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 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')