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 make_system(self, text_output):
sstm = system.System(ff_class='1')
count = 0 # counter of the lines in the input file
sys_idx = 0 # counter of the gas molecules to lookup
while count < len(text_output) - 1:
tmp = self.sst[sys_idx].copy()
dictn = text_output[count:(len(tmp.particles) + count)]
if self.__fit_atoms__(tmp, dictn):
for p in tmp.particles:
vals = dictn[p.tag - 1].split()
# Read the coordinates from the text output of the CASSANDRA simulation
p.x, p.y, p.z = map(float, vals[1:4])
# Force velocities of the particles to be 0
p.vx, p.vy, p.vz = 0.0, 0.0, 0.0
p.molecule.syst_tag = 0
if self.is_rigid[sys_idx]:
for p in tmp.particles:
p.is_rigid = True
sstm.add(tmp)
self.made_ins[sys_idx] += 1
count += len(tmp.particles)
sys_idx = 0
else:
sys_idx += 1
if sys_idx >= len(self.sst):
self.logger.error(
'Wasn\'t able to read CASSANDRA .chk file. '
'Please check either MC-simulation provided to PySIMM or the CASSANDRA '
'checkpoint file ')
exit(1)
sstm.update_tags()
sstm.objectify()
return sstm
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 Cl():
s = system.System()
m = s.molecules.add(system.Molecule())
f = forcefield.Dreiding()
dreiding_Na_ = s.particle_types.add(f.particle_types.get('Cl')[0].copy())
s.particles.add(system.Particle(type=dreiding_Na_, x=0, y=0, z=0, charge=-1, molecule=m))
s.apply_forcefield(f)
s.pair_style = 'lj/cut'
lmps.quick_min(s, min_style='fire')
return s
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')
from pysimm import system, lmps, forcefield
# create empty system
s = system.System()
# create new molecule in our system
m = s.molecules.add(system.Molecule())
# retrieve GAFF2 parameters
f = forcefield.Gaff2()
# get a copy of the c3 particle type object from GAFF
# get method returns a list, we need the first element
gaff_c3 = s.particle_types.add(f.particle_types.get('c3')[0].copy())
# we'll first make the carbon atom at the origin
# we'll include gasteiger charges later
c1 = s.particles.add(
system.Particle(type=gaff_c3, x=0, y=0, z=0, charge=0, molecule=m))
# get hc particle type object from GAFF
gaff_hc = f.particle_types.get('hc')[0].copy()
# add hc particle type to system
s.particle_types.add(gaff_hc)
# now we'll add 4 hydrogen atoms bonded to our carbon atom
# these atoms will be placed randomly 1.5 angstroms from the carbon atom
# we'll optimize the structure using LAMMPS afterwords
# we supply the GAFF forcefield object so that bond and angle types can be added as well
h1 = s.add_particle_bonded_to(
unwrap=True,
settings={
'np': 6,
'length': 25000,
'min_style': 'cg',
'etol': 1e-5,
'ftol': 1e-5,
'maxiter': int(1e+7),
'maxeval': int(1e+7)
})
chains.append(sngl_chain)
# remove litter
os.remove('polymer.xyz')
os.remove('polymer.lmps')
pim1_ld = system.System()
for prp in [
'ff_class', 'forcefield', 'pair_style', 'bond_style', 'angle_style',
'dihedral_style', 'improper_style'
]:
setattr(pim1_ld, prp, getattr(mono, prp))
pim1_ld.dim.dx = ld_box_size
pim1_ld.dim.dy = ld_box_size
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)
def run(test=False):
# create empty system
print('Example progress: Creating an empty system...')
s = system.System()
# create new molecule in our system
print(
'Example progress: Adding an empty molecule container to our system...'
)
m = s.molecules.add(system.Molecule())
# retrieve GAFF2 parameters
print('Example progress: Retrieving Dreiding force field parameters...')
f = forcefield.Gaff2()
s.forcefield = f.name
# get a copy of the c3 particle type object from GAFF
# get method returns a list, we need the first element
gaff_c3 = s.particle_types.add(f.particle_types.get('c3')[0].copy())
# get hc particle type object from GAFF
gaff_hc = s.particle_types.add(f.particle_types.get('hc')[0].copy())
# we'll first make the carbon atom at the origin
# we'll include gasteiger charges later
print('Example progress: Adding carbon atom at origin...')
c1 = s.particles.add(
system.Particle(type=gaff_c3, x=0, y=0, z=0, charge=0, molecule=m))
# now we'll add 4 hydrogen atoms bonded to our carbon atom
# these atoms will be placed randomly 1.5 angstroms from the carbon atom
# we'll optimize the structure using LAMMPS afterwords
# we supply the GAFF forcefield object so that bond and angle types can be added as well
print(
'Example progress: Adding 4 hydrogen atoms at random positions bonded to the carbon atom...'
)
h1 = s.add_particle_bonded_to(
system.Particle(type=gaff_hc, charge=0, molecule=m), c1, f)
h2 = s.add_particle_bonded_to(
system.Particle(type=gaff_hc, charge=0, molecule=m), c1, f)
h3 = s.add_particle_bonded_to(
system.Particle(type=gaff_hc, charge=0, molecule=m), c1, f)
h4 = s.add_particle_bonded_to(
system.Particle(type=gaff_hc, charge=0, molecule=m), c1, f)
# let's add gasteiger charges
print('Example progress: Deriving Gasteiger charges...')
s.apply_charges(f, charges='gasteiger')
# right now there is no simulation box defined
# we'll define a box surrounding our methane molecule with a 10 angstrom padding
print(
'Example progress: Constructing Simulation box surrounding our new molecule...'
)
s.set_box(padding=10)
# before we optimize our structure, LAMMPS needs to know what type of
# pair, bond, and angle interactions we are using
# these are determined by the forcefield being used
s.pair_style = 'lj'
s.bond_style = 'harmonic'
s.angle_style = 'harmonic'
# we'll perform energy minimization using the fire algorithm in LAMMPS
print('Example progress: Optimizing structure using LAMMPS...')
lmps.quick_min(s,
min_style='fire',
name='fire_min',
etol=1e-10,
ftol=1e-10)
# write xyz, YAML, LAMMPS data, and chemdoodle json files
print('Example progress: Saving structure to files...')
s.write_xyz('methane.xyz')
s.write_yaml('methane.yaml')
s.write_lammps('methane.lmps')
s.write_chemdoodle_json('methane.json')
print('Example progress: Complete!')
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')
