def write_lammps_data(self, f):
"""
write lammps structure data
from ase with custom modifications
"""
f.write(f.name + ' (written by mpinterfaces) \n\n')
symbols = self.atoms.get_chemical_symbols()
n_atoms = len(symbols)
f.write('%d \t atoms \n' % n_atoms)
if self.specorder is None:
species = [tos.symbol
for tos in self.structure.types_of_specie]
else:
species = self.specorder
n_atom_types = len(species)
f.write('%d atom types\n' % n_atom_types)
p = prism(self.atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
f.write('0.0 %s xlo xhi\n' % xhi)
f.write('0.0 %s ylo yhi\n' % yhi)
f.write('0.0 %s zlo zhi\n' % zhi)
if self.always_triclinic or p.is_skewed():
f.write('%s %s %s xy xz yz\n' % (xy, xz, yz))
f.write('\n\n')
f.write('Atoms \n\n')
for i, r in enumerate(map(p.pos_to_lammps_str,
self.atoms.get_positions())):
c = 0.0
if self.charges:
c = self.charges[symbols[i]]
s = species.index(symbols[i]) + 1
if 'atom_style' in self.parameters:
if self.parameters['atom_style'] == 'charge':
f.write('%6d %3d %6f %s %s %s\n' %
((i+1, s, c)+tuple(r)) )
else:
f.write('%6d %3d %s %s %s\n' % ((i+1, s)+tuple(r)))
if self.atoms.get_velocities() is not None:
f.write('\n\nVelocities \n\n')
for i, v in enumerate(self.atoms.get_velocities()):
f.write('%6d %s %s %s\n' % ((i+1,)+tuple(v)))
f.close()
def write_lammps_data(self, f):
"""
write lammps structure data
from ase with custom modifications
"""
f.write(f.name + ' (written by mpinterfaces) \n\n')
symbols = self.atoms.get_chemical_symbols()
n_atoms = len(symbols)
f.write('%d \t atoms \n' % n_atoms)
if self.specorder is None:
species = [tos.symbol
for tos in self.structure.types_of_specie]
else:
species = self.specorder
n_atom_types = len(species)
f.write('%d atom types\n' % n_atom_types)
p = prism(self.atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
f.write('0.0 %s xlo xhi\n' % xhi)
f.write('0.0 %s ylo yhi\n' % yhi)
f.write('0.0 %s zlo zhi\n' % zhi)
if self.always_triclinic or p.is_skewed():
f.write('%s %s %s xy xz yz\n' % (xy, xz, yz))
f.write('\n\n')
f.write('Atoms \n\n')
for i, r in enumerate(map(p.pos_to_lammps_str,
self.atoms.get_positions())):
c = 0.0
if self.charges:
c = self.charges[symbols[i]]
s = species.index(symbols[i]) + 1
if 'atom_style' in self.parameters:
if self.parameters['atom_style'] == 'charge':
f.write('%6d %3d %6f %s %s %s\n' %
((i+1, s, c)+tuple(r)) )
else:
f.write('%6d %3d %s %s %s\n' % ((i+1, s)+tuple(r)))
if self.atoms.get_velocities() is not None:
f.write('\n\nVelocities \n\n')
for i, v in enumerate(self.atoms.get_velocities()):
f.write('%6d %s %s %s\n' % ((i+1,)+tuple(v)))
f.close()
def write_lammps_data(structure=None, file="", write_tmp_file=True):
"""
write lammps structure data
from ase with custom modifications
Args:
structure: Structure object
file: intended file to write in
"""
structure.sort()
if write_tmp_file == True:
structure.to(fmt="poscar", filename="new_pymatgen_slab.vasp")
atoms = AseAtomsAdaptor().get_atoms(structure)
f = open(file, "w")
f.write("datafile (written by JARVIS-FF) \n\n")
symbols = atoms.get_chemical_symbols()
import ase.io.vasp
# ase.io.vasp.write_vasp("POSCAR.1x1x1",atoms, label='444supercell',direct=True,sort=False)
n_atoms = len(symbols)
f.write("%d \t atoms \n" % n_atoms)
species = [tos for tos in Poscar(structure).site_symbols]
# species = [tos.symbol
# for tos in structure.types_of_specie]
n_atom_types = len(species)
print("species", species)
f.write("%d atom types\n" % n_atom_types)
p = prism(atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
f.write("0.0 %s xlo xhi\n" % xhi)
f.write("0.0 %s ylo yhi\n" % yhi)
f.write("0.0 %s zlo zhi\n" % zhi)
f.write("%s %s %s xy xz yz\n" % (xy, xz, yz))
f.write("\n\n")
f.write("Atoms \n\n")
for i, r in enumerate(map(p.pos_to_lammps_str, atoms.get_positions())):
c = 0.0
s = species.index(symbols[i]) + 1
f.write("%6d %3d %6f %s %s %s\n" % ((i + 1, s, c) + tuple(r)))
f.close()
def write_lammps_atoms(self, atoms):
"""Write atoms infor for LAMMPS"""
fileobj = self.prefix + '_atoms'
if isinstance(fileobj, str):
fileobj = open(fileobj, 'w')
# header
fileobj.write(fileobj.name + ' (by ' + str(self.__class__) + ')\n\n')
fileobj.write(str(len(atoms)) + ' atoms\n')
fileobj.write(str(len(atoms.types)) + ' atom types\n')
btypes, blist = self.get_bonds(atoms)
if len(blist):
fileobj.write(str(len(blist)) + ' bonds\n')
fileobj.write(str(len(btypes)) + ' bond types\n')
atypes, alist = self.get_angles()
if len(alist):
fileobj.write(str(len(alist)) + ' angles\n')
fileobj.write(str(len(atypes)) + ' angle types\n')
dtypes, dlist = self.get_dihedrals(alist, atypes)
if len(dlist):
fileobj.write(str(len(dlist)) + ' dihedrals\n')
fileobj.write(str(len(dtypes)) + ' dihedral types\n')
# cell
p = prism(atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
fileobj.write('\n0.0 %s xlo xhi\n' % xhi)
fileobj.write('0.0 %s ylo yhi\n' % yhi)
fileobj.write('0.0 %s zlo zhi\n' % zhi)
# atoms
fileobj.write('\nAtoms\n\n')
tag = atoms.get_tags()
for i, r in enumerate(map(p.pos_to_lammps_str, atoms.get_positions())):
q = 0 # charge will be overwritten
fileobj.write('%6d %3d %3d %s %s %s %s' %
((i + 1, 1, tag[i] + 1, q) + tuple(r)))
fileobj.write(' # ' + atoms.types[tag[i]] + '\n')
# velocities
velocities = atoms.get_velocities()
if velocities is not None:
fileobj.write('\nVelocities\n\n')
for i, v in enumerate(velocities):
fileobj.write('%6d %g %g %g\n' % (i + 1, v[0], v[1], v[2]))
# masses
fileobj.write('\nMasses\n\n')
for i, typ in enumerate(atoms.types):
cs = atoms.split_symbol(typ)[0]
fileobj.write(
'%6d %g # %s -> %s\n' %
(i + 1, atomic_masses[chemical_symbols.index(cs)], typ, cs))
# bonds
if len(blist):
fileobj.write('\nBonds\n\n')
for ib, bvals in enumerate(blist):
fileobj.write(
