class MPINTLammps(LAMMPS, MSONable):
"""
setup LAMMPS for given structure and parameters
extends ase.calculators.lammpsrun.LAMMPS
"""
def __init__(
self, structure, parameters={}, label="mpintlmp", specorder=None, always_triclinic=True, no_data_file=False
):
LAMMPS.__init__(
self,
label=label,
parameters=parameters,
specorder=specorder,
files=[],
always_triclinic=always_triclinic,
no_data_file=no_data_file,
)
self.structure = structure
self.atoms = AseAtomsAdaptor().get_atoms(structure)
self.label = label
self.parameters = parameters
self.specorder = specorder
self.always_triclinic = always_triclinic
self.no_data_file = no_data_file
self.charges = None
if "charges" in self.parameters:
self.charges = self.parameters["charges"]
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()
# self.mplmp.write_lammps_in(lammps_in=lmp_in_fd,lammps_in1=lmp_in_fd1,lammps_in2=lmp_in_fd2,
# lammps_trj=lmp_trj_name,
# lammps_data=lmp_data_name)
# self.mplmp.write_lammps_in(lammps_in=lmp_in_fd,lammps_in1=lmp_in_fd1,
# lammps_trj=lmp_trj_name,
# lammps_data=lmp_data_name)
def write_lammps_in(self, lammps_in=None, lammps_in1=None, lammps_in2=None, lammps_trj=None, lammps_data=None):
"""
write lammps input file
from ase with custom modifications
"""
f = lammps_in
f1 = lammps_in1 # potential.mod
f2 = lammps_in2
parameters = self.parameters
if "units" in parameters:
if parameters["units"] == "real":
f.write(
('variable dump_file string "%s"\n' % lammps_trj)
+ ("variable up equal 1.0e-8\n")
+ ("variable cfac equal 1.01325e-4\n")
+ ("variable cunits string GPa\n")
+ ("variable etol equal 0\n")
+ ("variable ftol equal 1.0e-10\n")
+ ("variable maxiter equal 1000\n")
+ ("variable maxeval equal 10000\n")
+ ("variable dmax equal 1.0e-2\n")
+ ('variable data_file string "%s"\n' % lammps_data)
)
else:
f.write(
('variable dump_file string "%s"\n' % lammps_trj)
+ ("variable up equal 1.0e-8\n")
+ ("variable cfac equal 1.0e-4\n")
+ ("variable cunits string GPa\n")
+ ("variable etol equal 0\n")
+ ("variable ftol equal 1.0e-10\n")
+ ("variable maxiter equal 1000\n")
+ ("variable maxeval equal 10000\n")
+ ("variable dmax equal 1.0e-2\n")
+ ('variable data_file string "%s"\n' % lammps_data)
)
pbc = self.atoms.get_pbc()
if "control_file" in parameters:
f2.write("include %s \n" % parameters["control_file"])
# f2.write('include /home/kamal/inelast.mod \n')
if "units" in parameters:
f.write("units %s \n" % parameters["units"])
else:
f.write("units metal \n")
# f.write('units metal \n')
if "atom_style" in parameters:
f.write("atom_style %s \n" % parameters["atom_style"])
else:
f.write("atom_style atomic \n")
if "boundary" in parameters:
f.write("boundary %s \n" % parameters["boundary"])
else:
f.write("boundary %c %c %c \n" % tuple("sp"[x] for x in pbc))
f.write("atom_modify sort 0 0.0 \n")
for key in ("neighbor", "newton"):
if key in parameters:
f.write("%s %s \n" % (key, parameters[key]))
f.write("\n")
# If no_data_file,
# write the simulation box and the atoms
if self.no_data_file:
p = self.prism
f.write("lattice sc 1.0\n")
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
if self.always_triclinic or p.is_skewed():
f.write("region asecell prism 0.0 %s 0.0 %s 0.0 %s " % (xhi, yhi, zhi))
f.write("%s %s %s side in units box\n" % (xy, xz, yz))
else:
f.write(("region asecell block 0.0 %s 0.0 %s 0.0 %s " "side in units box\n") % (xhi, yhi, zhi))
symbols = self.atoms.get_chemical_symbols()
############KAMAL###########################################
# species = [tos.symbol for tos in self.structure.types_of_specie]
#
# for i, r in enumerate(map(p.pos_to_lammps_str,
# self.atoms.get_positions())):
# s = species.index(symbols[i]) + 1
################################################
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)
species_i = dict([(s, i + 1) for i, s in enumerate(species)])
f.write("create_box %i asecell\n" % n_atom_types)
for s, pos in zip(symbols, self.atoms.get_positions()):
