def run(test=False):
logFileName = 'steps.log'
# use an import from .yaml to get of previously created pmma-based 4-chain polymer structure
polymer = system.read_yaml(os.path.join(os.path.dirname(os.path.realpath(__file__)), "polymer.yaml"))
polymer.forcefield = 'dreiding'
# Initialize the wrapper object around the polymer that will organize the work with LAMMPS
print('Creating Simulation object with log-file in "{0:s}"\n'.format(logFileName))
sim = lmps.Simulation(polymer, log= 'steps.log')
# setting up the parameters for the energy optimization
# add_min() method will add the "Minimization" task to the task que of the
# Simulation object that is stored in sim.sim list
print('Creating and running energy-minimization task:')
sim.add_min(min_style = 'fire', name = 'min_fire', etol = 1.0e-5, ftol = 1.0e-5)
print('Creating and running molecular dynamics task:')
# Let's set up the Molecular dynamics task
sim.add_md(ensemble='nvt', timestep=0.5)
print('List of simulation tasks ready to run:')
print(sim.sim)
print('Input that will be passed to LAMMPS when the simulation is performed:')
sim.write_input()
print(sim.input)
# call run to run the simulation
sim.run()
def run(test=False):
# we'll create a pe monomer from the pysimm.models database
pe = monomer()
# we'll instantiate a Dreiding forcefield object for use later
f = forcefield.Dreiding()
# the monomers do not have any charges, so we will derive partial charges using the gasteiger algorithm
pe.apply_charges(f, charges='gasteiger')
# run the random_walk polymerization method making a chain of 10 repeat units
# the forcefield object is supplied to get new forcefield types not in the monomer system
polymer = random_walk(pe, 10, forcefield=f)
# write a few different file formats
polymer.write_xyz('polymer.xyz')
polymer.write_yaml('polymer.yaml')
polymer.write_lammps('polymer.lmps')
polymer.write_chemdoodle_json('polymer.json')
# if you want to restart a polymerization, the yaml file format retains linker information
# random_walk looks for the last head and tail linkers, so just run a copolymerization with the original polymer chain and new monomers
# we give the copolymer function a list of reference "monomers", but use the first polymer chain as the first "monomer" and only insert one
# then we use the pattern argument to define how many of each "monomers" to add. Let's add 5 more monomers to our chain
# first import the copolymer function
from pysimm.apps.random_walk import copolymer
# now read in the yaml file we saved after making our first polymer
original_polymer = system.read_yaml('polymer.yaml')
# we can use our original polyethylene monomer because it doesn't get modified during polymerization
# the total number of monomers we're adding is 6, 1 for the original polymer chain, and 5 for our new monomers
longer_polymer = copolymer([original_polymer, pe], 6, pattern=[1, 5], forcefield=f)
longer_polymer.write_xyz('longer_polymer.xyz')
longer_polymer.write_yaml('longer_polymer.yaml')
longer_polymer.write_lammps('longer_polymer.lmps')
longer_polymer.write_chemdoodle_json('longer_polymer.json')
s = system.read_lammps(args.lammps_data)
elif args.molfile:
s = system.read_mol(args.molfile)
if args.forcefield and args.forcefield in supported_forcefields:
if args.forcefield.lower() == 'dreiding':
print('typing with %s' % args.forcefield)
s.apply_forcefield(forcefield.Dreiding())
elif args.forcefield.lower() == 'pcff':
s.apply_forcefield(forcefield.Pcff())
elif args.forcefield:
print('forcefield %s is not supported in '
'command line interface at this time')
elif args.cml_file:
s = system.read_cml(args.cml_file)
elif args.yaml_file:
s = system.read_yaml(args.yaml_file)
elif args.lmps2xyz:
s = system.read_lammps(args.lmps2xyz[0])
if args.unwrap:
print(
'unwrapping system so bonds do no cross simulation boundaries...'
'this may take a while if your system is large')
s.unwrap()
s.write_xyz(args.lmps2xyz[1])
elif args.lmps2cdjson:
s = system.read_lammps(args.lmps2cdjson[0])
s.write_chemdoodle_json(args.lmps2cdjson[1])
if args.unwrap:
try:
print(