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:
sim = lmps.Simulation(s, name='initial optimization',
print_to_screen=False, nanohub=nanohub, custom=True)
sim.add(settings.polym.min.min_in)
sim.run(np=settings.np, nanohub=nanohub)
else:
sim = lmps.Simulation(s, name='initial optimization',
print_to_screen=False, nanohub=nanohub,
log=log_name
)
sim.add(lmps.Init(cutoff=settings.polym.min.nb_cutoff, forcefield=settings.forcefield))
sim.add_min(
min_style='sd',
etol=settings.polym.min.sd_etol,
ftol=settings.polym.min.sd_ftol,
maxiter=settings.polym.min.sd_maxiter,
maxeval=settings.polym.min.sd_maxeval,
)
sim.add_min(
min_style='cg',
etol=settings.polym.min.cg_etol,
ftol=settings.polym.min.cg_ftol,
maxiter=settings.polym.min.cg_maxiter,
maxeval=settings.polym.min.cg_maxeval,
)
sim.run(np=settings.np, nanohub=nanohub)
if settings.polym.min.cluster:
shutil.move(log_name, 'logs')
return True
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:
sim = lmps.Simulation(s, name='bond %d cycle npt' % bonds,
print_to_screen=False, nanohub=nanohub, custom=True)
sim.add(settings.polym.cycle_npt.step_in)
sim.run(np=settings.np, nanohub=nanohub)
else:
sim = lmps.Simulation(s, name='bond %d cycle npt' % bonds,
print_to_screen=False, nanohub=nanohub,
log=log_name
)
sim.add(lmps.Init(cutoff=settings.polym.cycle_npt.nb_cutoff, forcefield=settings.forcefield))
sim.add(lmps.Velocity(temperature=settings.polym.cycle_npt.temp))
sim.add_md(
ensemble='npt', temperature=settings.polym.cycle_npt.nb_cutoff,
run=settings.polym.cycle_npt.length,
pressure=settings.polym.cycle_npt.pressure,
)
sim.run(np=settings.np, nanohub=nanohub)
if settings.polym.cycle_npt.cluster:
shutil.move(log_name, 'logs')
return True
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:
sim = lmps.Simulation(s, name='bond %s attempt #%d' % (bonds + 1, attempt),
print_to_screen=False, nanohub=nanohub, custom=True)
sim.add(settings.polym.step.step_in)
sim.run(np=settings.np, nanohub=nanohub)
else:
sim = lmps.Simulation(s, name='bond %s: attempt #%d' % (bonds + 1, attempt),
print_to_screen=False, nanohub=nanohub,
log=log_name
)
sim.add(lmps.Init(cutoff=settings.polym.step.nb_cutoff, forcefield=settings.forcefield))
sim.add(lmps.Velocity(temperature=settings.polym.step.temp))
sim.add_md(
ensemble='nvt', temperature=settings.polym.step.temp,
run=settings.polym.step.length,
)
sim.run(np=settings.np, nanohub=nanohub)
if settings.polym.step.cluster:
shutil.move(log_name, 'logs')
return True
def monomer(ff, is_capped=False):
try:
s = system.read_pubchem_smiles('CCc1=cc=cc=c1')
except:
import os
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'topologies', 'CCc1=cc=cc=c1.mol'))
for b in s.bonds:
if b.a.bonds.count == 3 and b.b.bonds.count == 3:
b.order = 4
c1 = s.particles[1]
c5 = s.particles[5]
c1.linker = 'head'
c5.linker = 'tail'
if not is_capped:
for b in c1.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c1 else b.b
s.particles.remove(pb.tag, update=False)
break
for b in c5.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c5 else b.b
s.particles.remove(pb.tag, update=False)
break
s.remove_spare_bonding()
s.apply_forcefield(ff, charges='gasteiger')
s.set_box(padding=10)
sim = lmps.Simulation(s, print_to_screen=False, log='ps_mon_relax.log')