f.write(
"create_atoms %i single %s %s %s units box\n" % ((species_i[s],) + p.pos_to_lammps_fold_str(pos))
)
else:
f.write("read_data %s\n" % lammps_data)
# interaction
f.write("\n### interactions \n")
if "lib" in parameters:
lib = parameters["lib"]
f1.write("%s \n" % lib)
if ("pair_style" in parameters) and ("pair_coeff" in parameters):
pair_style = parameters["pair_style"]
f1.write("pair_style %s \n" % pair_style)
symbols = self.atoms.get_chemical_symbols()
species = set(symbols)
# species = [tos.symbol.replace("Mo","M") for tos in self.structure.types_of_specie]
species = [tos.symbol for tos in self.structure.types_of_specie]
tag = ""
for i in species:
tag = tag + " " + i
pair_coef = "* * " + str(parameters["pair_coeff"]) + " " + tag
f1.write("pair_coeff %s \n" % pair_coef)
# for pair_coeff in parameters['pair_coeff']:
# f.write('pair_coeff %s \n' % pair_coeff)
#
# if 'mass' in parameters:
# for mass in parameters['mass']:
# f.write('mass %s \n' % mass)
masses = set(self.atoms.get_masses())
count = 0
for i in masses:
count = count + 1
f.write("mass" + " " + str(count) + " " + str(i) + "\n")
else:
# default interaction
f.write("pair_style lj/cut 2.5 \n" + "pair_coeff * * 1 1 \n" + "mass * 1.0 \n")
# f.write('\n### run\n')
# if 'fix' in parameters:
# if parameters['fix']:
# for i in parameters['fix']:
# f.write('fix %s\n' % i)
# else:
# f.write('fix fix_nve all nve\n')
f1.write("neighbor 1.0 nsq\n")
f1.write("neigh_modify once no every 1 delay 0 check yes\n")
f1.write("min_style cg\n")
f1.write("min_modify dmax ${dmax} line quadratic\n")
f1.write("thermo 1\n")
f1.write("thermo_style custom step temp press cpu pxx pyy pzz pxy pxz pyz ke pe etotal vol lx ly lz atoms\n")
# f1.write('thermo_style custom step temp pe press pxx pyy pzz pxy pxz pyz lx ly lz vol\n' )
f1.write("thermo_modify norm no\n")
# if 'thermo_style' in parameters:
# f.write('thermo_style %s\n' % parameters['thermo_style'])
# else:
# f.write(('thermo_style custom %s\n') %
# (' '.join(self._custom_thermo_args)))
# if 'thermo_modify' in parameters:
# f.write('thermo_modify %s\n' % parameters['thermo_modify'])
# else:
# f.write('thermo_modify flush yes\n')
# if 'thermo' in parameters:
# f.write('thermo %s\n' % parameters['thermo'])
# else:
# f.write('thermo 1\n')
# if 'minimize' in parameters:
# f.write('minimize %s\n' % parameters['minimize'])
# if 'run' in parameters:
# f.write('run %s\n' % parameters['run'])
# if not (('minimize' in parameters) or ('run' in parameters)):
# f.write('run 0\n')
# if 'dump' in parameters:
# f.write('dump %s\n' % parameters['dump'])
# else:
# f.write('dump dump_all all custom 1 %s id type x y z vx vy vz fx fy fz\n' % lammps_trj)
# f.write('print __end_of_ase_invoked_calculation__\n')
# f.write('log /dev/stdout\n')
if "fix" in parameters:
if parameters["fix"]:
for i in parameters["fix"]:
f1.write("fix %s\n" % i)
f.close()
def as_dict(self):
d = dict(
structure=self.structure.as_dict(),
parameters=self.parameters,
label=self.label,
specorder=self.specorder,
always_triclinic=self.always_triclinic,
no_data_file=self.no_data_file,
)
d["@module"] = self.__class__.__module__
d["@class"] = self.__class__.__name__
return d
@classmethod
def from_dict(cls, d):
structure = Structure.from_dict(d["structure"])
return MPINTLammps(
structure,
parameters=d["parameters"],
label=d["label"],
specorder=d["specorder"],
always_triclinic=d["always_triclinic"],
no_data_file=d["no_data_file"],
)
def write_lammps_in(
structure=None,
lammps_in=None,
lammps_in1=None,
lammps_in2=None,
lammps_trj=None,
lammps_data=None,
parameters={},
):
"""
write lammps input file
from ase with custom modifications
LAMMPS input is devided into three parts
Args:
structure: Structure object
lammps_in: generally"init.mod", with unit and conversion factor information
lammps_in1: generally "potential.mod", with force-field/potential style and element tyoe information
