def write_config(sim, fields=None, precision=None):
"""
Write configurations to a trajectory file.
The trajectory format is taken from the passed Simulation
instance.
"""
# Initialize
# This will clear the variable in a new run
if sim.current_step == 0 or not hasattr(sim, '__init_write_config'):
sim.__init_write_config = False
if sim.restart:
sim.__init_write_config = True
# Header
if not sim.__init_write_config:
sim.__init_write_config = True
# TODO: folder-based trajectories should ensure that mode='w' clears up the folder
rmd(sim.output_path)
rmf(sim.output_path)
with sim.trajectory_class(sim.output_path, 'a') as t:
if precision is not None:
t.precision = precision
if fields is not None:
t.fields = fields
t.write(sim.system, sim.current_step)
def run(self, steps=None):
if steps is not None:
self.steps = steps
dirout = tempfile.mkdtemp()
file_tmp = os.path.join(dirout, 'lammps.atom')
file_inp = os.path.join(dirout, 'lammps.atom.inp')
# Update lammps startup file using self.system
# This will write the .inp startup file
with TrajectoryLAMMPS(file_tmp, 'w') as th:
th.write(self.system, 0)
# Do things in lammps order: units, read, commands, run. A
# better approach would be to parse commands and place
# read_data after units then pack commands again. Even better
# using PyLammps...
cmd = """\
units lj
atom_style atomic
read_data {file_inp}
{commands}
min_style {method}
minimize 0.0 {tolerance} {steps} {max_evaluations}
write_dump all custom {file_tmp} id type x y z modify sort id format line "%d %d %.15g %.15g %.15g"
""".format(file_tmp=file_tmp,
file_inp=file_inp,
commands=self.commands,
method=self.method,
tolerance=self.ftol,
steps=min(100000000, self.steps),
max_evaluations=min(100000000, self.max_evaluations))
stdout = _run_lammps_command(cmd)
if self.verbose:
print(stdout)
# Check if we have reached the number of maximum number of steps
if 'Stopping criterion = max iterations' in stdout:
self.reached_steps = True
else:
self.reached_steps = False
# Update internal reference to self.system
with TrajectoryLAMMPS(file_tmp) as th:
new_system = th[-1]
for i in range(len(self.system.particle)):
self.system.particle[i] = new_system.particle[i]
# Clean up
rmd(dirout)
def setUp(self):
self.dirname = '/tmp/test_folder'
rmd(self.dirname)
mkdir(self.dirname)
for i in range(10, 13):
fname = os.path.join(self.dirname, 'step_%d' % i)
with open(fname, 'w') as fh:
fh.write("""\
2
step:%d
A 1.0 -1.0 0.0
A 2.9 -2.9 0.0
""" % i)
def compute(self, observable, particle, cell):
# We use self.potential as lammps commands
dirout = tempfile.mkdtemp()
file_tmp = os.path.join(dirout, 'lammps.atom')
file_inp = os.path.join(dirout, 'lammps.atom.inp')
# Update lammps startup file using self.system
# This will write the .inp startup file
with TrajectoryLAMMPS(file_tmp, 'w') as th:
th.write(system.System(particle, cell), 0)
