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
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(
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')
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!')
