def run(test=False):
# we'll instantiate a Dreiding forcefield object for use later
f = forcefield.Dreiding()
# we'll make a polyethylene monomer and a polystyrene monomer from the pysimm models database
pe = pe_monomer(f)
ps = ps_monomer(f)
# the monomers do not have any charges, so we will derive partial charges using the gasteiger algorithm
pe.apply_charges(f, charges='gasteiger')
ps.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
pe.pair_style = 'lj/cut'
ps.pair_style = 'lj/cut'
# run the copolymer random walk method with 10 total repeat units, using an alternating pattern
polymer = copolymer([pe, ps], 10, pattern=[1, 1], 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')
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 run(test=False):
# we'll make a polyethylene monomer and a polystyrene monomer from the pysimm models database
pe = pe_monomer()
ps = ps_monomer()
# we'll instantiate a GAFF2 forcefield object for use later
f = forcefield.Gaff2()
# the monomers do not have any charges, so we will derive partial charges using the gasteiger algorithm
pe.apply_charges(f, charges='gasteiger')
ps.apply_charges(f, charges='gasteiger')
# run the copolymer random walk method with 10 total repeat units, using an alternating pattern
polymer = copolymer([pe, ps], 10, pattern=[1, 1], 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')
def run(test=False):
# we'll make a polyethylene monomer and a polystyrene monomer from the pysimm models database
pe = pe_monomer()
ps = ps_monomer()
ba = ba_monomer()
H20 = water_water()
dise = dise_monomer()
disg = disg_monomer()
disi = disi_monomer()
amide = amide_monomer()
peg = peg_monomer()
Na = pos_salt()
Cl = neg_salt()
# we'll instantiate a Dreiding forcefield object for use later
f = forcefield.gaff2()
# the monomers do not have any charges, so we will derive partial charges using the gasteiger algorithm
pe.apply_charges(f, charges='gasteiger')
ps.apply_charges(f, charges='gasteiger')
#H20.apply_charges(f,charges = 'gasteiger')
ba.apply_charges(f, charges='gasteiger')
peg.apply_charges(f, charges='gasteiger')
amide.apply_charges(f, charges='gasteiger')
dise.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
pe.pair_style = 'lj/cut'
ps.pair_style = 'lj/cut'
H20.pair_style = 'lj/cut'
ba.pair_style = 'lj/cut'
dise.pair_style = 'lj/cut'
disg.pair_style = 'lj/cut'
peg.pair_style = 'lj/cut'
amide.pair_style = 'lj/cut'
disi.pair_style = 'lj/cut'
Na.pair_style = 'lj/cut'
Cl.pair_style = 'lj/cut'
######## Heres the Paramaters you can edit ##########
##### Specifiy What Monomer that you are going to use and the frequency of each Monomer
polist = [ba, amide, disg, disi, dise]
monlist = [10, 80, 5, 4, 1]
n_molecules = 50000 # Number of Water Molecules Try to keep it at 10,000
##Current Monomers available
# PEG5 : peg
# Butyl Acrylate : ba
# amide monomer: amide
# Ethelyne: pa
# Polystyrene: ps
# MethylAcrylate: pmma
# disulfideG: disg
# disulfideI: disi
# disulfideE: dise
####################################################################################
pattern = shuffle(monlist, polist)
# run the copolymer random walk method with 10 total repeat units, using an alternating pattern
z = np.ones(len(pattern))
setter = []
for elem in range(0, len(z)):
setter.append(int(z[elem]))
print(setter)
polymer = copolymer(pattern, len(pattern), pattern=setter, forcefield=f)
polymer.write_xyz('polymernonsolvated.xyz')
charge = 0
for pb in polymer.particles:
charge = charge + pb.charge
print("The System has: " + str(charge) + " charge")
numSa = round(charge)
if charge < 0:
salt = 'Na'
charg = +1
else:
salt = 'Cl'
charg = -1
partition = n_molecules / (abs(numSa) + 1)
if round(charge) == 0:
system.replicate([H20], n_molecules, s_=polymer, density=0.6)
else:
for iters in range(0, abs(numSa) + 1):
system.replicate([H20],
abs(int(partition)),
s_=polymer,
density=0.6)
if iters == abs(numSa):
lmps.quick_min(polymer, min_style='sd')
break
m = polymer.molecules.add(system.Molecule())
dreiding_salt_ = polymer.particle_types.add(
f.particle_types.get(salt)[0].copy())
polymer.particles.add(
system.Particle(type=dreiding_salt_,
x=polymer.dim.dx / 2,
y=polymer.dim.dy / 2,
z=polymer.dim.dz / 2,
charge=charg,
molecule=m))
lmps.quick_min(polymer, min_style='sd')
charge = 0
for pb in polymer.particles:
charge = charge + pb.charge
print("The System has: " + str(charge) + " charge")
if charge < 0:
salt = 'Na'
charg = +1
else:
salt = 'Cl'
charg = -1
m = polymer.molecules.add(system.Molecule())
dreiding_salt_ = polymer.particle_types.add(
f.particle_types.get(salt)[0].copy())
polymer.particles.add(
system.Particle(type=dreiding_salt_,
x=polymer.dim.dx / 2,
y=polymer.dim.dy / 2,
z=polymer.dim.dz / 2,
charge=-charge,
molecule=m))
lmps.quick_min(polymer, min_style='sd')
charge = 0
for pb in polymer.particles:
charge = charge + pb.charge
print("The System has: " + str(charge) + " charge")
# write a few different file formats
polymer.write_xyz('polymersolvated.xyz')
# polymer.write_yaml('polymer.yaml')
polymer.write_lammps('polymer.lmps')
ps.particles[7].linker = 'tail'
# like in example 3, we need to identify the bonds in the ring as aromatic
for b in ps.bonds:
if (not b.a.linker
and not b.b.linker) and b.a.elem == 'C' and b.b.elem == 'C':
b.order = 'A'
# 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
ps.apply_forcefield(f, charges='gasteiger')
# do a quick minimization of the monomer
lmps.quick_min(ps, min_style='fire')
# write a yaml file for the ps monomer
ps.write_yaml('ps_monomer.yaml')
# run the copolymer random walk method with 10 total repeat units, using an alternating pattern
# here, settings is passed to the LAMMPS simulations during the polymerization, and we will use 2 processors
polymer = copolymer([pe, ps],
10,
pattern=[1, 1],
forcefield=f,
settings={'np': 2})
# 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')