'%8d %6d %6d %6d ' %
(ib + 1, bvals[0] + 1, bvals[1] + 1, bvals[2] + 1))
fileobj.write('# ' + btypes[bvals[0]] + '\n')
# angles
if len(alist):
fileobj.write('\nAngles\n\n')
for ia, avals in enumerate(alist):
fileobj.write('%8d %6d %6d %6d %6d ' %
(ia + 1, avals[0] + 1, avals[1] + 1,
avals[2] + 1, avals[3] + 1))
fileobj.write('# ' + atypes[avals[0]] + '\n')
# dihedrals
if len(dlist):
fileobj.write('\nDihedrals\n\n')
for i, dvals in enumerate(dlist):
fileobj.write('%8d %6d %6d %6d %6d %6d ' %
(i + 1, dvals[0] + 1, dvals[1] + 1, dvals[2] + 1,
dvals[3] + 1, dvals[4] + 1))
fileobj.write('# ' + dtypes[dvals[0]] + '\n')
return btypes, atypes, dtypes
def write_lammps_atoms(self, atoms, connectivities):
"""Write atoms input for LAMMPS"""
fname = self.prefix + '_atoms'
fileobj = open(fname, 'w')
# header
fileobj.write(fileobj.name + ' (by ' + str(self.__class__) + ')\n\n')
fileobj.write(str(len(atoms)) + ' atoms\n')
fileobj.write(str(len(atoms.types)) + ' atom types\n')
blist = connectivities['bonds']
if len(blist):
btypes = connectivities['bond types']
fileobj.write(str(len(blist)) + ' bonds\n')
fileobj.write(str(len(btypes)) + ' bond types\n')
alist = connectivities['angles']
if len(alist):
atypes = connectivities['angle types']
fileobj.write(str(len(alist)) + ' angles\n')
fileobj.write(str(len(atypes)) + ' angle types\n')
dlist = connectivities['dihedrals']
if len(dlist):
dtypes = connectivities['dihedral types']
fileobj.write(str(len(dlist)) + ' dihedrals\n')
fileobj.write(str(len(dtypes)) + ' dihedral types\n')
# cell
p = prism(atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
fileobj.write('\n0.0 %s xlo xhi\n' % xhi)
fileobj.write('0.0 %s ylo yhi\n' % yhi)
fileobj.write('0.0 %s zlo zhi\n' % zhi)
# atoms
fileobj.write('\nAtoms\n\n')
tag = atoms.get_tags()
if atoms.has('molid'):
molid = atoms.get_array('molid')
else:
molid = [1] * len(atoms)
for i, r in enumerate(map(p.pos_to_lammps_str,
atoms.get_positions())):
q = self.data['one'][atoms.types[tag[i]]][2]
fileobj.write('%6d %3d %3d %s %s %s %s' % ((i + 1, molid[i],
tag[i] + 1,
q)
+ tuple(r)))
fileobj.write(' # ' + atoms.types[tag[i]] + '\n')
# velocities
velocities = atoms.get_velocities()
if velocities is not None:
fileobj.write('\nVelocities\n\n')
for i, v in enumerate(velocities):
fileobj.write('%6d %g %g %g\n' %
(i + 1, v[0], v[1], v[2]))
# masses
fileobj.write('\nMasses\n\n')
for i, typ in enumerate(atoms.types):
cs = atoms.split_symbol(typ)[0]
fileobj.write('%6d %g # %s -> %s\n' %
(i + 1,
atomic_masses[chemical_symbols.index(cs)],
typ, cs))
# bonds
if len(blist):
fileobj.write('\nBonds\n\n')
for ib, bvals in enumerate(blist):
fileobj.write('%8d %6d %6d %6d ' %
(ib + 1, bvals[0] + 1, bvals[1] + 1,
bvals[2] + 1))
try:
fileobj.write('# ' + btypes[bvals[0]])
except:
pass
fileobj.write('\n')
# angles
if len(alist):
fileobj.write('\nAngles\n\n')
