def test_gas_unwrap(self):
# Read molecular system from the file and decorate the frame with fixed property
test_sst = system.read_lammps(osp.join(self.data_path, 'wrapped_co2.lmps'))
css = cassandra.Cassandra(test_sst)
for p in css.system.particles:
p.is_fixed = False
# Assert that gas molecules are wrapped
bnd_lng = []
for p in test_sst.particles:
if p.type.name == 'C':
for i in [1, 2]:
bnd_lng.append(
(css.system.particles[p.tag].x - css.system.particles[p.tag + i].x) ** 2 +
(css.system.particles[p.tag].y - css.system.particles[p.tag + i].y) ** 2 +
(css.system.particles[p.tag].z - css.system.particles[p.tag + i].z) ** 2)
self.assertFalse(all([(1.344 < el) and (el < 1.346) for el in bnd_lng]))
css.unwrap_gas()
# Assert that gas molecules are unwrapped
bnd_lng = []
for p in test_sst.particles:
if p.type.name == 'C':
for i in [1, 2]:
bnd_lng.append(
(css.system.particles[p.tag].x - css.system.particles[p.tag + i].x) ** 2 +
(css.system.particles[p.tag].y - css.system.particles[p.tag + i].y) ** 2 +
(css.system.particles[p.tag].z - css.system.particles[p.tag + i].z) ** 2)
self.assertTrue(all([(1.344 < el) and (el < 1.346) for el in bnd_lng]))
def run(test=False):
# Setup the empty cubic box with
bx_size = 60
sst = system.System()
sst.dim = system.Dimension(dx=bx_size,
dy=bx_size,
dz=bx_size,
center=[bx_size / 2, bx_size / 2, bx_size / 2])
sst.forcefield = 'trappe/amber'
molec = system.read_lammps('c2h4.lmps')
molec.forcefield = 'trappe/amber'
cs = cassandra.Cassandra(sst)
npt_props = cs.read_input('props.inp')
npt_props['Pressure_Info'] = 25 # Simulated pressure in bars
npt_props['Start_Type'] = {'start_type': 'make_config', 'species': 300}
npt_props['Run_Type'] = {'type': 'equilibration', 'steps': [1000, 100]}
npt_props['Simulation_Length_Info'] = {'run': 10000}
npt_props['Property_Info'] = {
'prop1': 'energy_total',
'prop2': 'volume',
'prop3': 'mass_density'
}
cs.add_simulation('NPT',
species=molec,
is_rigid=True,
out_folder='results',
**npt_props)
cs.run()
lmps.check_lmps_attr(cs.system)
cs.system.write_lammps('final_conf.lmps')
def run(test=False):
# Setup the box with acetelene molecules on the regular grid
sst = system.System()
bx_size = 30
sst.dim = system.Dimension(dx=bx_size,
dy=bx_size,
dz=bx_size,
center=[bx_size / 2, bx_size / 2, bx_size / 2])
sst.forcefield = 'trappe/amber'
molec = system.read_lammps('c2h4.lmps')
molec.forcefield = 'trappe/amber'
cs = cassandra.Cassandra(sst)
nvt_props = cs.read_input('props.inp')
nvt_props['Temperature_Info'] = 400
nvt_props['Start_Type'] = {'start_type': 'make_config', 'species': 300}
nvt_props['Simulation_Length_Info'] = {'run': 300000}
nvt_props['Property_Info'] = {
'prop1': 'energy_total',
'prop2': 'pressure',
'prop3': 'mass_density'
}
cs.add_nvt(species=molec, is_rigid=True, out_folder='results', **nvt_props)
cs.run()
lmps.check_lmps_attr(cs.system)
cs.system.write_lammps('final_conf.lmps')
def test_nonames_mc(self):
sst = system.System()
sst.dim = system.Dimension(dx=40, dy=40, dz=40, center=[0, 0, 0])
sst.forcefield = 'trappe/amber'
css = cassandra.Cassandra(sst)
my_gcmc_props = css.read_input(osp.join(self.data_path, 'props.inp'))
specie = system.read_lammps(osp.join(self.data_path, 'toluene_nonames.lmps'))
specie.forcefield = 'trappe/amber'
with pytest.raises(SystemExit) as err_back:
css.add_gcmc(species=specie, is_rigid=True, max_ins=200,
chem_pot=-30.34, out_folder=self.data_path, **my_gcmc_props)
assert err_back.type == SystemExit
def run(test=False):
# In order to run CASSANDRA GCMC one need to create the CASSANDRA object
sst = system.System()
sst.dim = system.Dimension(dx=40, dy=40, dz=45, center=[0, 0, 0])
sst.forcefield = 'trappe/amber'
lmps.check_lmps_attr(sst)
css = cassandra.Cassandra(sst)
