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"""
Stream input commands to lammps to perform desired simulations
"""
from ase.parallel import paropen
from ase.calculators.lammps.unitconvert import convert
# "End mark" used to indicate that the calculation is done
CALCULATION_END_MARK = "__end_of_ase_invoked_calculation__"
def lammps_create_atoms(fileobj, parameters, atoms, prismobj):
"""Create atoms in lammps with 'create_box' and 'create_atoms'
:param fileobj: open stream for lammps input
:param parameters: dict of all lammps parameters
:type parameters: dict
:param atoms: Atoms object
:type atoms: Atoms
:param prismobj: coordinate transformation between ase and lammps
:type prismobj: Prism
"""
if parameters["verbose"]:
fileobj.write("## Original ase cell\n".encode("utf-8"))
fileobj.write(
"".join(
[
"# {0:.16} {1:.16} {2:.16}\n".format(*x)
for x in atoms.get_cell()
]
).encode("utf-8")
)
fileobj.write("lattice sc 1.0\n".encode("utf-8"))
# Get cell parameters and convert from ASE units to LAMMPS units
xhi, yhi, zhi, xy, xz, yz = convert(prismobj.get_lammps_prism(),
"distance", "ASE", parameters.units)
if parameters["always_triclinic"] or prismobj.is_skewed():
fileobj.write(
"region asecell prism 0.0 {0} 0.0 {1} 0.0 {2} ".format(
xhi, yhi, zhi
).encode("utf-8")
)
fileobj.write(
"{0} {1} {2} side in units box\n".format(xy, xz, yz).encode(
"utf-8"
)
)
else:
fileobj.write(
"region asecell block 0.0 {0} 0.0 {1} 0.0 {2} "
"side in units box\n".format(xhi, yhi, zhi).encode("utf-8")
)
symbols = atoms.get_chemical_symbols()
try:
# By request, specific atom type ordering
species = parameters["specorder"]
except AttributeError:
# By default, atom types in alphabetic order
species = sorted(set(symbols))
species_i = {s: i + 1 for i, s in enumerate(species)}
fileobj.write(
"create_box {0} asecell\n" "".format(len(species)).encode("utf-8")
)
for sym, pos in zip(symbols, atoms.get_positions()):
# Convert position from ASE units to LAMMPS units
pos = convert(pos, "distance", "ASE", parameters.units)
if parameters["verbose"]:
fileobj.write(
"# atom pos in ase cell: {0:.16} {1:.16} {2:.16}\n"
"".format(*tuple(pos)).encode("utf-8")
)
fileobj.write(
"create_atoms {0} single {1} {2} {3} remap yes units box\n".format(
*((species_i[sym],) + tuple(prismobj.vector_to_lammps(pos)))
).encode("utf-8")
)
def write_lammps_in(lammps_in, parameters, atoms, prismobj,
lammps_trj=None, lammps_data=None):
"""Write a LAMMPS in_ file with run parameters and settings."""
