def __check_params__(self):
"""pysimm.cassandra.upd_simulation
Private method designed for update the fields of the GCMC object to make them conformed with each other
"""
# Synchronizing the simulation box parameters
if self.fxd_sst:
dx = self.fxd_sst.dim.xhi - self.fxd_sst.dim.xlo
dy = self.fxd_sst.dim.yhi - self.fxd_sst.dim.ylo
dz = self.fxd_sst.dim.zhi - self.fxd_sst.dim.zlo
if (dx == dy) and (dy == dz):
box_type = 'cubic'
box_dims = str(dx)
else:
box_type = 'orthogonal'
box_dims = '{0:} {1:} {2:}'.format(dx, dy, dz)
upd_vals = OrderedDict([('box_count', 1), ('box_type', box_type),
('box_size', box_dims)])
if ('Box_Info' in self.props.keys()) and isinstance(
self.props['Box_Info'], InpSpec):
self.props['Box_Info'] = InpSpec('Box_Info', upd_vals, None,
**{'new_line': True})
else:
self.props['Box_Info'] = upd_vals
tmp = self.props['Box_Info'].value['box_size']
if self.props['Box_Info'].value['box_type'] == 'cubic':
tmp = [tmp] * 3
self.tot_sst.dim = system.Dimension(center=True,
dx=float(tmp[0]),
dy=float(tmp[1]),
dz=float(tmp[2]))
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 setUp(self):
self.sst = system.read_pubchem_cid(6360)
self.sst.dim = system.Dimension(xlo=-10,
ylo=-10,
zlo=-10,
xhi=10,
yhi=10,
zhi=10)
self.sst.apply_forcefield(forcefield.Pcff(), charges='gasteiger')
self.fname_temp = 'testfile.output.{}'
self.fname = ''
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')
if p.bonds.count == 4:
p.type = o_3
else:
p.type = o_r
if p.elem == 'C':
p.type = c_r
if p.elem == 'Zn':
p.type = zn
if p.elem == 'H':
p.type = h_
f.assign_btypes(s)
f.assign_atypes(s)
f.assign_dtypes(s)
f.assign_itypes(s)
# Assign the calculation box size assuming it is cubic
cc_bnd_lngth = 1.363
dim = cc_bnd_lngth / 2 + max(df['x'].values) - min(df['x'].values)
s.dim = system.Dimension(dx=dim,
dy=dim,
dz=dim,
center=[dim / 2, dim / 2, dim / 2])
s.forcefield = 'dreiding-lj'
s.pair_style = 'lj'
s.bond_style = 'harmonic'
s.angle_style = 'harmonic'
s.dihedral_style = 'harmonic'
s.improper_style = 'harmonic'
s.write_lammps('irmof-14.lmps')
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')