lammps_in2: generally "in.elastic", a generic main input file to be fed in LAMMPS usin lmp_*<...,parameters['exec']
parameters: input parameters
"""
structure.sort()
f = open(lammps_in, "w")
f1 = open(lammps_in1, "w") # potential.mod
f2 = open(lammps_in2, "w")
f.write(
('variable dump_file string "%s"\n' % lammps_trj)
+ ("variable up equal 1.0e-6\n")
+ ("variable cfac equal 1.0e-4\n")
+ ("variable cunits string GPa\n")
+ ("variable etol equal 0\n")
+ ("variable ftol equal 1.0e-10\n")
+ ("variable maxiter equal 1000\n")
+ ("variable maxeval equal 10000\n")
+ ("variable dmax equal 1.0e-2\n")
+ ('variable data_file string "%s"\n' % "data")
)
atoms = AseAtomsAdaptor().get_atoms(structure)
pbc = atoms.get_pbc()
if "control_file" in parameters:
f2.write("include %s \n" % parameters["control_file"])
if "units" in parameters:
f.write("units %s \n" % parameters["units"])
else:
f.write("units metal \n")
if "atom_style" in parameters:
f.write("atom_style %s \n" % parameters["atom_style"])
else:
f.write("atom_style atomic \n")
if "boundary" in parameters:
f.write("boundary %s \n" % parameters["boundary"])
else:
f.write("boundary %c %c %c \n" % tuple("sp"[x] for x in pbc))
f.write("atom_modify sort 0 0.0 \n")
for key in ("neighbor", "newton"):
if key in parameters:
f.write("%s %s \n" % (key, parameters[key]))
f.write("\n")
# If no_data_file,
# write the simulation box and the 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)
species_i = dict([(s, i + 1) for i, s in enumerate(species)])
f.write("read_data %s\n" % "data")
# interaction
f.write("\n### interactions \n")
if "lib" in parameters:
lib = parameters["lib"]
f1.write("%s \n" % lib)
if ("pair_style" in parameters) and ("pair_coeff" in parameters):
pair_style = parameters["pair_style"]
f1.write("pair_style %s \n" % pair_style)
symbols = atoms.get_chemical_symbols()
# species = [tos.symbol.replace("Mo","M") for tos in structure.types_of_specie] #For REBO Mo-S
# species = [tos.symbol for tos in structure.types_of_specie]
print("site symbolss", Poscar(structure).site_symbols)
species = [tos for tos in Poscar(structure).site_symbols]
if parameters["pair_style"] == "rebomos":
species = [tos.replace("Mo", "M") for tos in Poscar(structure).site_symbols]
tag = ""
for i in species:
tag = tag + " " + i
pair_coef = "* * " + str(parameters["pair_coeff"]) + " " + tag
f1.write("pair_coeff %s \n" % pair_coef)
masses = []
for m in atoms.get_masses():
if m not in masses:
masses.append(m)
count = 0
for i in masses:
count = count + 1
f.write("mass" + " " + str(count) + " " + str(i) + "\n")
else:
# default interaction
f.write("pair_style lj/cut 2.5 \n" + "pair_coeff * * 1 1 \n" + "mass * 1.0 \n")
f1.write("neighbor 1.0 nsq\n")
f1.write("neigh_modify once no every 1 delay 0 check yes\n")
if "min" not in parameters:
f1.write("min_style cg\n")
f1.write("min_modify dmax ${dmax} line quadratic\n")
f1.write("thermo 1\n")
f1.write(
"thermo_style custom step temp press cpu pxx pyy pzz pxy pxz pyz ke pe etotal vol lx ly lz atoms\n"
)
# f1.write('thermo_style custom step temp pe press pxx pyy pzz pxy pxz pyz lx ly lz vol\n' )
f1.write("thermo_modify norm no\n")
# if 'thermo_style' in parameters:
# f.write('thermo_style %s\n' % parameters['thermo_style'])
# else:
# f.write(('thermo_style custom %s\n') %
# (' '.join(self._custom_thermo_args)))
# if 'thermo_modify' in parameters:
# f.write('thermo_modify %s\n' % parameters['thermo_modify'])
# else:
# f.write('thermo_modify flush yes\n')
# if 'thermo' in parameters:
# f.write('thermo %s\n' % parameters['thermo'])
# else:
# f.write('thermo 1\n')
# if 'minimize' in parameters:
# f.write('minimize %s\n' % parameters['minimize'])
# if 'run' in parameters:
# f.write('run %s\n' % parameters['run'])
# if not (('minimize' in parameters) or ('run' in parameters)):
# f.write('run 0\n')
# if 'dump' in parameters:
# f.write('dump %s\n' % parameters['dump'])
# else:
# f.write('dump dump_all all custom 1 %s id type x y z vx vy vz fx fy fz\n' % lammps_trj)
# f.write('print __end_of_ase_invoked_calculation__\n')
# f.write('log /dev/stdout\n')
if "fix" in parameters:
