def run(self, set_atoms=False):
"""Method which explicitly runs LAMMPS."""
self.calls += 1
# set LAMMPS command from environment variable
if 'LAMMPS_COMMAND' in os.environ:
lammps_cmd_line = shlex.split(os.environ['LAMMPS_COMMAND'],
posix=(os.name == 'posix'))
if len(lammps_cmd_line) == 0:
self.clean()
raise RuntimeError('The LAMMPS_COMMAND environment variable '
'must not be empty')
# want always an absolute path to LAMMPS binary when calling from
# self.dir
lammps_cmd_line[0] = os.path.abspath(lammps_cmd_line[0])
else:
self.clean()
raise RuntimeError(
'Please set LAMMPS_COMMAND environment variable')
if 'LAMMPS_OPTIONS' in os.environ:
lammps_options = shlex.split(os.environ['LAMMPS_OPTIONS'],
posix=(os.name == 'posix'))
else:
lammps_options = shlex.split('-echo log -screen none',
posix=(os.name == 'posix'))
# change into subdirectory for LAMMPS calculations
cwd = os.getcwd()
os.chdir(self.tmp_dir)
# setup file names for LAMMPS calculation
label = '{0}{1:>06}'.format(self.label, self.calls)
lammps_in = uns_mktemp(prefix='in_' + label, dir=self.tmp_dir)
lammps_log = uns_mktemp(prefix='log_' + label, dir=self.tmp_dir)
lammps_trj_fd = NamedTemporaryFile(prefix='trj_' + label,
dir=self.tmp_dir,
delete=(not self.keep_tmp_files))
lammps_trj = lammps_trj_fd.name
if self.no_data_file:
lammps_data = None
else:
lammps_data_fd = NamedTemporaryFile(
prefix='data_' + label,
dir=self.tmp_dir,
delete=(not self.keep_tmp_files))
self.write_lammps_data(lammps_data=lammps_data_fd)
lammps_data = lammps_data_fd.name
lammps_data_fd.flush()
# see to it that LAMMPS is started
if not self._lmp_alive():
# Attempt to (re)start lammps
self._lmp_handle = Popen(
#### lammps_cmd_line + lammps_options + ['-log', '/dev/stdout'],
lammps_cmd_line + lammps_options,
stdin=PIPE,
stdout=PIPE)
lmp_handle = self._lmp_handle
# Create thread reading lammps stdout (for reference, if requested,
# also create lammps_log, although it is never used)
if self.keep_tmp_files:
lammps_log_fd = open(lammps_log, 'wb')
fd = SpecialTee(lmp_handle.stdout, lammps_log_fd)
else:
fd = lmp_handle.stdout
thr_read_log = Thread(target=self.read_lammps_log, args=(fd, ))
thr_read_log.start()
# write LAMMPS input (for reference, also create the file lammps_in,
# although it is never used)
if self.keep_tmp_files:
lammps_in_fd = open(lammps_in, 'wb')
fd = SpecialTee(lmp_handle.stdin, lammps_in_fd)
else:
fd = lmp_handle.stdin
self.write_lammps_in(lammps_in=fd,
lammps_trj=lammps_trj,
lammps_data=lammps_data)
if self.keep_tmp_files:
lammps_in_fd.close()
# Wait for log output to be read (i.e., for LAMMPS to finish)
# and close the log file if there is one
thr_read_log.join()
if self.keep_tmp_files:
lammps_log_fd.close()
if not self.keep_alive:
self._lmp_end()
exitcode = lmp_handle.poll()
if exitcode and exitcode != 0:
cwd = os.getcwd()
raise RuntimeError(
'LAMMPS exited in {0} with exit code: {1}.'.format(
cwd, exitcode))
# A few sanity checks
if len(self.thermo_content) == 0:
raise RuntimeError('Failed to retrieve any thermo_style-output')
if int(self.thermo_content[-1]['atoms']) != len(self.atoms):
# This obviously shouldn't happen, but if prism.fold_...() fails,
# it could
raise RuntimeError('Atoms have gone missing')
self.read_lammps_trj(lammps_trj=lammps_trj, set_atoms=set_atoms)
lammps_trj_fd.close()
if not self.no_data_file:
lammps_data_fd.close()
os.chdir(cwd)
def run(self, set_atoms=False):
# !TODO: split this function
"""Method which explicitly runs LAMMPS."""