sim.add(lmps.Init())
sim.add_min(min_style='fire')
sim.run()
s.add_particle_bonding()
return s
pim1_ld.dim.dz = ld_box_size
for idx in range(10):
tmp = chains[idx].copy()
tmp.shift_particles(*displ[2 * idx])
pim1_ld.add(tmp, change_dim=False)
pim1_ld.wrap()
pim1_ld.set_density()
print('Density of the system is: {:} g/cc'.format(pim1_ld.density))
# pim1_ld = system.replicate(new_chains, [1] * len(new_chains), density=0.05, rand=False)
mimi = lmps.Simulation(pim1_ld, print_to_screen=False, log='mimimization.log')
mimi.add(
lmps.Init(cutoff=14.0,
special_bonds='amber',
pair_modify={'mix': 'arithmetic'}))
mimi.add_min(min_style='sd',
eol=1e-5,
ftol=1e-5,
maxiter=int(1e+5),
maxeval=int(1e+6))
mimi.add_min(min_style='cg',
eol=1e-5,
ftol=1e-5,
maxiter=int(1e+5),
maxeval=int(1e+6))
mimi.run(np=6)
pim1_ld.write_lammps('pim1.smpl1.rndwlk.lmps')
def mc_md(gas_sst,
fixed_sst=None,
mcmd_niter=None,
sim_folder=None,
mc_props=None,
md_props=None,
**kwargs):
"""pysimm.apps.mc_md
Performs the iterative hybrid Monte-Carlo/Molecular Dynamics (MC/MD) simulations using :class:`~pysimm.lmps` for
MD and :class:`~pysimm.cassandra` for MC
Args:
gas_sst (list of :class:`~pysimm.system.System`) : list items describe a different molecule to be
inserted by MC
fixed_sst (:class:`~pysimm.system.System`) : fixed during th MC steps group of atoms (default: None)
Keyword Args:
mcmd_niter (int) : number of MC-MD iterations (default: 10)
sim_folder (str): relative path to the folder with all simulation files (default: 'results')
mc_props (dictionary) : description of all MC properties needed for simulations (see
:class:`~pysimm.cassandra.GCMC` and :class:`~pysimm.cassandra.GCMC.props` for details)
md_props (dictionary): description of all Molecular Dynamics settings needed for simulations (see
:class:`~pysimm.lmps.Simulation` and :class:`~pysimm.lmps.MolecularDynamics` for details)
Returns:
:class:`~pysimm.system.System`:
Final state of the simulated system
"""
nonrig_group_name = 'nonrigid_b'
rig_group_name = 'rigid_b'
n_iter = mcmd_niter or 10
sim_folder = sim_folder or 'results'
xyz_fname = os.path.join(sim_folder, 'MD{:}_out.xyz')
l = 1
# Creating fixed polymer system
fs = None
if fixed_sst:
if isinstance(fixed_sst, system.System):
fs = fixed_sst
fs.wrap()
else:
print(
'Cannot setup the fixed system for the simulations. Skipping this'
)
# Set the one-molecule gas systems
gases = []
if gas_sst:
if isinstance(gas_sst, system.System):
gases = [gas_sst]
elif isinstance(gas_sst, types.ListType):
for g in cassandra.make_iterable(gas_sst):
if isinstance(g, system.System):
gases.append(g)
if not gases:
print(
'There are no gas molecules were specified correctely\nThe gas molecules are needed to start the '
'MC-MD simulations\nExiting...')
exit(1)
css = cassandra.Cassandra(fixed_sst)
# Set the Monte-Carlo properties:
mcp = mc_props
if mcp:
CHEM_POT = cassandra.make_iterable(mcp.get('Chemical_Potential_Info'))
if not CHEM_POT:
print('Missing chemical potential info\nExiting...')
exit(1)
else:
print('Missing the MC Simulation settings\nExiting...')
exit(1)
mcp['Start_Type'] = OrderedDict([('species', [1] + [0] * len(CHEM_POT))])
# Set the Molecular-Dynamics properties:
sim = None
mdp = md_props
if not mdp:
print('Missing the MD Simulation settings\nExiting...')