def write_model_post_and_masses(fileobj, parameters):
# write additional lines needed for some LAMMPS potentials
if 'model_post' in parameters:
mlines = parameters['model_post']
for ii in range(0,len(mlines)):
fileobj.write(mlines[ii].encode('utf-8'))
if "masses" in parameters:
for mass in parameters["masses"]:
# Note that the variable mass is a string containing
# the type number and value of mass separated by a space
fileobj.write("mass {0} \n".format(mass).encode("utf-8"))
if isinstance(lammps_in, str):
fileobj = paropen(lammps_in, "wb")
close_in_file = True
else:
# Expect lammps_in to be a file-like object
fileobj = lammps_in
close_in_file = False
if parameters["verbose"]:
fileobj.write("# (written by ASE)\n".encode("utf-8"))
# Write variables
fileobj.write(
(
"clear\n"
'variable dump_file string "{0}"\n'
'variable data_file string "{1}"\n'
)
.format(lammps_trj, lammps_data)
.encode("utf-8")
)
if "package" in parameters:
fileobj.write(
(
"\n".join(
["package {0}".format(p) for p in parameters["package"]]
)
+ "\n"
).encode("utf-8")
)
# setup styles except 'pair_style'
for style_type in ("atom", "bond", "angle",
"dihedral", "improper", "kspace"):
style = style_type + "_style"
if style in parameters:
fileobj.write('{} {} \n'.format(style, parameters[style]).encode("utf-8"))
# write initialization lines needed for some LAMMPS potentials
if 'model_init' in parameters:
mlines = parameters['model_init']
for ii in range(0,len(mlines)):
fileobj.write(mlines[ii].encode('utf-8'))
# write units
if 'units' in parameters:
units_line = 'units ' + parameters['units'] + '\n'
fileobj.write(units_line.encode('utf-8'))
else:
fileobj.write('units metal\n'.encode('utf-8'))
pbc = atoms.get_pbc()
if "boundary" in parameters:
fileobj.write(
"boundary {0} \n".format(parameters["boundary"]).encode("utf-8")
)
else:
fileobj.write(
"boundary {0} {1} {2} \n".format(
*tuple("sp"[int(x)] for x in pbc)
).encode("utf-8")
)
fileobj.write("atom_modify sort 0 0.0 \n".encode("utf-8"))
for key in ("neighbor", "newton"):
if key in parameters:
fileobj.write(
"{0} {1} \n".format(key, parameters[key]).encode("utf-8")
)
fileobj.write("\n".encode("utf-8"))
# write the simulation box and the atoms
if not lammps_data:
lammps_create_atoms(fileobj, parameters, atoms, prismobj)
# or simply refer to the data-file
else:
fileobj.write("read_data {0}\n".format(lammps_data).encode("utf-8"))
# Write interaction stuff
fileobj.write("\n### interactions\n".encode("utf-8"))
if "kim_interactions" in parameters:
fileobj.write("{}\n".format(parameters["kim_interactions"]).encode("utf-8"))
write_model_post_and_masses(fileobj, parameters)
elif ("pair_style" in parameters) and ("pair_coeff" in parameters):
pair_style = parameters["pair_style"]
fileobj.write("pair_style {0} \n".format(pair_style).encode("utf-8"))
for pair_coeff in parameters["pair_coeff"]:
fileobj.write(
"pair_coeff {0} \n" "".format(pair_coeff).encode("utf-8")
)
write_model_post_and_masses(fileobj, parameters)
else:
# simple default parameters
# that should always make the LAMMPS calculation run
fileobj.write(
"pair_style lj/cut 2.5 \n"
"pair_coeff * * 1 1 \n"
"mass * 1.0 \n".encode("utf-8")
)
if "group" in parameters:
fileobj.write(
(
"\n".join(["group {0}".format(p) for p in parameters["group"]])
+ "\n"
).encode("utf-8")
)
fileobj.write("\n### run\n" "fix fix_nve all nve\n".encode("utf-8"))
if "fix" in parameters:
fileobj.write(
(
"\n".join(["fix {0}".format(p) for p in parameters["fix"]])
+ "\n"
).encode("utf-8")
)
fileobj.write(
"dump dump_all all custom {1} {0} id type x y z vx vy vz "
"fx fy fz\n"
"".format(lammps_trj, parameters["dump_period"]).encode("utf-8")
)
fileobj.write(
"thermo_style custom {0}\n"
"thermo_modify flush yes format float %23.16g\n"
"thermo 1\n".format(" ".join(parameters["thermo_args"])).encode(
"utf-8"
)
)
if "timestep" in parameters:
fileobj.write(
"timestep {0}\n".format(parameters["timestep"]).encode("utf-8")
)
if "minimize" in parameters:
fileobj.write(
"minimize {0}\n".format(parameters["minimize"]).encode("utf-8")
)
if "run" in parameters:
fileobj.write("run {0}\n".format(parameters["run"]).encode("utf-8"))
if not (("minimize" in parameters) or ("run" in parameters)):
fileobj.write("run 0\n".encode("utf-8"))
fileobj.write(
'print "{0}" \n'.format(CALCULATION_END_MARK).encode("utf-8")
)
# Force LAMMPS to flush log
fileobj.write("log /dev/stdout\n".encode("utf-8"))
fileobj.flush()
if close_in_file:
fileobj.close()
|