for ia, avals in enumerate(alist):
fileobj.write('%8d %6d %6d %6d %6d ' %
(ia + 1, avals[0] + 1,
avals[1] + 1, avals[2] + 1, avals[3] + 1))
try:
fileobj.write('# ' + atypes[avals[0]])
except:
pass
fileobj.write('\n')
# dihedrals
if len(dlist):
fileobj.write('\nDihedrals\n\n')
for i, dvals in enumerate(dlist):
fileobj.write('%8d %6d %6d %6d %6d %6d ' %
(i + 1, dvals[0] + 1,
dvals[1] + 1, dvals[2] + 1,
dvals[3] + 1, dvals[4] + 1))
try:
fileobj.write('# ' + dtypes[dvals[0]])
except:
pass
fileobj.write('\n')
def write_lammps_atoms(self, atoms):
"""Write atoms infor for LAMMPS"""
fileobj = self.prefix + '_atoms'
if isinstance(fileobj, str):
fileobj = open(fileobj, 'w')
# header
fileobj.write(fileobj.name + ' (by ' + str(self.__class__) + ')\n\n')
fileobj.write(str(len(atoms)) + ' atoms\n')
fileobj.write(str(len(atoms.types)) + ' atom types\n')
btypes, blist = self.get_bonds(atoms)
if len(blist):
fileobj.write(str(len(blist)) + ' bonds\n')
fileobj.write(str(len(btypes)) + ' bond types\n')
atypes, alist = self.get_angles()
if len(alist):
fileobj.write(str(len(alist)) + ' angles\n')
fileobj.write(str(len(atypes)) + ' angle types\n')
dtypes, dlist = self.get_dihedrals(alist, atypes)
if len(dlist):
fileobj.write(str(len(dlist)) + ' dihedrals\n')
fileobj.write(str(len(dtypes)) + ' dihedral types\n')
# cell
p = prism(atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
fileobj.write('\n0.0 %s xlo xhi\n' % xhi)
fileobj.write('0.0 %s ylo yhi\n' % yhi)
fileobj.write('0.0 %s zlo zhi\n' % zhi)
# atoms
fileobj.write('\nAtoms\n\n')
tag = atoms.get_tags()
for i, r in enumerate(map(p.pos_to_lammps_str,
atoms.get_positions())):
q = 0 # charge will be overwritten
fileobj.write('%6d %3d %3d %s %s %s %s' % ((i + 1, 1,
tag[i] + 1,
q)
+ tuple(r)))
fileobj.write(' # ' + atoms.types[tag[i]] + '\n')
# velocities
velocities = atoms.get_velocities()
if velocities is not None:
fileobj.write('\nVelocities\n\n')
for i, v in enumerate(velocities):
fileobj.write('%6d %g %g %g\n' %
(i + 1, v[0], v[1], v[2]))
# masses
fileobj.write('\nMasses\n\n')
for i, typ in enumerate(atoms.types):
cs = atoms.split_symbol(typ)[0]
fileobj.write('%6d %g # %s -> %s\n' %
(i + 1,
atomic_masses[chemical_symbols.index(cs)],
typ, cs))
# bonds
if len(blist):
fileobj.write('\nBonds\n\n')
for ib, bvals in enumerate(blist):
fileobj.write('%8d %6d %6d %6d ' %
(ib + 1, bvals[0] + 1, bvals[1] + 1,
bvals[2] + 1))
fileobj.write('# ' + btypes[bvals[0]] + '\n')
# angles
if len(alist):
fileobj.write('\nAngles\n\n')
for ia, avals in enumerate(alist):
fileobj.write('%8d %6d %6d %6d %6d ' %
(ia + 1, avals[0] + 1,
avals[1] + 1, avals[2] + 1, avals[3] + 1))
fileobj.write('# ' + atypes[avals[0]] + '\n')
# dihedrals
if len(dlist):
fileobj.write('\nDihedrals\n\n')
for i, dvals in enumerate(dlist):
fileobj.write('%8d %6d %6d %6d %6d %6d ' %
(i + 1, dvals[0] + 1,