# Do things in lammps order: units, read, commands, run. A
# better approach would be to parse commands and place
# read_data after units then pack commands again. Even better
# using PyLammps...
cmd = """\
units lj
atom_style atomic
read_data {}
{}
run 0
write_dump all custom {} fx fy fz modify format line "%.15g %.15g %.15g"
""".format(file_inp, self.potential, file_tmp)
stdout = _run_lammps_command(cmd)
found = False
for line in stdout.split('\n'):
if 'Step' in line:
found = True
elif found:
if 'MPI' in line:
continue
_, T, U, _, _, P = [float(x) for x in line.split()]
rho = len(particle) / cell.volume
ndim = len(cell.side)
self.energy = U * len(particle)
self.virial = (P - rho * T) * ndim * cell.volume
break
with TrajectoryLAMMPS(file_tmp) as th:
new_system = th[-1]
self.forces = new_system.interaction.forces
# Clean up
rmd(dirout)
def _run_lammps_command(cmd):
"""Run a lammps script from the command line"""
dirout = tempfile.mkdtemp()
file_tmp = os.path.join(dirout, 'cmd.lammps')
with open(file_tmp, 'w') as fh:
fh.write(cmd)
opt = '-n {}'.format(lammps_mpi_tasks) if lammps_mpi else ''
shell_cmd = '{} {} {} -in {}'.format(lammps_mpi, opt, lammps_command,
file_tmp)
try:
stdout = subprocess.check_output(shell_cmd,
executable='/bin/bash',
stderr=subprocess.STDOUT,
shell=True)
except subprocess.CalledProcessError as exception:
print(''.join(exception.output))
raise
# Clean up
rmd(dirout)
return stdout.decode()
def tearDown(self):
rmf(self.inpfile)
rmd(self.inpdir)
def test_rmd(self):
utils.rmd(self.dirbase)
def tearDown(self):
rmd('/tmp/test_simulation')
def tearDown(self):
from atooms.core.utils import rmd
rmd('/tmp/test_xyz')
def close(self):
if self.archive:
rmd(self.dirname)
def tearDown(self):
from atooms.core.utils import rmf, rmd
rmf('/tmp/test_backends*')
rmd('/tmp/test_backends')
def run(self, steps):
dirout = tempfile.mkdtemp()
file_tmp = os.path.join(dirout, 'lammps.atom')
file_inp = os.path.join(dirout, 'lammps.atom.inp')
if self.restart:
file_res = os.path.join(self.tmpdir, 'lammps.restart')
# Update lammps startup file using self.system
# This will write the .inp startup file
with TrajectoryLAMMPS(file_tmp, 'w') as th:
th.write(self.system, 0)
# Set fixes from the system if we find thermostat / barostat
if self.system.thermostat is not None and self.system.barostat is not None:
# NPT ensemble
fix = 'fix 1 all npt temp {0.temperature} {0.temperature} {0.relaxation_time} iso {1.pressure} {1.pressure} {1.relaxation_time}'.format(
self.system.thermostat, self.system.barostat)
elif self.system.thermostat is not None:
# NVT ensemble
fix = 'fix 1 all nvt temp {0.temperature} {0.temperature} {0.relaxation_time}'.format(
self.system.thermostat)
elif not 'fix' in self.commands:
# NVE ensemble
fix = 'fix 1 all nve'
else:
# The integrator is already contained in the commands
fix = ''
# Do things in lammps order: units, read, commands, run. A
# better approach would be to parse commands and place
# read_data after units then pack commands again. Even better
# using PyLammps...
cmd = """\
units lj
atom_style atomic
"""
# Read restart file if it exists
if self.restart and os.path.exists(file_res):
cmd += """
read_restart {}
""".format(file_res)
else:
cmd += """
read_data {}
""".format(file_inp)
# Rest of commands
cmd += """
{commands}
{fix}
run {steps}
write_dump all custom {file_tmp} id type x y z vx vy vz modify sort id format line "%d %d %.15g %.15g %.15g %.15g %.15g %.15g"
""".format(commands=self.commands, fix=fix, steps=steps, file_tmp=file_tmp)
if self.restart:
cmd += """
write_restart {}
""".format(file_res)
# Execute LAMMPS command
stdout = _run_lammps_command(cmd)
if self.verbose:
print(stdout)
# Update internal reference to self.system
# Note that the thermostat and barostat are not touched
with TrajectoryLAMMPS(file_tmp) as th:
new_system = th[-1]
for i in range(len(self.system.particle)):
self.system.particle[i] = new_system.particle[i]
# Clean up
rmd(dirout)
def tearDown(self):
rmd('/tmp/test_lammps.d')
rmf('/tmp/test_lammps*')