# Read the CASSANDRA .inp parameters file -- common way to setup simulations.
# Any of the read properties can be modified here afterwards
my_gcmc_props = css.read_input('props.inp')
# The prefix for the all files that will be created by this run
my_gcmc_props['Run_Name'] = 'gas_adsorb'
# Set the gas (gas system) to be purged in a box
specie1 = system.read_lammps('co2.lmps')
specie2 = system.read_lammps('ch4.lmps')
specie3 = system.read_lammps('m-xylene.lmps')
for s in [specie1, specie2, specie3]:
s.forcefield = 'trappe/amber'
css.add_gcmc(species=[specie1, specie2, specie3],
is_rigid=[True, False, True],
max_ins=[2000, 1000, 500],
chem_pot=[-27.34, -29.34, -24.59],
out_folder='gas_adsorb_results',
**my_gcmc_props)
css.run()
for pt in css.system.particle_types:
pt.elem = pt.real_elem
css.system.write_lammps('gas_adsorb.lmps')
css.system.write_xyz('gas_adsorb.xyz')
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 run(test=False):
# Set to False if you **do not** want to recalculate pure gas adsorption isotherms
is_simulate_loadings = False
loadings_file = 'loadings.dat'
# Option to draw the isotherms: it is either **'ToFile'** or **'ToScreen'** (case insensitive).
# Any other value will be interpreted as no graphics
graphing = 'none'
# Gas names as they will be referred through simulations
gas_names = ['ch4', 'co2']
# Corresponding mole fractions of gases that will allow us to calculate their partial pressures through the Dalton's law
mol_frac = [0.5, 0.5]
# Calibrated previously functional forms of chemical potentials of gases for GCMC simulations as a functions of pressure
chem_pots = [
lambda x: 2.4153 * numpy.log(x) - 36.722,
lambda x: 2.40 * numpy.log(x) - 40.701
]
# Root directory for some data (For PySIMM examples it is )
data_dir = osp.join('..', '09_cassandra_simulations', 'gcmc')
# Setup of adsorbate model
gases = []
for gn in gas_names:
gases.append(system.read_lammps(osp.join(data_dir, gn + '.lmps')))
gases[-1].forcefield = 'trappe/amber'
# Setup of adsorbent model
frame = system.read_lammps('pim.lmps')
frame.forcefield = 'trappe/amber'
# Constant for loadings calculations
molec2mmols_g = 1e+3 / frame.mass
# Setup of the GCMC simulations
css = cassandra.Cassandra(frame)
sim_settings = css.read_input('run_props.inp')
# This function in given context will calculate the loading from short GCMC simulations
def calculate_isotherm_point(gas_name, press):
run_fldr = osp.join(gas_name, str(press))
idx = gas_names.index(gas_name)
# sim_settings.update({'Run_Name': 'gcmc'})
css.add_gcmc(species=gases[idx],
is_new=True,
chem_pot=chem_pots[idx](press),
out_folder=run_fldr,
props_file='gcmc.inp',
**sim_settings)
css.run()
full_prp = css.run_queue[0].get_prp()
return molec2mmols_g * numpy.average(
full_prp[3][int(len(2 * full_prp[3]) / 3):])
# This function in given context will load the pre-calculated loading value from previously done GCMC simulations
def load_isotherm_point(gas_name, press):
with open(loadings_file, 'r') as pntr:
stream = pntr.read()
tmp = stream.split('\n' + gas_name)[1]
idx = re.search('[a-zA-Z]|\Z', tmp)
value = re.findall('\n{:}\s+\d+\.\d+'.format(press),
tmp[:idx.start()])[0]
return float(re.split('\s+', value)[-1])