pbc = self.atoms.get_pbc()
if all(pbc):
cell = self.atoms.get_cell()
elif not any(pbc):
# large enough cell for non-periodic calculation -
# LAMMPS shrink-wraps automatically via input command
# "periodic s s s"
# below
cell = 2 * np.max(np.abs(self.atoms.get_positions())) * np.eye(3)
else:
warnings.warn(
"semi-periodic ASE cell detected - translation "
+ "to proper LAMMPS input cell might fail"
)
cell = self.atoms.get_cell()
self.prism = Prism(cell)
self.set_missing_parameters()
self.calls += 1
# change into subdirectory for LAMMPS calculations
cwd = os.getcwd()
os.chdir(self.parameters.tmp_dir)
# setup file names for LAMMPS calculation
label = "{0}{1:>06}".format(self.label, self.calls)
lammps_in = uns_mktemp(
prefix="in_" + label, dir=self.parameters.tmp_dir
)
lammps_log = uns_mktemp(
prefix="log_" + label, dir=self.parameters.tmp_dir
)
lammps_trj_fd = NamedTemporaryFile(
prefix="trj_" + label,
suffix=(".bin" if self.parameters.binary_dump else ""),
dir=self.parameters.tmp_dir,
delete=(not self.parameters.keep_tmp_files),
)
lammps_trj = lammps_trj_fd.name
if self.parameters.no_data_file:
lammps_data = None
else:
lammps_data_fd = NamedTemporaryFile(
prefix="data_" + label,
dir=self.parameters.tmp_dir,
delete=(not self.parameters.keep_tmp_files),
mode='w',
encoding='ascii'
)
write_lammps_data(
lammps_data_fd,
self.atoms,
specorder=self.parameters.specorder,
force_skew=self.parameters.always_triclinic,
velocities=self.parameters.write_velocities,
prismobj=self.prism,
units=self.parameters.units,
atom_style=self.parameters.atom_style
)
lammps_data = lammps_data_fd.name
lammps_data_fd.flush()
# see to it that LAMMPS is started
if not self._lmp_alive():
command = self.get_lammps_command()
# Attempt to (re)start lammps
self._lmp_handle = Popen(
shlex.split(command, posix=(os.name == "posix")),
stdin=PIPE,
stdout=PIPE,
)
lmp_handle = self._lmp_handle
# Create thread reading lammps stdout (for reference, if requested,
# also create lammps_log, although it is never used)
if self.parameters.keep_tmp_files:
lammps_log_fd = open(lammps_log, "wb")
fd = SpecialTee(lmp_handle.stdout, lammps_log_fd)
else:
fd = lmp_handle.stdout
thr_read_log = Thread(target=self.read_lammps_log, args=(fd,))
thr_read_log.start()
# write LAMMPS input (for reference, also create the file lammps_in,
# although it is never used)
if self.parameters.keep_tmp_files:
lammps_in_fd = open(lammps_in, "wb")
fd = SpecialTee(lmp_handle.stdin, lammps_in_fd)
else:
fd = lmp_handle.stdin
write_lammps_in(
lammps_in=fd,
parameters=self.parameters,
atoms=self.atoms,
prismobj=self.prism,
lammps_trj=lammps_trj,
lammps_data=lammps_data,
)
if self.parameters.keep_tmp_files:
lammps_in_fd.close()
# Wait for log output to be read (i.e., for LAMMPS to finish)
# and close the log file if there is one
thr_read_log.join()
if self.parameters.keep_tmp_files:
lammps_log_fd.close()
if not self.parameters.keep_alive:
self._lmp_end()
exitcode = lmp_handle.poll()
if exitcode and exitcode != 0:
cwd = os.getcwd()
raise RuntimeError(
"LAMMPS exited in {} with exit code: {}."
"".format(cwd, exitcode)
)
# A few sanity checks
if len(self.thermo_content) == 0:
raise RuntimeError("Failed to retrieve any thermo_style-output")
if int(self.thermo_content[-1]["atoms"]) != len(self.atoms):
# This obviously shouldn't happen, but if prism.fold_...() fails,
# it could
raise RuntimeError("Atoms have gone missing")
trj_atoms = read_lammps_dump(
infileobj=lammps_trj,
order=False,
index=-1,
prismobj=self.prism,
specorder=self.parameters.specorder,
)
if set_atoms:
self.atoms = trj_atoms.copy()
self.forces = trj_atoms.get_forces()
# !TODO: trj_atoms is only the last snapshot of the system; Is it
# desirable to save also the inbetween steps?
if self.parameters.trajectory_out is not None:
# !TODO: is it advisable to create here temporary atoms-objects
self.trajectory_out.write(trj_atoms)
tc = self.thermo_content[-1]
self.results["energy"] = convert(
tc["pe"], "energy", self.parameters["units"], "ASE"
)
self.results["free_energy"] = self.results["energy"]
self.results["forces"] = self.forces.copy()
stress = np.array(
[-tc[i] for i in ("pxx", "pyy", "pzz", "pyz", "pxz", "pxy")]
)
# We need to apply the Lammps rotation stuff to the stress:
xx, yy, zz, yz, xz, xy = stress
stress_tensor = np.array([[xx, xy, xz],
[xy, yy, yz],
[xz, yz, zz]])
R = self.prism.rot_mat
stress_atoms = np.dot(R, stress_tensor)
stress_atoms = np.dot(stress_atoms, R.T)
stress_atoms = stress_atoms[[0, 1, 2, 1, 0, 0],
[0, 1, 2, 2, 2, 1]]
stress = stress_atoms
self.results["stress"] = convert(
stress, "pressure", self.parameters["units"], "ASE"
)
lammps_trj_fd.close()
if not self.parameters.no_data_file:
lammps_data_fd.close()
os.chdir(cwd)
def run(self):
"""Method which explicitely runs LAMMPS."""