exit(1)
while l < n_iter + 1:
mcp['Run_Name'] = str(l) + '.gcmc'
css.add_gcmc(species=gases,
is_new=True,
chem_pot=CHEM_POT,
is_rigid=mcp.get('rigid_type') or [False] * len(gases),
out_folder=sim_folder,
props_file=str(l) + '.gcmc_props.inp',
**mcp)
css.run()
# >>> 2N: MD (LAMMPS) step:
sim_sst = css.system
sim_sst.write_lammps(
os.path.join(sim_folder,
str(l) + '.before_md.lmps'))
sim = lmps.Simulation(sim_sst,
debug=True,
log=os.path.join(sim_folder,
str(l) + '.md.log'))
sim.add(lmps.Init(cutoff=mdp.get('cutoff')))
# custom definitions for the neighbour list updates
sim.add_custom(
'neighbor 1.0 nsq \nneigh_modify once no every 1 delay 0 check yes'
)
# adding group definitions to separate rigid and non-rigid bodies
sim.add(
lmps.Group('matrix', 'id',
css.run_queue[0].group_by_id('matrix')[0]))
sim.add(
lmps.Group(nonrig_group_name, 'id',
css.run_queue[0].group_by_id('nonrigid')[0]))
rigid_mols = css.run_queue[0].group_by_id('rigid')[0]
if rigid_mols:
sim.add(lmps.Group(rig_group_name, 'id', rigid_mols))
# adding "run 0" line before velocities rescale for correct temperature init of the system with rigid molecules
sim.add(lmps.Velocity(style='create'))
if rigid_mols:
sim.add_custom('run 0')
sim.add(lmps.Velocity(style='scale'))
# create the description of the molecular dynamics simulation
sim.add_md(
lmps.MolecularDynamics(
name='main_fix',
group=nonrig_group_name if rigid_mols else 'all',
ensemble='npt',
timestep=mdp.get('timestep'),
temperature=mdp.get('temp'),
pressure=mdp.get('pressure'),
run=False,
extra_keywords={'dilate': 'all'} if rigid_mols else {}))
# create the second NVT fix for rigid molecules that cannot be put in NPT fix
if rigid_mols:
sim.add(
lmps.MolecularDynamics(name='rig_fix',
ensemble='rigid/nvt/small molecule',
timestep=mdp.get('timestep'),
length=mdp.get('length'),
group=rig_group_name,
temperature=mdp.get('temp'),
pressure=mdp.get('pressure'),
run=False))
# add the "spring tether" fix to the geometrical center of the system to avoid system creep
sim.add_custom(
'fix tether_fix matrix spring tether 30.0 0.0 0.0 0.0 0.0')
sim.add(
lmps.OutputSettings(thermo=mdp.get('thermo'),
dump={
'filename':
os.path.join(sim_folder,
str(l) + '.md.dump'),
'freq':
int(mdp.get('dump'))
}))
sim.add_custom('run {:}\n'.format(mdp.get('length')))
# The input for correct simulations is set, starting LAMMPS:
sim.run(np=mdp.get('np', 1))
# Updating the size of the fixed system from the MD simulations and saving the coordinates for the next MC
css.system.dim = sim.system.dim
sim.system.write_xyz(xyz_fname.format(l))
mcp['Start_Type']['file_name'] = xyz_fname.format(l)
mcp['Start_Type']['species'] = [1] + [0] * len(CHEM_POT)
l += 1
return sim.system if sim else None
def mc_md(gas_sst, fixed_sst=None, mc_props=None, md_props=None, **kwargs):
"""pysimm.apps.mc_md
Performs the iterative hybrid Monte-Carlo/Molecular Dynamics (MC/MD) simulations using :class:`~pysimm.lmps` for
MD and :class:`~pysimm.cassandra` for MC
Args:
gas_sst (list of :class:`~pysimm.system.System`) : list items describe a different molecule to be
inserted by MC
fixed_sst (:class:`~pysimm.system.System`) : fixed during th MC steps group of atoms (default: None)
Keyword Args:
mcmd_niter (int) : number of MC-MD iterations (default: 10)
sim_folder (str): relative path to the folder with all simulation files (default: 'results')
mc_props (dictionary) : description of all MC properties needed for simulations (see
:class:`~pysimm.cassandra.GCMC` and :class:`~pysimm.cassandra.GCMC.props` for details)