# Calculation of adsorption isotherms for pure CH4 and CO2 gases for further usage in IAST simulations.
# This is the **MOST TIME CONSUMING STEP** in this example, if you want to skip it switch the key is_simulated to False
# The IAST will be done using PyIAST package, thus isotherms are wrapped into the corresponding object
gas_press = [0.1, 1, 5, 10, 25, 50]
lk = 'Loading(mmol/g)'
pk = 'Pressure(bar)'
isotherms = []
loadings = dict.fromkeys(gas_names)
for gn in gas_names:
loadings[gn] = []
for p in gas_press:
if is_simulate_loadings:
data = calculate_isotherm_point(gn, p)
else:
data = load_isotherm_point(gn, p)
loadings[gn].append(data)
isotherms.append(
pyiast.ModelIsotherm(pandas.DataFrame(zip(gas_press, loadings[gn]),
columns=[pk, lk]),
loading_key=lk,
pressure_key=pk,
model='BET',
optimization_method='Powell'))
# The PyIAST run for calculating of mixed adsorption isotherm
# Initial guesses of adsorbed mole fractions do span broad range of values, because PyIAST might not find
# solution at certain values of mole fractions and through an exception
guesses = [[a, 1 - a] for a in numpy.linspace(0.01, 0.99, 50)]
for in_g in guesses:
mix_loadings = []
try:
for p in gas_press:
mix_loadings.append(
list(
pyiast.iast(p * numpy.array(mol_frac),
isotherms,
verboseflag=False,
adsorbed_mole_fraction_guess=in_g)))
mix_loadings = numpy.array(mix_loadings)
break
except:
print('Initial guess {:} had failed to converge'.format(in_g))
continue
mix_loadings = numpy.sum(mix_loadings, axis=1)
mix_isotherm = pyiast.ModelIsotherm(pandas.DataFrame(zip(
gas_press, mix_loadings),
columns=[pk, lk]),
loading_key=lk,
pressure_key=pk,
model='BET',
optimization_method='L-BFGS-B')
# Output: Graphing of constructed isotherms
def _plot_isotherms(ax, loc_gp, loc_isoth, loc_mix_load, loc_mix_isoth):
rng = numpy.linspace(min(loc_gp), max(loc_gp), 100)
ax.plot(loc_gp,
loadings[gas_names[0]],
'og',
lw=2.5,
label='{:} loadings'.format(gas_names[0].upper()))
ax.plot(rng, [loc_isoth[0].loading(t) for t in rng],
'--g',
lw=2,
label='BET fit of {:} loadings'.format(gas_names[0].upper()))
ax.plot(loc_gp,
loadings[gas_names[1]],
'or',
lw=2.5,
label='{:} loadings'.format(gas_names[1].upper()))
ax.plot(rng, [loc_isoth[1].loading(t) for t in rng],
'--r',
lw=2,
label='BET fit of {:} loadings'.format(gas_names[1].upper()))
ax.plot(loc_gp,
loc_mix_load,
'ob',
lw=2.5,
label='1-to-1 mixture loadings')
ax.plot(rng, [loc_mix_isoth.loading(t) for t in rng],
'--b',
lw=2,
label='BET fit of 1-to-1 mixture loadings')
ax.set_xlabel('Gas pressure [bar]', fontsize=20)
ax.set_ylabel('Loading [mmol / g]', fontsize=20)
ax.tick_params(axis='both', labelsize=16)
ax.grid(True)
ax.legend(fontsize=16)
mplp.tight_layout()
if graphing.lower() == 'tofile':
fig, axs = mplp.subplots(1, 1, figsize=(10, 5))
_plot_isotherms(axs, gas_press, isotherms, mix_loadings, mix_isotherm)
mplp.savefig('pim1_mix_adsorption.png', dpi=192)
elif graphing.lower() == 'toscreen':
mplp.figure()
axs = mplp.gca()
_plot_isotherms(axs, gas_press, isotherms, mix_loadings, mix_isotherm)
mplp.show()
with open('iast_loadings.dat', 'w') as pntr:
pntr.write('{:}\t\t{:}\n'.format(pk, lk))
pntr.write('{:}-{:} 1-to-1\n'.format(gas_names[0], gas_names[1]))
for p, ml in zip(gas_press, mix_loadings):
pntr.write('{:}\t\t{:}\n'.format(p, ml))
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
from pysimm import system, cassandra
from collections import OrderedDict
# In order to run CASSANDRA GCMC one need to create the CASSANDRA object
sst = system.System()
sst.dim = system.Dimension(dx=45, dy=45, dz=45, center=[0, 0, 0])
css = cassandra.Cassandra(sst)
