def run(test=False):
# we'll create a pmma monomer from the pysimm.models database
pmma = monomer()
# we'll instantiate a Dreiding forcefield object for use later
f = forcefield.Dreiding()
pmma.pair_style = 'lj/cut'
# we're going to make 4 chains, each of 5 repeat units
# the first system we make will be used as the initial system and then replicated to form 4 chains
# in this case the system.replicate function take a system input(polymer),
# replicates a defined number of times(4), and inserts the new replication randomly(rand=True) at the specified density(0.022)
print('Building polymer chain 1...')
polymer = random_walk(pmma, nmon=5, forcefield=f)
print('Replicating polymer chain...')
uniform_polymer = system.replicate(polymer, 4, density=0.022, rand=True)
# next we're going to make 4 chains, with lengths of 2, 4, 6, and 8 monomer units
# the first system we make will be used as the initial system for the subsequent random walk calls
print('Building polymer chain 1...')
nonuniform_polymer = random_walk(pmma, nmon=2, forcefield=f, density=0.3/4)
print('Building polymer chain 2...')
nonuniform_polymer = random_walk(pmma, nmon=4, s_=nonuniform_polymer, forcefield=f)
print('Building polymer chain 3...')
nonuniform_polymer = random_walk(pmma, nmon=6, s_=nonuniform_polymer, forcefield=f)
print('Building polymer chain 4...')
nonuniform_polymer = random_walk(pmma, nmon=8, s_=nonuniform_polymer, forcefield=f)
# now that we have our two polymer systems, let's calculate their molecular weight dispersity
uniform_polymer.set_mm_dist()
nonuniform_polymer.set_mm_dist()
print('')
print('Uniform polymer')
print('---------------')
print('Number average molecular weight: {}'.format(uniform_polymer.mn))
print('Weight average molecular weight: {}'.format(uniform_polymer.mw))
print('Dispersity: {}'.format(uniform_polymer.dispersity))
print('')
print('Nonuniform polymer')
print('------------------')
print('Number average molecular weight: {}'.format(nonuniform_polymer.mn))
print('Weight average molecular weight: {}'.format(nonuniform_polymer.mw))
print('Dispersity: {}'.format(nonuniform_polymer.dispersity))
# write a few different file formats
uniform_polymer.write_yaml('uniform_polymer.yaml')
uniform_polymer.write_xyz('uniform_polymer.xyz')
nonuniform_polymer.write_yaml('nonuniform_polymer.yaml')
nonuniform_polymer.write_xyz('nonuniform_polymer.xyz')
def polymer_system(chains=10, mn=1000, pdi=1, density=0.3):
if pdi != 1:
print('disperse molecular weight distributions not supported yet')
return
mon = monomer()
chain_length = int(mn/mon.mass)
polym = random_walk(mon, chain_length, density=density/chains, forcefield=forcefield.Dreiding())
for chain in range(chains-1):
polym = random_walk(mon, chain_length, s_=polym, density=None, forcefield=forcefield.Dreiding())
return polym
def grow_polymer(self):
self.polymer = random_walk(self.monomer,
self.chain_length,
forcefield=self.ff,
density=self.growth_density,
settings={'np': self.nproc})
self.polymer.forcefield = self.ff.name
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')
def polymer_chain(length):
mon = monomer()
polym = random_walk(mon, length, forcefield=forcefield.Dreiding())
return polym
for x, y, z in zip(np.ndarray.flatten(X), np.ndarray.flatten(Y),
np.ndarray.flatten(Z))]
for ch in range(1, nchains + 1):
mloc = mono.copy()
mloc.dim.translate(*displ[2 * ch])
mloc.shift_particles(*displ[2 * ch])
sngl_chain = random_walk(mloc,
10,
density=0.01,
geometry_rule=position_rule_pim1,
extra_bonds=[1, 0],
traj=False,
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',
cntrion_tp = ff.particle_types.get('SOD')[0].copy()
chrg = 1
elif abs(monomer.charge - 1) < 0.1:
print('\tAdding CLORINE counterion to equilibrate the system chargewise')
cntrion_tp = ff.particle_types.get('CLA')[0].copy()
chrg = -1
else:
cntrion_tp = None
if cntrion_tp:
monomer.particle_types.add(cntrion_tp)
monomer.particles.add(system.Particle(x=monomer.cog[0], y=monomer.cog[1], z=monomer.cog[2] + 5.0, type=cntrion_tp,
charge=chrg, molecule=monomer.molecules[1]))
# -------------> Polymer construction and tacticity check <--------------
sngl_chain = random_walk(monomer, chain_len, forcefield=ff, density=0.01, print_to_screen='true', traj=False, unwrap=True)
if is_cap:
cap_with_methyls(sngl_chain, ff)
# After polymerisation and possibly capping is done let's cleanup: remove all counterions and reshape the simulation
# box so that the chain is in the center of a cube with padding of 3 nm
sngl_chain.center(what='particles', at=[0.0, 0.0, 0.0], move_both=False)
if cntrion_tp:
for p in sngl_chain.particles:
if p.type.name == cntrion_tp.name:
sngl_chain.particles.remove(p.tag, update=False)
sngl_chain.molecules[p.molecule.tag].particles.remove(p.tag, update=False)
sngl_chain.objectify()
def polymer_chain(length, ff):
return random_walk(monomer(ff), length, forcefield=ff)
# we'll instantiate a GAFF2 forcefield object for use later
f = forcefield.Gaff2()
# particles 1 and 2 in the monomer are going to be the head and tail linkers
s.particles[1].linker = 'head'
s.particles[2].linker = 'tail'
# the resulting system has sufficient information to type with the forcefield object we made earlier
# we will also determine partial charges using the gasteiger algorithm
s.apply_forcefield(f, charges='gasteiger')
# do a quick minimization of the monomer
lmps.quick_min(s, min_style='fire')
# write a few different file formats
s.write_xyz('pe_monomer.xyz')
s.write_yaml('pe_monomer.yaml')
s.write_lammps('pe_monomer.lmps')
s.write_chemdoodle_json('pe_monomer.json')
# 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(s, 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')
# we'll instantiate a GAFF2 forcefield object for use later
f = forcefield.Gaff2()
# particles 3 and 6 in the monomer are going to be the head and tail linkers
pmma.particles[3].linker = 'head'
pmma.particles[6].linker = 'tail'
# the resulting system has sufficient information to type with the forcefield object we made earlier
# we will also determine partial charges using the gasteiger algorithm
pmma.apply_forcefield(f, charges='gasteiger')
# do a quick minimization of the monomer
lmps.quick_min(pmma, min_style='fire')
# write a yaml file for the pmma monomer
pmma.write_yaml('pmma_monomer.yaml')
# we're going to make 4 chains, each of 5 repeat units
# the first system we make will be used as the initial system for the subsequent random walk calls
polymer = random_walk(pmma, nmon=5, forcefield=f, density=0.3 / 4)
polymer = random_walk(pmma, nmon=5, s_=polymer, forcefield=f)
polymer = random_walk(pmma, nmon=5, s_=polymer, forcefield=f)
polymer = random_walk(pmma, nmon=5, s_=polymer, 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')