def check_lmps_attr(s):
# sync of the forcefield-style properties
if hasattr(s, 'forcefield'):
styles_list = FF_SETTINGS['dreiding'].keys()
if s.forcefield in FF_SETTINGS.keys():
for st_prop in styles_list:
setattr(s, st_prop, FF_SETTINGS[s.forcefield][st_prop])
else:
warning_print('Cannot synchronize given forcefield with LAMMPS representation types. '
'The forcefield is not present in the FF_SETTINGS of the pysimm.lmps module')
else:
warning_print('The forcefield attribute of the system is not defined. Some i/o methods of lmps '
'module will not be acessible')
def call_lammps(simulation, np, nanohub, prefix='mpiexec'):
"""pysimm.lmps.call_lammps
Wrapper to call LAMMPS using executable name defined in pysimm.lmps module.
Args:
simulation: :class:`~pysimm.lmps.Simulation` object reference
np: number of threads to use
nanohub: dictionary containing nanohub resource information default=None
prefix: prefix for running LAMMPS (i.e. - mpiexec)
Returns:
None
"""
log_name = simulation.log or 'log.lammps'
if nanohub:
with open('temp.in', 'w') as f:
f.write(simulation.input)
if simulation.name:
print('%s: sending %s simulation to computer cluster at nanoHUB' %
(strftime('%H:%M:%S'), simulation.name))
else:
print('%s: sending simulation to computer cluster at nanoHUB' %
strftime('%H:%M:%S'))
sys.stdout.flush()
cmd = ('submit -n %s -w %s -i temp.lmps -i temp.in '
'lammps-09Dec14-parallel -e both -l none -i temp.in' %
(nanohub.get('cores'), nanohub.get('walltime')))
cmd = shlex.split(cmd)
exit_status, stdo, stde = RapptureExec(cmd)
else:
if simulation.name:
print('%s: starting %s LAMMPS simulation' %
(strftime('%H:%M:%S'), simulation.name))
else:
print('%s: starting LAMMPS simulation' % strftime('%H:%M:%S'))
if np:
p = Popen([prefix, '-np',
str(np), LAMMPS_EXEC, '-e', 'both'],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
else:
p = Popen([LAMMPS_EXEC, '-e', 'both'],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
simulation.write_input()
if simulation.debug:
print(simulation.input)
warning_print(
'debug setting involves streaming output from LAMMPS process and can degrade performance'
)
warning_print(
'only use debug for debugging purposes, use print_to_screen to collect stdout after process finishes'
)
p.stdin.write(simulation.input.encode('utf-8'))
q = Queue()
t = Thread(target=enqueue_output, args=(p.stdout, q))
t.daemon = True
t.start()
while t.is_alive() or not q.empty():
try:
line = q.get_nowait()
except Empty:
pass
else:
if simulation.debug:
sys.stdout.write(line.decode('utf-8'))
sys.stdout.flush()
else:
stdo, stde = p.communicate(simulation.input.encode('utf-8'))
if simulation.print_to_screen:
print(stdo.decode('utf-8'))
print(stde.decode('utf-8'))
simulation.system.read_lammps_dump('pysimm.dump.tmp')
try:
os.remove('temp.lmps')
except OSError as e:
print(str(e))
if os.path.isfile('pysimm.qeq.tmp'):
os.remove('pysimm.qeq.tmp')
try:
os.remove('pysimm.dump.tmp')
if simulation.name:
print('%s: %s simulation using LAMMPS successful' %
(strftime('%H:%M:%S'), simulation.name))
else:
print('%s: simulation using LAMMPS successful' %
(strftime('%H:%M:%S')))
except OSError as e:
if simulation.name:
raise PysimmError('%s simulation using LAMMPS UNsuccessful' %
simulation.name)
else:
raise PysimmError('simulation using LAMMPS UNsuccessful')