if parameters["fix"]:
for i in parameters["fix"]:
f1.write("fix %s\n" % i)
f.close()
f1.close()
f2.close()
class MPINTLammps(LAMMPS, MSONable):
"""
setup LAMMPS for given structure and parameters
extends ase.calculators.lammpsrun.LAMMPS
"""
def __init__(self, structure, parameters={},
label='mpintlmp', specorder=None,
always_triclinic=True, no_data_file=False):
LAMMPS.__init__(self, label=label,
parameters=parameters,
specorder=specorder, files=[],
always_triclinic=always_triclinic,
no_data_file=no_data_file)
self.structure = structure
self.atoms = AseAtomsAdaptor().get_atoms(structure)
self.label = label
self.parameters = parameters
self.specorder = specorder
self.always_triclinic = always_triclinic
self.no_data_file = no_data_file
self.charges = None
if 'charges' in self.parameters:
self.charges = self.parameters['charges']
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()
# self.mplmp.write_lammps_in(lammps_in=lmp_in_fd,lammps_in1=lmp_in_fd1,lammps_in2=lmp_in_fd2,
# lammps_trj=lmp_trj_name,
# lammps_data=lmp_data_name)
# self.mplmp.write_lammps_in(lammps_in=lmp_in_fd,lammps_in1=lmp_in_fd1,
# lammps_trj=lmp_trj_name,
# lammps_data=lmp_data_name)
def write_lammps_in(self, lammps_in=None,lammps_in1=None,lammps_in2=None, lammps_trj=None,
lammps_data=None):
"""
write lammps input file
from ase with custom modifications
"""
f = lammps_in
f1 = lammps_in1 #potential.mod
f2 = lammps_in2
parameters = self.parameters
if 'units' in parameters:
if parameters['units']=='real':
f.write(('variable dump_file string "%s"\n' % lammps_trj) +
('variable up equal 1.0e-8\n' )+
('variable cfac equal 1.01325e-4\n' )+
('variable cunits string GPa\n' )+
('variable etol equal 0\n' )+
('variable ftol equal 1.0e-10\n' )+
('variable maxiter equal 1000\n' )+
('variable maxeval equal 10000\n' )+
('variable dmax equal 1.0e-2\n' )+
('variable data_file string "%s"\n' % lammps_data))
else:
f.write(('variable dump_file string "%s"\n' % lammps_trj) +
('variable up equal 1.0e-8\n' )+
('variable cfac equal 1.0e-4\n' )+
('variable cunits string GPa\n' )+
('variable etol equal 0\n' )+
('variable ftol equal 1.0e-10\n' )+
('variable maxiter equal 1000\n' )+
('variable maxeval equal 10000\n' )+
('variable dmax equal 1.0e-2\n' )+
('variable data_file string "%s"\n' % lammps_data))
pbc = self.atoms.get_pbc()
if 'control_file' in parameters:
f2.write('include %s \n'% parameters['control_file'])
#f2.write('include /home/kamal/inelast.mod \n')
if 'units' in parameters:
f.write('units %s \n' % parameters['units'])
else:
f.write('units metal \n')
#f.write('units metal \n')
if 'atom_style' in parameters:
f.write('atom_style %s \n' % parameters['atom_style'])
else:
f.write('atom_style atomic \n')
if 'boundary' in parameters:
f.write('boundary %s \n' % parameters['boundary'])
else:
f.write('boundary %c %c %c \n' %
tuple('sp'[x] for x in pbc))
f.write('atom_modify sort 0 0.0 \n')
for key in ('neighbor' ,'newton'):
if key in parameters:
f.write('%s %s \n' % (key, parameters[key]))
f.write('\n')
# If no_data_file,
# write the simulation box and the atoms
if self.no_data_file:
p = self.prism
f.write('lattice sc 1.0\n')
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
if self.always_triclinic or p.is_skewed():
f.write('region asecell prism 0.0 %s 0.0 %s 0.0 %s ' %
(xhi, yhi, zhi))
f.write('%s %s %s side in units box\n' % (xy, xz, yz))
else:
f.write(('region asecell block 0.0 %s 0.0 %s 0.0 %s '
'side in units box\n') % (xhi, yhi, zhi))
symbols = self.atoms.get_chemical_symbols()
############KAMAL###########################################
# species = [tos.symbol for tos in self.structure.types_of_specie]
#
# for i, r in enumerate(map(p.pos_to_lammps_str,
# self.atoms.get_positions())):
# s = species.index(symbols[i]) + 1
################################################