md_props (dictionary): description of all Molecular Dynamics settings needed for simulations (see
:class:`~pysimm.lmps.Simulation` and :class:`~pysimm.lmps.MolecularDynamics` for details)
Returns:
:class:`~pysimm.system.System`:
Final state of the simulated system
"""
nonrig_group_name = 'nonrigid_b'
rig_group_name = 'rigid_b'
n_iter = kwargs.get('mcmd_niter', 10)
sim_folder = kwargs.get('sim_folder', 'results')
xyz_fname = os.path.join(sim_folder, '{:}.md_out.xyz')
lmps_fname = os.path.join(sim_folder, '{:}.before_md.lmps')
# Define whether the simulations should be continued or start from the scratch
l = 1
is_restart = kwargs.get('restart')
if is_restart:
for f in glob.glob(lmps_fname.format('*')):
l = max(l, int(re.match('\A\d+', os.path.split(f)[1]).group()))
to_purge = glob.glob(os.path.join(sim_folder, '{:}.*'.format(l + 1))) + \
glob.glob(os.path.join(sim_folder, '{:}.md*'.format(l)))
for f in to_purge:
os.remove(f)
# Creating fixed polymer system
fs = None
if fixed_sst:
if isinstance(fixed_sst, system.System):
fs = fixed_sst
fs.wrap()
else:
print('Cannot setup the fixed system for the simulations. Skipping this')
# Set the one-molecule gas systems
gases = []
if gas_sst:
if isinstance(gas_sst, system.System):
gases = [gas_sst]
elif isinstance(gas_sst, types.ListType):
for g in cassandra.make_iterable(gas_sst):
if isinstance(g, system.System):
gases.append(g)
if not gases:
print('There are no gas molecules were specified correctely\nThe gas molecules are needed to start the '
'MC-MD simulations\nExiting...')
exit(1)
css = cassandra.Cassandra(fixed_sst)
# Set the Monte-Carlo properties:
mcp = mc_props
if mcp:
CHEM_POT = cassandra.make_iterable(mcp.get('Chemical_Potential_Info'))
if not CHEM_POT:
print('Missing chemical potential info\nExiting...')
exit(1)
else:
print('Missing the MC Simulation settings\nExiting...')
exit(1)
mcp['Start_Type'] = OrderedDict([('species', [1] + [0] * len(CHEM_POT))])
# Set the Molecular-Dynamics properties:
sim = None
mdp = md_props
if not mdp:
print('Missing the MD Simulation settings\nExiting...')
exit(1)
# De-synchronizing type names of the framework and the gases to avoid consolidation of types that PySIMM system does
for gi, g in enumerate(gases):
for pt in g.particle_types:
pt.name += '_g' + str(gi + 1)
while l < n_iter + 1:
# >>> MC (CASSANDRA) step:
mcp['Run_Name'] = str(l) + '.gcmc'
css.add_gcmc(species=gases, is_new=True, chem_pot=CHEM_POT,
is_rigid=mcp.get('rigid_type') or [False] * len(gases),
out_folder=sim_folder, props_file=str(l) + '.gcmc_props.inp', **mcp)
if is_restart:
# Set gas particles positions from the .chk file, and update some properties
css.run_queue[-1].upd_simulation()
css.system = css.run_queue[-1].tot_sst.copy()
# Set frame particles position and box size dimension from the .lmps file
tmp_sst = system.read_lammps(lmps_fname.format(l))
for p in css.system.particles:
p.x = tmp_sst.particles[p.tag].x
p.y = tmp_sst.particles[p.tag].y
p.z = tmp_sst.particles[p.tag].z
css.system.dim = tmp_sst.dim
is_restart = False
else:
css.run()
css.system.write_lammps(lmps_fname.format(l))
nm_treads = '1'
if 'OMP_NUM_THREADS' in os.environ.keys():
nm_treads = os.environ['OMP_NUM_THREADS']
os.environ['OMP_NUM_THREADS'] = '1'
# >>> MD (LAMMPS) step:
sim_sst = css.system.copy()
sim_sst.write_lammps(os.path.join(sim_folder, str(l) + '.before_md.lmps'))
sim = lmps.Simulation(sim_sst, print_to_screen=mdp.get('print_to_screen', False),
log=os.path.join(sim_folder, str(l) + '.md.log'))
