def run(test=False):
# we'll make a vinyl-type polynorbornene monomer from the pysimm models database
A = NbTMS(isomer="exo_exo")
setattr(A.particles[1], 'rnd_wlk_tag', 'tail_cap')
setattr(A.particles[49], 'rnd_wlk_tag', 'head_cap')
# 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
A.apply_charges(f, charges='gasteiger')
# the buckingham potential isn't great at small distances, and therefore we use the LJ potential while growing the polymer
A.pair_style = 'lj/cut'
# run the polymer random walk tacticity method with 10 total repeat units, all isotactic insertions, no minimizations
polymer = random_walk_tacticity(A,
10,
forcefield=f,
capped=True,
tacticity='isotactic',
sim='no',
rotation=180)
write_file_formats(polymer, "isotactic_PNB_nosim10")
# run the polymer random walk tacticity method with 10 total repeat units, all syndiotactic insertions, no minimizations
polymer = random_walk_tacticity(A,
10,
forcefield=f,
capped=True,
tacticity='syndiotactic',
sim='no',
rotation=180)
write_file_formats(polymer, "syndiotactic_PNB_nosim10")
# run the polymer random walk tacticity method with 50 total repeat units with minimizations and error
# checking (when a hardcore overlap is found, the last inserted monomer shrunken and gradually re-expanded)
polymer = random_walk_tacticity(A,
50,
forcefield=f,
capped=True,
tacticity='syndiotactic',
error_check=True,
rotation=180,
md_spacing=1)
write_file_formats(polymer, "syndiotactic_PNB_sim50")
# pack and equilibrate eight 20mers of exo_exo and exo_endo isomers to compare densities
pack_and_equil(A, 20, 8, f, "exo")
A = NbTMS(isomer="exo_endo")
A.apply_charges(f, charges='gasteiger')
A.pair_style = 'lj/cut'
pack_and_equil(A, 20, 8, f, "endo")
def run(test=False):
# we'll take a polystyrene monomer from the pysimm models database
monomer = ps(is_capped=True)
# we'll decorate atoms of PS monomer with tags that are needed for more elaborate polymerisation
# procedure that takes into account tacticity
setattr(monomer.particles[9], 'linker', 'mirror')
setattr(monomer.particles[9], 'rnd_wlk_tag', 'head_cap')
setattr(monomer.particles[13], 'rnd_wlk_tag', 'tail_cap')
# 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
monomer.apply_charges(f, charges='gasteiger')
# the buckingham potential isn't great at small distances, and therefore we use the LJ potential while growing the polymer
monomer.pair_style = 'lj/cut'
# run the polymer random walk tacticity method with 10 total repeat units
polymer = random_walk_tacticity(monomer, 10, forcefield=f, tacticity='isotactic', sim='no')
# write a few different file formats
polymer.write_xyz('isotactic.xyz')
polymer.write_yaml('isotactic.yaml')
polymer.write_lammps('isotactic.lmps')
polymer.write_chemdoodle_json('isotactic.json')
# run the polymer random walk tacticity method with 10 total repeat units
polymer = random_walk_tacticity(monomer, 10, forcefield=f, tacticity='syndiotactic', sim='no')
# write a few different file formats
polymer.write_xyz('syndiotactic.xyz')
polymer.write_yaml('syndiotactic.yaml')
polymer.write_lammps('syndiotactic.lmps')
polymer.write_chemdoodle_json('syndiotactic.json')
# run the polymer random walk tacticity method with 10 total repeat units
polymer = random_walk_tacticity(monomer, 10, forcefield=f, tacticity=0.2, sim='no')
# write a few different file formats
polymer.write_xyz('iso_20_syndio_80.xyz')
polymer.write_yaml('iso_20_syndio_80.yaml')
polymer.write_lammps('iso_20_syndio_80.lmps')
polymer.write_chemdoodle_json('iso_20_syndio_80.json')
tmp = 1.54 * tmp / numpy.linalg.norm(tmp)
# add new capping particle along the defined direction
new_p = new_monomer.add_particle_bonded_to(system.Particle(x=p.x + tmp[0], y=p.y + tmp[1],
z=p.z + tmp[2], type=captype), p, f=ff)
# decorate particle with '****_cap' tag
new_p.rnd_wlk_tag = p.linker + '_cap'
if p.linker == 'head':
setattr(new_p, 'linker', 'mirror')
new_monomer.objectified = False
new_monomer.objectify()
new_monomer.write_pdb('2.monomer_to_rndwlk-tacticity.pdb')
# first random walk **without** simulations
polymer = random_walk_tacticity(new_monomer, chain_len + 1, forcefield=ff, tacticity='syndiotactic', sim='no')
polymer.write_pdb('3.polymer_rndwlk-tacticity.no-sim.pdb')
tacticity_stat = check_tacticity(polymer, tacticity_order, len(monomer.particles))
print('\t Polymer chain built without MD contains {:}/{:} meso- and {:}/{:} racemo- diads'.format(
tacticity_stat[1].count(True), chain_len, tacticity_stat[1].count(False), chain_len))
# second, random walk **with** simulations
polymer = random_walk_tacticity(new_monomer, chain_len + 1, forcefield=ff, tacticity='syndiotactic')
