def lmps_min(s, name, settings):
"""pysimm.apps.polymatic.lmps_min
Runs LAMMPS minimization for the Polymatic algorithm.
Args:
s: :class:`~pysimm.system.System` to minimize
name: name of simulation
settings: object containing Polymatic settings
Returns:
result from :func:`~pysimm.lmps.minimize`
"""
if settings.polym.min.cluster:
nanohub = {
'cores': int(settings.polym.min.nanohub_cores),
'walltime': int(settings.polym.min.nanohub_walltime)
}
log_name = '%s' % '_'.join(name.split())
else:
nanohub = {}
log_name = 'logs/%s' % '_'.join(name.split())
if settings.polym.min.user_input:
lmps.run(s,
lammps_in=settings.polym.min.min_in,
name='initial optimization',
print_to_screen=False,
nanohub=nanohub)
else:
result = lmps.minimize(s,
name=name,
cutoff=settings.polym.min.nb_cutoff,
sd_etol=settings.polym.min.sd_etol,
sd_ftol=settings.polym.min.sd_ftol,
sd_maxiter=settings.polym.min.sd_maxiter,
sd_maxeval=settings.polym.min.sd_maxeval,
cg_etol=settings.polym.min.cg_etol,
cg_ftol=settings.polym.min.cg_ftol,
cg_maxiter=settings.polym.min.cg_maxiter,
cg_maxeval=settings.polym.min.cg_maxeval,
log=log_name,
np=settings.np,
nanohub=nanohub)
if settings.polym.min.cluster:
shutil.move(log_name, 'logs')
return result
def lmps_cycle_npt_md(s, bonds, settings):
"""pysimm.apps.polymatic.lmps_cycle_npt_md
Runs LAMMPS npt cycle md for the Polymatic algorithm.
Args:
s: :class:`~pysimm.system.System` to minimize
bonds: number of bond to be made
settings: object containing Polymatic settings
Returns:
result from lmps.md
"""
if settings.polym.cycle_npt.cluster:
nanohub = {
'cores': int(settings.polym.cycle_npt.nanohub_cores),
'walltime': int(settings.polym.cycle_npt.nanohub_walltime)
}
log_name = 'cycle_npt_%03d' % bonds
else:
nanohub = {}
log_name = 'logs/cycle_npt_%03d' % bonds
if settings.polym.cycle_npt.user_input:
lmps.run(s,
lammps_in=settings.polym.cycle_npt.step_in,
name='bond %d cycle npt' % bonds,
print_to_screen=False,
nanohub=nanohub)
else:
result = lmps.md(s,
name='bond %d cycle npt' % bonds,
ensemble='nvt',
cutoff=settings.polym.cycle_npt.nb_cutoff,
temp=settings.polym.cycle_npt.temp,
new_v=True,
pressure=settings.polym.cycle_npt.pressure,
length=settings.polym.cycle_npt.length,
log=log_name,
np=settings.np,
nanohub=nanohub)
if settings.polym.cycle_npt.cluster:
shutil.move(log_name, 'logs')
return result
def lmps_step_md(s, bonds, attempt, settings):
"""pysimm.apps.polymatic.lmps_step_md
Runs LAMMPS step md for the Polymatic algorithm.
Args:
s: :class:`~pysimm.system.System` to minimize
bonds: number of bond to be made
attempt: number of bonding attempt
settings: object containing Polymatic settings
Returns:
result from :func:`~pysimm.lmps.md`
"""
if settings.polym.step.cluster:
nanohub = {
'cores': int(settings.polym.step.nanohub_cores),
'walltime': int(settings.polym.step.nanohub_walltime)
}
log_name = 'step_%03d_%03d' % (bonds, attempt)
else:
nanohub = {}
log_name = 'logs/step_%03d_%03d' % (bonds, attempt)
if settings.polym.step.user_input:
lmps.run(s,
lammps_in=settings.polym.step.step_in,
name='bond %s attempt #%d' % (bonds + 1, attempt),
print_to_screen=False,
nanohub=nanohub)
else:
result = lmps.md(s,
name='bond %s: attempt #%d' % (bonds + 1, attempt),
ensemble='nvt',
cutoff=settings.polym.step.nb_cutoff,
temp=settings.polym.step.temp,
new_v=True,
length=settings.polym.step.length,
log=log_name,
np=settings.np,
nanohub=nanohub)
if settings.polym.step.cluster:
shutil.move(log_name, 'logs')
return result