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)
species_i = dict([(s,i+1) for i,s in enumerate(species)])
f.write('create_box %i asecell\n' % n_atom_types)
for s, pos in zip(symbols, self.atoms.get_positions()):
f.write('create_atoms %i single %s %s %s units box\n'%
((species_i[s],)+p.pos_to_lammps_fold_str(pos)))
else:
f.write('read_data %s\n' % lammps_data)
# interaction
f.write('\n### interactions \n')
if ( 'lib' in parameters ):
lib = parameters['lib']
f1.write('%s \n' % lib)
if ( ('pair_style' in parameters) and ('pair_coeff' in parameters) ):
pair_style = parameters['pair_style']
f1.write('pair_style %s \n' % pair_style)
symbols = self.atoms.get_chemical_symbols()
species = set(symbols)
#species = [tos.symbol.replace("Mo","M") for tos in self.structure.types_of_specie]
species = [tos.symbol for tos in self.structure.types_of_specie]
tag=''
for i in species:
tag=tag+' '+i
pair_coef = '* * '+str(parameters['pair_coeff'])+' '+tag
f1.write('pair_coeff %s \n' % pair_coef)
# for pair_coeff in parameters['pair_coeff']:
# f.write('pair_coeff %s \n' % pair_coeff)
#
# if 'mass' in parameters:
# for mass in parameters['mass']:
# f.write('mass %s \n' % mass)
masses = set(self.atoms.get_masses())
count=0
for i in masses:
count=count+1
f.write('mass'+' '+str(count)+' '+str(i)+'\n')
else:
# default interaction
f.write('pair_style lj/cut 2.5 \n' +
'pair_coeff * * 1 1 \n' +
'mass * 1.0 \n')
# f.write('\n### run\n')
# if 'fix' in parameters:
# if parameters['fix']:
# for i in parameters['fix']:
# f.write('fix %s\n' % i)
# else:
# f.write('fix fix_nve all nve\n')
f1.write('neighbor 1.0 nsq\n' )
f1.write('neigh_modify once no every 1 delay 0 check yes\n' )
f1.write('min_style cg\n' )
f1.write('min_modify dmax ${dmax} line quadratic\n' )
f1.write('thermo 1\n' )
f1.write('thermo_style custom step temp press cpu pxx pyy pzz pxy pxz pyz ke pe etotal vol lx ly lz atoms\n' )
#f1.write('thermo_style custom step temp pe press pxx pyy pzz pxy pxz pyz lx ly lz vol\n' )
f1.write('thermo_modify norm no\n' )
# if 'thermo_style' in parameters:
# f.write('thermo_style %s\n' % parameters['thermo_style'])
# else:
# f.write(('thermo_style custom %s\n') %
# (' '.join(self._custom_thermo_args)))
# if 'thermo_modify' in parameters:
# f.write('thermo_modify %s\n' % parameters['thermo_modify'])
# else:
# f.write('thermo_modify flush yes\n')
# if 'thermo' in parameters:
# f.write('thermo %s\n' % parameters['thermo'])
# else:
# f.write('thermo 1\n')
# if 'minimize' in parameters:
# f.write('minimize %s\n' % parameters['minimize'])
# if 'run' in parameters:
# f.write('run %s\n' % parameters['run'])
# if not (('minimize' in parameters) or ('run' in parameters)):
# f.write('run 0\n')
# if 'dump' in parameters:
# f.write('dump %s\n' % parameters['dump'])
# else:
# f.write('dump dump_all all custom 1 %s id type x y z vx vy vz fx fy fz\n' % lammps_trj)
# f.write('print __end_of_ase_invoked_calculation__\n')
# f.write('log /dev/stdout\n')
if 'fix' in parameters:
if parameters['fix']:
for i in parameters['fix']:
f1.write('fix %s\n' % i)
f.close()
def as_dict(self):
d = dict(structure=self.structure.as_dict(),
parameters=self.parameters, label=self.label,
specorder=self.specorder,
always_triclinic=self.always_triclinic,
no_data_file=self.no_data_file)
d["@module"] = self.__class__.__module__
d["@class"] = self.__class__.__name__
return d
@classmethod
def from_dict(cls, d):
structure = Structure.from_dict(d["structure"])
return MPINTLammps(structure, parameters=d["parameters"],
label=d["label"],
specorder=d["specorder"],
always_triclinic=d["always_triclinic"],
no_data_file=d["no_data_file"])
class MPINTLammps(LAMMPS, PMGSONable):
"""
setup LAMMPS for given structure and parameters
extends ase.calculators.lammpsrun.LAMMPS
"""
def __init__(self, structure, parameters={},
label='mpintlmp', specorder=None,
always_triclinic=False, no_data_file=False):