polymer.write_pdb('4.polymer_rndwlk-tacticity.pdb')
tacticity_stat = check_tacticity(polymer, tacticity_order, len(monomer.particles))
print('\t Polymer chain built using MD contains {:}/{:} meso- and {:}/{:} racemo- diads'.format(
tacticity_stat[1].count(True), chain_len, tacticity_stat[1].count(False), chain_len))
def pack_and_equil(A, n, x, f, prefix):
# A: monomer
# n: number of monomers
# x: number of chains
# f: forcefield
# prefix: prefix for output files
# run the polymer random walk tacticity method with n total repeat units
polymer = random_walk_tacticity(A,
n,
forcefield=f,
capped=True,
tacticity='syndiotactic',
rotation=180,
error_check=False,
sim=0)
write_file_formats(polymer, prefix + "_1", unwrap=True)
# quick opt of polymer
lmps.quick_min(polymer, min_style='fire', etol=1.0e-4, maxiter=100000)
# write a few different file formats
polymer.unwrap()
write_file_formats(polymer, prefix + "_1_fire")
# pack x copies of polymer
polymers = system.replicate(polymer, x, density=0.005)
# polymers = polymer
write_file_formats(polymers, prefix + "_" + str(x))
lmps.quick_min(polymers, min_style='fire', etol=1.0e-4, maxiter=100000)
write_file_formats(polymers, prefix + "_" + str(x) + "_fire")
# quickmd
nvt_settings = {
'name': 'nvt_md',
'print_to_screen': True,
'ensemble': 'nvt',
'temperature': {
'start': 100,
'stop': 300
},
'new_v': True,
'length': 10000
}
npt_settings = {
'name': 'npt_md',
'print_to_screen': True,
'ensemble': 'npt',
'temperature': 300,
'new_v': True,
'pressure': {
'start': 1000,
'stop': 1
},
'length': 100000,
'thermo_style': 'custom step temp press density'
}
# npt calcs need "add neigh_modify" command to reneighbor more often during compression of npt step
sim = lmps.Simulation(polymers, name='npt_reneighbor', debug=True)
sim.add_custom('neigh_modify delay 0')
sim.add(lmps.Velocity(temperature=1000))
sim.add_md(length=10000, ensemble='npt', temperature=1000, pressure=5000)
sim.run()
write_file_formats(polymers, prefix + "_" + str(x) + "_npt")
write_file_formats(polymers,
prefix + "_" + str(x) + "_npt_unwrapped",
unwrap=True)
# 21-step equilibration
equil(polymers, np=1, pmax=50000)
write_file_formats(polymers, prefix + "_" + str(x) + "_equil")
write_file_formats(polymers,
prefix + "_" + str(x) + "_equil_unwrapped",
unwrap=True)
def run(test=False):
# we'll make a polystyrene monomer from the pysimm models database
A = NbTMS(isomer="exoexo")
# 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
A.apply_charges(f, charges='gasteiger')
# the buckingham potential isn't great at small distances, and therefore we use the LJ potential while growing the polymer
A.pair_style = 'lj/cut'
# run the polymer random walk tacticity method with 10 total repeat units
polymer = random_walk_tacticity(A,
20,
forcefield=f,
capped=True,
tacticity='syndiotactic',
rotation=180,
errorCheck=False,
sim=0)
writeFileFormats(polymer, "polymer", unwrap=True)
#quick opt of polymer
lmps.quick_min(polymer, min_style='fire', etol=1.0e-4, maxiter=100000)
# write a few different file formats
polymer.unwrap()
writeFileFormats(polymer, "polymer_fired")
#pack multiple copies of polymer
polymers = system.replicate(polymer, 8, density=0.005)
#polymers = polymer
writeFileFormats(polymers, "polymers")
lmps.quick_min(polymers, min_style='fire', etol=1.0e-4, maxiter=100000)
writeFileFormats(polymers, "polymers_fired")
#quickmd
nvt_settings = {
'name': 'nvt_md',
'print_to_screen': True,
'ensemble': 'nvt',
'temperature': {
'start': 100,
'stop': 300
},
'new_v': True,
'length': 10000
}
npt_settings = {
'name': 'npt_md',
'print_to_screen': True,
'ensemble': 'npt',
'temperature': 300,
'new_v': True,
'pressure': {
'start': 1000,
'stop': 1
},
'length': 100000,
'thermo_style': 'custom step temp press density'
}
#nvt runs okay, but npt fails...need to add neigh_modify command to reneighbor more often during compression of npt step
#lmps.quick_md(polymers, debug=True, **nvt_settings)
#writeFileFormats(polymers,"polymers_nvt")
#lmps.quick_md(polymers, debug=True, **npt_settings)
#lmps.quick_md(polymers)
#writeFileFormats(polymers,"polymers_npt")
sim = lmps.Simulation(polymers, name='nptAndReneighbor', debug=True)
sim.add_custom('neigh_modify delay 0')
sim.add(lmps.Velocity(temperature=1000))
sim.add_md(length=10000, ensemble='npt', temperature=1000, pressure=5000)
sim.run()
writeFileFormats(polymers, "polymers_npt")
writeFileFormats(polymers, "polymers_npt_unwrapped", unwrap=True)
#21-step equilibration
equil(polymers, np=1, pmax=50000)
writeFileFormats(polymers, "polymers_equil")
polymers.unwrap()
writeFileFormats(polymers, "polymers_equil_unwrap")