sim.add(lmps.Init(cutoff=mdp.get('cutoff'),
special_bonds=mdp.get('special_bonds'),
pair_modify=mdp.get('pair_modify')))
# custom definitions for the neighbour list updates
sim.add_custom('neighbor 1.0 nsq \nneigh_modify once no every 1 delay 0 check yes')
# adding group definitions to separate rigid and non-rigid bodies
sim.add(lmps.Group('matrix', 'id', css.run_queue[0].group_by_id('matrix')[0]))
sim.add(lmps.Group(nonrig_group_name, 'id', css.run_queue[0].group_by_id('nonrigid')[0]))
rigid_mols = css.run_queue[0].group_by_id('rigid')[0]
if rigid_mols:
sim.add(lmps.Group(rig_group_name, 'id', rigid_mols))
# create the description of the molecular dynamics simulation
if type(mdp.get('timestep')) == list:
sim.add(lmps.OutputSettings(thermo=mdp.get('thermo'),
dump={'filename': os.path.join(sim_folder, str(l) + '.md.dump'),
'freq': int(mdp.get('dump'))}))
for it, (t, lng) in enumerate(zip(mdp.get('timestep'), mdp.get('length'))):
sim.add(lmps.Velocity(style='create'))
# adding "run 0" line before velocities rescale for correct temperature init of the
# system with rigid molecules
if rigid_mols:
sim.add_custom('run 0')
sim.add(lmps.Velocity(style='scale'))
sim.add_md(lmps.MolecularDynamics(name='main_fix_{}'.format(it),
group=nonrig_group_name if rigid_mols else 'all',
ensemble='npt',
timestep=t,
temperature=mdp.get('temp'),
pressure=mdp.get('pressure'),
run=False,
extra_keywords={'dilate': 'all'} if rigid_mols else {}))
# create the second NVT fix for rigid molecules that cannot be put in NPT fix
if rigid_mols:
sim.add(lmps.MolecularDynamics(name='rig_fix_{}'.format(it),
ensemble='rigid/nvt/small molecule',
timestep=t,
length=mdp.get('length'),
group=rig_group_name,
temperature=mdp.get('temp'),
pressure=mdp.get('pressure'),
run=False))
sim.add_custom('fix tether_fix_{} matrix spring tether 30.0 0.0 0.0 0.0 0.0'.format(it))
sim.add_custom('run {:}\n'.format(lng))
sim.add_custom('unfix main_fix_{:}'.format(it))
sim.add_custom('unfix rig_fix_{:}'.format(it))
sim.add_custom('unfix tether_fix_{:}'.format(it))
else:
sim.add_md(lmps.MolecularDynamics(name='main_fix',
group=nonrig_group_name if rigid_mols else 'all',
ensemble='npt',
timestep=mdp.get('timestep'),
temperature=mdp.get('temp'),
pressure=mdp.get('pressure'),
run=False,
extra_keywords={'dilate': 'all'} if rigid_mols else {}))
# create the second NVT fix for rigid molecules that cannot be put in NPT fix
if rigid_mols:
sim.add(lmps.MolecularDynamics(name='rig_fix',
ensemble='rigid/nvt/small molecule',
timestep=mdp.get('timestep'),
length=mdp.get('length'),
group=rig_group_name,
temperature=mdp.get('temp'),
pressure=mdp.get('pressure'),
run=False))
# add the "spring tether" fix to the geometrical center of the system to avoid system creep
sim.add_custom('fix tether_fix matrix spring tether 30.0 0.0 0.0 0.0 0.0')
sim.add(lmps.OutputSettings(thermo=mdp.get('thermo'),
dump={'filename': os.path.join(sim_folder, str(l) + '.md.dump'),
'freq': int(mdp.get('dump'))}))
sim.add_custom('run {:}\n'.format(mdp.get('length')))
# The input for correct simulations is set, starting LAMMPS:
sim.run(prefix=[''])
os.environ['OMP_NUM_THREADS'] = nm_treads
# Updating the size of the fixed system from the MD simulations and saving the coordinates for the next MC
# css.system.dim = sim.system.dim
css.system = sim.system.copy()
css.unwrap_gas()
css.system.write_xyz(xyz_fname.format(l))
mcp['Start_Type']['file_name'] = xyz_fname.format(l)
mcp['Start_Type']['species'] = [1] + css.run_queue[-1].mc_sst.made_ins
l += 1
return sim.system if sim else None