LAMMPS.__init__(self, label=label,
parameters=parameters,
specorder=specorder, files=[],
always_triclinic=always_triclinic,
no_data_file=no_data_file)
self.structure = structure
self.atoms = AseAtomsAdaptor().get_atoms(structure)
self.label = label
self.parameters = parameters
self.specorder = specorder
self.always_triclinic = always_triclinic
self.no_data_file = no_data_file
self.charges = None
if 'charges' in self.parameters:
self.charges = self.parameters['charges']
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_in(self, lammps_in=None, lammps_trj=None,
lammps_data=None):
"""
write lammps input file
from ase with custom modifications
"""
f = lammps_in
f.write('clear\n' +
('variable dump_file string "%s"\n' % lammps_trj) +
('variable data_file string "%s"\n' % lammps_data))
parameters = self.parameters
pbc = self.atoms.get_pbc()
f.write('units metal \n')
if 'atom_style' in parameters:
f.write('atom_style %s \n' % parameters['atom_style'])
else:
f.write('atom_style atomic \n')
if 'boundary' in parameters:
f.write('boundary %s \n' % parameters['boundary'])
else:
f.write('boundary %c %c %c \n' %
tuple('sp'[x] for x in pbc))
f.write('atom_modify sort 0 0.0 \n')
for key in ('neighbor' ,'newton'):
if key in parameters:
f.write('%s %s \n' % (key, parameters[key]))
f.write('\n')
# If no_data_file,
# write the simulation box and the atoms
if self.no_data_file:
p = self.prism
f.write('lattice sc 1.0\n')
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
if self.always_triclinic or p.is_skewed():
f.write('region asecell prism 0.0 %s 0.0 %s 0.0 %s ' %
(xhi, yhi, zhi))
f.write('%s %s %s side in units box\n' % (xy, xz, yz))
else:
f.write(('region asecell block 0.0 %s 0.0 %s 0.0 %s '
'side in units box\n') % (xhi, yhi, zhi))
symbols = self.atoms.get_chemical_symbols()
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)
species_i = dict([(s,i+1) for i,s in enumerate(species)])
f.write('create_box %i asecell\n' % n_atom_types)
for s, pos in zip(symbols, self.atoms.get_positions()):
f.write('create_atoms %i single %s %s %s units box\n'%
((species_i[s],)+p.pos_to_lammps_fold_str(pos)))
else:
f.write('read_data %s\n' % lammps_data)
# interaction
f.write('\n### interactions \n')
if ( ('pair_style' in parameters) and ('pair_coeff' in parameters) ):
pair_style = parameters['pair_style']
f.write('pair_style %s \n' % pair_style)
for pair_coeff in parameters['pair_coeff']:
f.write('pair_coeff %s \n' % pair_coeff)
if 'mass' in parameters:
for mass in parameters['mass']:
f.write('mass %s \n' % mass)
else:
# default interaction
f.write('pair_style lj/cut 2.5 \n' +
'pair_coeff * * 1 1 \n' +
'mass * 1.0 \n')
f.write('\n### run\n')
if 'fix' in parameters:
if parameters['fix']:
for i in parameters['fix']:
f.write('fix %s\n' % i)
else:
f.write('fix fix_nve all nve\n')
if 'thermo_style' in parameters:
f.write('thermo_style %s\n' % parameters['thermo_style'])
else:
f.write(('thermo_style custom %s\n') %
(' '.join(self._custom_thermo_args)))
if 'thermo_modify' in parameters:
f.write('thermo_modify %s\n' % parameters['thermo_modify'])
else:
f.write('thermo_modify flush yes\n')
if 'thermo' in parameters:
f.write('thermo %s\n' % parameters['thermo'])
else:
f.write('thermo 1\n')
if 'minimize' in parameters:
f.write('minimize %s\n' % parameters['minimize'])
if 'run' in parameters:
f.write('run %s\n' % parameters['run'])
if not (('minimize' in parameters) or ('run' in parameters)):
f.write('run 0\n')
if 'dump' in parameters:
f.write('dump %s\n' % parameters['dump'])
else:
f.write('dump dump_all all custom 1 %s id type x y z vx vy vz fx fy fz\n' % lammps_trj)
f.write('print __end_of_ase_invoked_calculation__\n')
f.write('log /dev/stdout\n') # Force LAMMPS to flush log
f.close()
def as_dict(self):
d = dict(structure=self.structure.as_dict(),
parameters=self.parameters, label=self.label,
specorder=self.specorder,
always_triclinic=self.always_triclinic,
no_data_file=self.no_data_file)