dvals[1] + 1, dvals[2] + 1,
dvals[3] + 1, dvals[4] + 1))
fileobj.write('# ' + dtypes[dvals[0]] + '\n')
return btypes, atypes, dtypes
def write_lammps_atoms(self, atoms, connectivities):
"""Write atoms input for LAMMPS"""
fname = self.prefix + '_atoms'
fileobj = open(fname, 'w')
# header
fileobj.write(fileobj.name + ' (by ' + str(self.__class__) + ')\n\n')
fileobj.write(str(len(atoms)) + ' atoms\n')
fileobj.write(str(len(atoms.types)) + ' atom types\n')
blist = connectivities['bonds']
if len(blist):
btypes = connectivities['bond types']
fileobj.write(str(len(blist)) + ' bonds\n')
fileobj.write(str(len(btypes)) + ' bond types\n')
alist = connectivities['angles']
if len(alist):
atypes = connectivities['angle types']
fileobj.write(str(len(alist)) + ' angles\n')
fileobj.write(str(len(atypes)) + ' angle types\n')
dlist = connectivities['dihedrals']
if len(dlist):
dtypes = connectivities['dihedral types']
fileobj.write(str(len(dlist)) + ' dihedrals\n')
fileobj.write(str(len(dtypes)) + ' dihedral types\n')
# cell
p = prism(atoms.get_cell())
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
fileobj.write('\n0.0 %s xlo xhi\n' % xhi)
fileobj.write('0.0 %s ylo yhi\n' % yhi)
fileobj.write('0.0 %s zlo zhi\n' % zhi)
# atoms
fileobj.write('\nAtoms\n\n')
tag = atoms.get_tags()
if atoms.has('molid'):
molid = atoms.get_array('molid')
else:
molid = [1] * len(atoms)
for i, r in enumerate(map(p.pos_to_lammps_str, atoms.get_positions())):
q = self.data['one'][atoms.types[tag[i]]][2]
fileobj.write('%6d %3d %3d %s %s %s %s' %
((i + 1, molid[i], tag[i] + 1, q) + tuple(r)))
fileobj.write(' # ' + atoms.types[tag[i]] + '\n')
# velocities
velocities = atoms.get_velocities()
if velocities is not None:
fileobj.write('\nVelocities\n\n')
for i, v in enumerate(velocities):
fileobj.write('%6d %g %g %g\n' % (i + 1, v[0], v[1], v[2]))
# masses
fileobj.write('\nMasses\n\n')
for i, typ in enumerate(atoms.types):
cs = atoms.split_symbol(typ)[0]
fileobj.write(
'%6d %g # %s -> %s\n' %
(i + 1, atomic_masses[chemical_symbols.index(cs)], typ, cs))
# bonds
if len(blist):
fileobj.write('\nBonds\n\n')
for ib, bvals in enumerate(blist):
fileobj.write(
'%8d %6d %6d %6d ' %
(ib + 1, bvals[0] + 1, bvals[1] + 1, bvals[2] + 1))
try:
fileobj.write('# ' + btypes[bvals[0]])
except:
pass
fileobj.write('\n')
# angles
if len(alist):
fileobj.write('\nAngles\n\n')
for ia, avals in enumerate(alist):
fileobj.write('%8d %6d %6d %6d %6d ' %
(ia + 1, avals[0] + 1, avals[1] + 1,
avals[2] + 1, avals[3] + 1))
try:
fileobj.write('# ' + atypes[avals[0]])
except:
pass
fileobj.write('\n')
# dihedrals
if len(dlist):
fileobj.write('\nDihedrals\n\n')
for i, dvals in enumerate(dlist):
fileobj.write('%8d %6d %6d %6d %6d %6d ' %
(i + 1, dvals[0] + 1, dvals[1] + 1, dvals[2] + 1,
dvals[3] + 1, dvals[4] + 1))
try:
fileobj.write('# ' + dtypes[dvals[0]])
except:
pass
fileobj.write('\n')
