self._get_pair(parts[1])[1])
system['style'] = self._get_pair(parts[2])[1]
elif line.startswith("Kspace style"):
system['kspace_style'] = self._get_pair(line)[1]
elif line.startswith("Dimensions"):
system['dimensions'] = int(self._get_pair(line)[1])
elif line.startswith("Orthogonal box"):
system['orthogonal_box'] = [float(x) for x in self._get_pair(line)[1].split('x')]
elif line.startswith("Boundaries"):
system['boundaries'] = self._get_pair(line)[1]
elif line.startswith("xlo"):
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("ylo"):
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("zlo"):
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['ndihedraltypes'] = 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):
comm = {}
comm['nprocs'] = self.lmp.extract_setting("world_size")
comm['nthreads'] = self.lmp.extract_setting("nthreads")
for line in output:
if line.startswith("MPI library"):
@ -779,10 +768,6 @@ class PyLammps(object):
comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')]
elif line.startswith("Communicate velocities for ghost atoms"):
comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes")
elif line.startswith("Nprocs"):
parts = self._split_values(line)
comm['nprocs'] = int(self._get_pair(parts[0])[1])
comm['nthreads'] = int(self._get_pair(parts[1])[1])
return comm
def _parse_element_list(self, output):