d["@module"] = self.__class__.__module__
d["@class"] = self.__class__.__name__
return d
@classmethod
def from_dict(cls, d):
structure = Structure.from_dict(d["structure"])
return MPINTLammps(structure, parameters=d["parameters"],
label=d["label"],
specorder=d["specorder"],
always_triclinic=d["always_triclinic"],
no_data_file=d["no_data_file"])
class MPINTLammps(LAMMPS, MSONable):
"""
setup LAMMPS for given structure and parameters
extends ase.calculators.lammpsrun.LAMMPS
"""
def __init__(self,
structure,
parameters={},
label='mpintlmp',
specorder=None,
always_triclinic=False,
no_data_file=False):
LAMMPS.__init__(self,
label=label,
parameters=parameters,
specorder=specorder,
files=[],
always_triclinic=always_triclinic,
no_data_file=no_data_file)
self.structure = structure
self.atoms = AseAtomsAdaptor().get_atoms(structure)
self.label = label
self.parameters = parameters
self.specorder = specorder
self.always_triclinic = always_triclinic
self.no_data_file = no_data_file
self.charges = None
if 'charges' in self.parameters:
self.charges = self.parameters['charges']
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_in(self,
lammps_in=None,
lammps_trj=None,
lammps_data=None):
"""
write lammps input file
from ase with custom modifications
"""
f = lammps_in
f.write('clear\n' + ('variable dump_file string "%s"\n' % lammps_trj) +
('variable data_file string "%s"\n' % lammps_data))
parameters = self.parameters
pbc = self.atoms.get_pbc()
f.write('units metal \n')
if 'atom_style' in parameters:
f.write('atom_style %s \n' % parameters['atom_style'])
else:
f.write('atom_style atomic \n')
if 'boundary' in parameters:
f.write('boundary %s \n' % parameters['boundary'])
else:
f.write('boundary %c %c %c \n' % tuple('sp'[x] for x in pbc))
f.write('atom_modify sort 0 0.0 \n')
for key in ('neighbor', 'newton'):
if key in parameters:
f.write('%s %s \n' % (key, parameters[key]))
f.write('\n')
# If no_data_file,
# write the simulation box and the atoms
if self.no_data_file:
p = self.prism
f.write('lattice sc 1.0\n')
xhi, yhi, zhi, xy, xz, yz = p.get_lammps_prism_str()
if self.always_triclinic or p.is_skewed():
f.write('region asecell prism 0.0 %s 0.0 %s 0.0 %s ' %
(xhi, yhi, zhi))
f.write('%s %s %s side in units box\n' % (xy, xz, yz))
else:
f.write(('region asecell block 0.0 %s 0.0 %s 0.0 %s '
'side in units box\n') % (xhi, yhi, zhi))
symbols = self.atoms.get_chemical_symbols()
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)
species_i = dict([(s, i + 1) for i, s in enumerate(species)])
f.write('create_box %i asecell\n' % n_atom_types)
for s, pos in zip(symbols, self.atoms.get_positions()):
f.write('create_atoms %i single %s %s %s units box\n' %
((species_i[s], ) + p.pos_to_lammps_fold_str(pos)))
else:
f.write('read_data %s\n' % lammps_data)
# interaction
f.write('\n### interactions \n')
if (('pair_style' in parameters) and ('pair_coeff' in parameters)):
pair_style = parameters['pair_style']
f.write('pair_style %s \n' % pair_style)
for pair_coeff in parameters['pair_coeff']:
f.write('pair_coeff %s \n' % pair_coeff)
if 'mass' in parameters:
for mass in parameters['mass']:
f.write('mass %s \n' % mass)
else:
# default interaction
f.write('pair_style lj/cut 2.5 \n' + 'pair_coeff * * 1 1 \n' +
'mass * 1.0 \n')
f.write('\n### run\n')
if 'fix' in parameters:
if parameters['fix']:
for i in parameters['fix']:
f.write('fix %s\n' % i)
else:
f.write('fix fix_nve all nve\n')
if 'thermo_style' in parameters:
f.write('thermo_style %s\n' % parameters['thermo_style'])
else:
f.write(('thermo_style custom %s\n') %
(' '.join(self._custom_thermo_args)))
if 'thermo_modify' in parameters:
f.write('thermo_modify %s\n' % parameters['thermo_modify'])
else:
f.write('thermo_modify flush yes\n')
if 'thermo' in parameters:
f.write('thermo %s\n' % parameters['thermo'])
else:
f.write('thermo 1\n')
if 'minimize' in parameters:
f.write('minimize %s\n' % parameters['minimize'])
if 'run' in parameters:
f.write('run %s\n' % parameters['run'])
if not (('minimize' in parameters) or ('run' in parameters)):
f.write('run 0\n')
if 'dump' in parameters:
f.write('dump %s\n' % parameters['dump'])
else:
f.write(
'dump dump_all all custom 1 %s id type x y z vx vy vz fx fy fz\n'
% lammps_trj)
f.write('print __end_of_ase_invoked_calculation__\n')
f.write('log /dev/stdout\n')
f.close()
def as_dict(self):
d = dict(structure=self.structure.as_dict(),
parameters=self.parameters,
label=self.label,
specorder=self.specorder,
always_triclinic=self.always_triclinic,
no_data_file=self.no_data_file)
d["@module"] = self.__class__.__module__
d["@class"] = self.__class__.__name__
return d
@classmethod
def from_dict(cls, d):
structure = Structure.from_dict(d["structure"])
return MPINTLammps(structure,
parameters=d["parameters"],
label=d["label"],
specorder=d["specorder"],
always_triclinic=d["always_triclinic"],
no_data_file=d["no_data_file"])
def write_lammps_in( structure=None,lammps_in=None,lammps_in1=None,lammps_in2=None, lammps_trj=None,
lammps_data=None,parameters={}):
"""
write lammps input file
from ase with custom modifications
"""
structure.sort()
f = open(lammps_in,"w")
f1 = open(lammps_in1,"w") #potential.mod
f2 = open(lammps_in2,"w")
f.write(('variable dump_file string "%s"\n' % lammps_trj) +
('variable up equal 1.0e-6\n' )+
('variable cfac equal 1.0e-4\n' )+
('variable cunits string GPa\n' )+
('variable etol equal 0\n' )+
('variable ftol equal 1.0e-10\n' )+
('variable maxiter equal 1000\n' )+
('variable maxeval equal 10000\n' )+
('variable dmax equal 1.0e-2\n' )+
('variable data_file string "%s"\n' % "data"))
atoms = AseAtomsAdaptor().get_atoms(structure)
pbc = atoms.get_pbc()
if 'control_file' in parameters:
f2.write('include %s \n'% parameters['control_file'])
if 'units' in parameters:
f.write('units %s \n' % parameters['units'])
else:
f.write('units metal \n')
if 'atom_style' in parameters:
f.write('atom_style %s \n' % parameters['atom_style'])
else:
f.write('atom_style atomic \n')
if 'boundary' in parameters:
f.write('boundary %s \n' % parameters['boundary'])
else:
f.write('boundary %c %c %c \n' %
tuple('sp'[x] for x in pbc))
f.write('atom_modify sort 0 0.0 \n')
for key in ('neighbor' ,'newton'):
if key in parameters:
f.write('%s %s \n' % (key, parameters[key]))
f.write('\n')
species = [tos for tos in Poscar(structure).site_symbols]
n_atom_types = len(species)
species_i = dict([(s,i+1) for i,s in enumerate(species)])
f.write('read_data %s\n' % "data")
f.write('\n### interactions \n')
if ( 'lib' in parameters ):
lib = parameters['lib']
f1.write('%s \n' % lib)
if ( ('pair_style' in parameters) and ('pair_coeff' in parameters) ):
pair_style = parameters['pair_style']
f1.write('pair_style %s \n' % pair_style)
symbols = atoms.get_chemical_symbols()
#print "site symbolss",Poscar(structure).site_symbols
species = [tos for tos in Poscar(structure).site_symbols]
if parameters['pair_style']=='rebomos':
species = [tos.replace("Mo","M") for tos in Poscar(structure).site_symbols]
tag=''
for i in species:
tag=tag+' '+i
pair_coef = '* * '+str(parameters['pair_coeff'])+' '+tag
f1.write('pair_coeff %s \n' % pair_coef)
masses=[]
for m in atoms.get_masses():
if m not in masses:
masses.append(m)
count=0
for i in masses:
count=count+1
f.write('mass'+' '+str(count)+' '+str(i)+'\n')
else:
f.write('pair_style lj/cut 2.5 \n' +
'pair_coeff * * 1 1 \n' +
'mass * 1.0 \n')
f1.write('neighbor 1.0 nsq\n' )
f1.write('neigh_modify once no every 1 delay 0 check yes\n' )
if 'min' not in parameters:
f1.write('min_style cg\n' )
f1.write('min_modify dmax ${dmax} line quadratic\n' )
f1.write('thermo 1\n' )
f1.write('thermo_style custom step temp press cpu pxx pyy pzz pxy pxz pyz ke pe etotal vol lx ly lz atoms\n' )
f1.write('thermo_modify norm no\n' )
if 'fix' in parameters:
if parameters['fix']:
for i in parameters['fix']:
f1.write('fix %s\n' % i)
f.close()
f1.close()
f2.close()