def run(self, np=None, nanohub=None, save_input=True, prefix='mpiexec'):
"""pysimm.lmps.Simulation.run
Begin LAMMPS simulation.
Args:
np: number of threads to use (serial by default) default=None
nanohub: dictionary containing nanohub resource information default=None
init: True to write initialization part of LAMMPS input script (set to False if using complete custom input)
save_input: True to save input as pysimm.sim.in
prefix: prefix for running LAMMPS (i.e. - mpiexec)
"""
if isinstance(save_input, str):
with open(save_input, 'w') as f:
f.write(self.input)
elif save_input is True:
with open('pysimm.sim.in', 'w') as f:
f.write(self.input)
try:
call_lammps(self, np, nanohub, prefix=prefix)
except OSError:
raise PysimmError(
'There was a problem calling LAMMPS with {}'.format(prefix))
except IOError:
if check_lmps_exec():
raise PysimmError(
'There was a problem running LAMMPS. The process started but did not finish successfully. Check the log file, or rerun the simulation with debug=True to debug issue from LAMMPS output'
)
else:
raise PysimmError(
'There was a problem running LAMMPS. LAMMPS is not configured properly. Make sure the LAMMPS_EXEC environment variable is set to the correct LAMMPS executable path. The current path is set to:\n\n{}'
.format(LAMMPS_EXEC))
def __init__(self, fname):
if not pd:
raise PysimmError('pysimm.lmps.LogFile function requires pandas')
self.filename = fname
self.data = pd.DataFrame()
self._read(self.filename)
def write(self, sim=None):
"""pysimm.lmps.Init.write
Prepare LAMMPS input with initialization settings
Args:
sim: :class:`~pysimm.lmps.Simulation` object reference
Returns:
string of LAMMPS input
"""
if sim:
s = sim.system
else:
s = None
if self.forcefield is None and s and s.forcefield is not None:
if s.forcefield in ['gaff', 'gaff2']:
self.forcefield = 'amber'
elif s.forcefield in ['cgenff']:
self.forcefield = 'charmm'
else:
self.forcefield = s.forcefield
elif self.forcefield is None and sim and sim.forcefield is not None:
self.forcefield = sim.forcefield
if self.special_bonds is None and self.forcefield is not None:
self.special_bonds = FF_SETTINGS[self.forcefield]['special_bonds']
if self.forcefield is not None:
pair_modify = FF_SETTINGS[self.forcefield]['pair_modify']
if self.pair_modify:
pair_modify.update(self.pair_modify)
self.pair_modify = pair_modify
if self.charge is None and s is not None:
for p in s.particles:
if p.charge:
self.charge = True
break
if self.charge is None:
self.charge = False
lammps_input = ''
lammps_input += '\n' + '#' * 80 + '\n'
lammps_input += '#' * 34 + ' Init ' + '#' * 34 + '\n'
lammps_input += '#' * 80 + '\n'
lammps_input += '{:<15} {}\n'.format('units', self.units)
lammps_input += '{:<15} {}\n'.format('atom_style', self.atom_style)
if self.create_box and self.create_box.region and type(
self.create_box.region) is Region:
lammps_input += self.create_box.region.write(None)
lammps_input += self.create_box.write(None)
if self.pair_style:
lammps_input += '{:<15} {}'.format('pair_style', self.pair_style)
elif self.forcefield:
self.pair_style = FF_SETTINGS[self.forcefield]['pair_style']
lammps_input += '{:<15} {}'.format('pair_style', self.pair_style)
if self.charge:
lammps_input += '/coul/long'
self.pair_style += '/coul/long'
else:
raise PysimmError(
'A pair_style must be defined during initialization')
if self.cutoff:
if (self.forcefield == 'charmm') and self.cutoff.get('inner_lj'):
lammps_input += ' {} '.format(self.cutoff['inner_lj'])
lammps_input += ' {} '.format(self.cutoff['lj'])
if self.charge and self.cutoff.get('coul'):
lammps_input += ' {} '.format(self.cutoff['coul'])
lammps_input += '\n'
if self.charge:
lammps_input += '{:<15} {}\n'.format('kspace_style',
self.kspace_style)
if self.bond_style is None and s and s.bonds.count > 0:
if self.forcefield:
self.bond_style = FF_SETTINGS[self.forcefield]['bond_style']
if self.bond_style:
lammps_input += '{:<15} {}\n'.format('bond_style', self.bond_style)
if self.angle_style is None and s and s.angles.count > 0:
if self.forcefield:
self.angle_style = FF_SETTINGS[self.forcefield]['angle_style']
if self.angle_style:
lammps_input += '{:<15} {}\n'.format('angle_style',
self.angle_style)
if self.dihedral_style is None and s and s.dihedrals.count > 0:
if self.forcefield:
self.dihedral_style = FF_SETTINGS[
self.forcefield]['dihedral_style']
if self.dihedral_style:
lammps_input += '{:<15} {}\n'.format('dihedral_style',
self.dihedral_style)
if self.improper_style is None and s and s.impropers.count > 0:
if self.forcefield:
self.improper_style = FF_SETTINGS[
self.forcefield]['improper_style']
if self.improper_style:
lammps_input += '{:<15} {}\n'.format('improper_style',
self.improper_style)
if self.special_bonds:
lammps_input += '{:<15} {}\n'.format('special_bonds',
self.special_bonds)
if self.pair_modify:
lammps_input += '{:<15} '.format('pair_modify')
for k, v in self.pair_modify.items():
lammps_input += '{} {} '.format(k, v)
lammps_input += '\n'
if self.read_data:
lammps_input += '{:<15} {}\n'.format('read_data', self.read_data)
elif s:
s.write_lammps('temp.lmps')
lammps_input += '{:<15} temp.lmps\n'.format('read_data')
if self.pair_style and self.pair_style.startswith('buck'):
for pt1 in s.particle_types:
for pt2 in s.particle_types:
if pt1.tag <= pt2.tag:
a = pow(pt1.a * pt2.a, 0.5)
c = pow(pt1.c * pt2.c, 0.5)
rho = 0.5 * (pt1.rho + pt2.rho)
lammps_input += '{:<15} {} {} {} {} {}\n'.format(
'pair_coeff', pt1.tag, pt2.tag, a, rho, c)
lammps_input += '#' * 80 + '\n\n'
return lammps_input
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')