# Read the CASSANDRA .inp parameters file -- common way to setup simulations.
# Any of the read properties can be modified here afterwards
my_gcmc_props = css.read_input('props.inp')
# The prefix for the all files that will be created by this run
my_gcmc_props['Run_Name'] = 'gas_adsorb'
# Set the gas (gas system) to be purged in a box
specie1 = system.read_lammps('co2.lmps')
specie2 = system.read_lammps('ch4.lmps')
specie3 = system.read_lammps('m-xylene.lmps')
css.add_gcmc(species=[specie1, specie2, specie3],
max_ins=[2000, 1000, 500],
chem_pot=[-27.34, -29.34, -24.59],
out_folder='gas_adsorb_results',
**my_gcmc_props)
css.run()
for pt in css.final_sst.particle_types:
pt.elem = pt.real_elem
css.final_sst.write_lammps('gas_adsorb.lmps')
# Setup of adsorbate model
gases = []
for gn in gas_names:
gases.append(system.read_lammps(osp.join(data_dir, gn + '.lmps')))
gases[-1].forcefield = 'trappe/amber'
# Setup of adsorbent model
frame = system.read_lammps('pim.lmps')
frame.forcefield = 'trappe/amber'
# Constant for loadings calculations
molec2mmols_g = 1e+3 / frame.mass
# Setup of the GCMC simulations
css = cassandra.Cassandra(frame)
sim_settings = css.read_input('run_props.inp')
# This function in given context will calculate the loading from short GCMC simulations
def calculate_isotherm_point(gas_name, press):
run_fldr = osp.join(gas_name, str(press))
idx = gas_names.index(gas_name)
# sim_settings.update({'Run_Name': 'gcmc'})
css.add_gcmc(species=gases[idx],
is_new=True,
chem_pot=chem_pots[idx](press),
out_folder=run_fldr,
props_file='gcmc.inp',
**sim_settings)
css.run()
def mc_md(gas_sst, fixed_sst=None, **kwargs):
"""pysimm.apps.mc_md
Performs the iterative hybrid Monte-Carlo/Molecular Dynamics (MC-MD) simulations using pysimm.lmps for MD and
pysimm.cassandra for MD
Args:
gas_sst: list of pysimm.system.System objects each of which describes a different molecule to be inserted by MC
fixed_sst: fixed during th MC steps group of atoms (default: None)
mcmd_niter: number of MC-MD iteradions (default: 10)
sim_folder: relative path to the folder with all simulation files (default: 'results')
mc_props: dictionary describing all MC properties needed for simulations (see pysimm.cassandra.GCMC and
pysimm.cassandra.GCMC.props for details)
md_props: dictionary containing all Molecular Dynamics settings needed for simulations (see
pysimm.lmps.Simulation and pysimm.lmps.MolecularDynamics for details)
"""
nonrig_group_name = 'nonrigid_b'
rig_group_name = 'rigid_b'
n_iter = kwargs.get('mcmd_niter') or 10
sim_folder = kwargs.get('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, str):
fs = system.read_lammps(fixed_sst)
fs.wrap()
elif 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 = []
for g in cassandra.make_iterable(gas_sst):
if isinstance(g, str):
try:
gases.append(system.read_lammps(g))
except IOError:
print('Cannot read file: {}\nExiting...'.format(g))
exit(1)
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 = kwargs.get('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:
mdp = kwargs.get('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.final_sst
sim_sst.write_lammps(os.path.join(sim_folder, str(l) + '.before_md.lmps'))
sim = lmps.Simulation(sim_sst,
log=os.path.join(sim_folder, str(l) + '.md.log'),
print_to_screen=mdp.get('print_to_screen'),
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
grp_tmpl = 'group {:} id {:}'
sim.add_custom(grp_tmpl.format('matrix', css.run_queue[0].group_by_id('matrix')[0]))
sim.add_custom(grp_tmpl.format(nonrig_group_name, 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_custom(grp_tmpl.format(rig_group_name, rigid_mols))
# create the description of the molecular dynamics simulation
tmp_md = lmps.MolecularDynamics(ensemble=mdp.get('ensemble'),
timestep=mdp.get('timestep'),
length=int(mdp.get('length')),
thermo=mdp.get('thermo'),
temp=mdp.get('temp'),
pressure=mdp.get('pressure'),
dump=int(mdp.get('dump')),
dump_name=os.path.join(sim_folder, str(l) + '.md.dump'),
scale_v=True)
# obtain the simulation (LAMMPS) input in order to customly modify it later
tmp_md.write(sim)
# replace single default fix with two separate fixes for rigid and nonrigid bodies separately
old_line = re.search('(?<=(\nfix)).*', tmp_md.input).group(0)
corr_fix = re.sub('all', nonrig_group_name, old_line)
if rigid_mols:
corr_fix += ' dilate all\n'
else:
corr_fix += '\n'
if rigid_mols:
corr_fix += 'fix' + re.sub('iso\s+\d+[.\d]*\s+\d+[.\d]*\s+\d+[.\d]*', '', old_line).\
replace('1', '2', 1). \
replace('all', rig_group_name). \
replace('npt', 'rigid/nvt/small molecule') + '\n'
# adding the spring fix to the geometrical center of the system to avoid system creep
corr_fix += 'fix {:} {:} spring tether {:} {:} {:} {:} {:}\n'.format(3, 'matrix', 30.0, 0.0, 0.0, 0.0, 0.0)
# saving all fixes to the input
tmp_md.input = tmp_md.input.replace(old_line, corr_fix)
# adding "run 0" line for correct temperature scaling of the system with rigid molecules
tmp_md.input = tmp_md.input.replace('velocity all scale',
'velocity all create {:} {:}\nrun 0\nvelocity all scale'
.format(mdp.get('temp'), random.randint(int(1e+5), int(1e+6) - 1)))
# The input for correct simulations is set, starting LAMMPS:
sim.add_custom(tmp_md.input)
sim.run(np=1)
# Updating the size of the fixed system from the MD simulations and saving the coordinates for the next MC
css.init_sst.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