self.calls += 1
# set LAMMPS command from environment variable
if 'LAMMPS_COMMAND' in os.environ:
lammps_cmd_line = shlex.split(os.environ['LAMMPS_COMMAND'])
if len(lammps_cmd_line) == 0:
self.clean()
raise RuntimeError('The LAMMPS_COMMAND environment variable '
'must not be empty')
# want always an absolute path to LAMMPS binary when calling from self.dir
lammps_cmd_line[0] = os.path.abspath(lammps_cmd_line[0])
else:
self.clean()
raise RuntimeError('Please set LAMMPS_COMMAND environment variable')
if 'LAMMPS_OPTIONS' in os.environ:
lammps_options = shlex.split(os.environ['LAMMPS_OPTIONS'])
else:
lammps_options = shlex.split('-echo log -screen none')
# change into subdirectory for LAMMPS calculations
cwd = os.getcwd()
os.chdir(self.tmp_dir)
# setup file names for LAMMPS calculation
label = '%s%06d' % (self.label, self.calls)
lammps_in = uns_mktemp(prefix='in_'+label, dir=self.tmp_dir)
lammps_log = uns_mktemp(prefix='log_'+label, dir=self.tmp_dir)
lammps_trj_fd = NamedTemporaryFile(prefix='trj_'+label, dir=self.tmp_dir,
delete=(not self.keep_tmp_files))
lammps_trj = lammps_trj_fd.name
if self.no_data_file:
lammps_data = None
else:
lammps_data_fd = NamedTemporaryFile(prefix='data_'+label, dir=self.tmp_dir,
delete=(not self.keep_tmp_files))
self.write_lammps_data(lammps_data=lammps_data_fd)
lammps_data = lammps_data_fd.name
lammps_data_fd.flush()
#Save names of the files just in case
self.trajfile = lammps_trj_fd.name
self.infile = lammps_in
self.logfile = lammps_log
self.datafile = lammps_data
# see to it that LAMMPS is started
if not self._lmp_alive():
# Attempt to (re)start lammps
self._lmp_handle = Popen(lammps_cmd_line+lammps_options+['-log', '/dev/stdout'],
stdin=PIPE, stdout=PIPE)
lmp_handle = self._lmp_handle
# Create thread reading lammps stdout (for reference, if requested,
# also create lammps_log, although it is never used)
if self.keep_tmp_files:
lammps_log_fd = open(lammps_log, 'w')
fd = special_tee(lmp_handle.stdout, lammps_log_fd)
else:
fd = lmp_handle.stdout
thr_read_log = Thread(target=self.read_lammps_log, args=(fd,))
thr_read_log.start()
# write LAMMPS input (for reference, also create the file lammps_in,
# although it is never used)
if self.keep_tmp_files:
lammps_in_fd = open(lammps_in, 'w')
fd = special_tee(lmp_handle.stdin, lammps_in_fd)
else:
fd = lmp_handle.stdin
self.write_lammps_in(lammps_in=fd, lammps_trj=lammps_trj, lammps_data=lammps_data)
if self.keep_tmp_files:
lammps_in_fd.close()
# Wait for log output to be read (i.e., for LAMMPS to finish)
# and close the log file if there is one
thr_read_log.join()
if self.keep_tmp_files:
lammps_log_fd.close()
if not self.keep_alive:
self._lmp_end()
exitcode = lmp_handle.poll()
if exitcode and exitcode != 0:
cwd = os.getcwd()
raise RuntimeError('LAMMPS exited in %s with exit code: %d.' %\
(cwd,exitcode))
# A few sanity checks
if len(self.thermo_content) == 0:
raise RuntimeError('Failed to retreive any thermo_style-output')
if int(self.thermo_content[-1]['atoms']) != len(self.atoms):
# This obviously shouldn't happen, but if prism.fold_...() fails, it could
raise RuntimeError('Atoms have gone missing')
self.read_lammps_trj(lammps_trj=lammps_trj, set_atoms=True)
lammps_trj_fd.close()
if not self.no_data_file:
lammps_data_fd.close()
os.chdir(cwd)
