def initialize(job):
water = create_spce_water()
water.name = 'SOL'
pore = mb.recipes.GraphenePoreSolvent(
pore_width=1.0,
pore_length=1.0,
pore_depth=1.1,
n_sheets=1,
slit_pore_dim=2,
solvent=water,
n_solvent=24,
x_bulk=0,
)
ff = foyer.Forcefield(get_ff("pore-spce.xml"))
water = mb.Compound()
gph = mb.Compound()
for child in pore.children:
if child.name == 'SOL':
water.add(mb.clone(child))
else:
gph.add(mb.clone(child))
typed_water = ff.apply(water, residues='SOL', combining_rule='lorentz')
typed_gph = ff.apply(gph, combining_rule='lorentz')
typed_pore = typed_gph + typed_water
typed_pore.box[1] = 20
with job:
write_lammpsdata(typed_pore, 'data.spce')
typed_pore.save('init.mol2', overwrite=True)
typed_pore.save('init.gro', combine='all', overwrite=True)
def initialize(job):
water = create_spce_water()
water.name = 'SOL'
pore = mb.recipes.GraphenePoreSolvent(
pore_width=2.0,
pore_length=3.0,
pore_depth=3.0,
n_sheets=3,
slit_pore_dim=2,
solvent=water,
n_solvent=job.sp.nwater,
x_bulk=0,
)
pore.periodicity[1] = 6.0
ff = foyer.Forcefield(get_ff("pore-spce.xml"))
water = mb.Compound()
gph = mb.Compound()
for child in pore.children:
if child.name == 'SOL':
water.add(mb.clone(child))
else:
gph.add(mb.clone(child))
typed_water = ff.apply(water, residues='SOL', combining_rule='lorentz')
typed_gph = ff.apply(gph, combining_rule='lorentz')
typed_pore = typed_gph + typed_water
typed_pore.box[1] = 60
with job:
typed_pore.save('init.gro', combine='all', overwrite=True)
typed_pore.save('init.top', combine='all', overwrite=True)
typed_pore.save('init.mol2', overwrite=True)
#add_settles('init.top')
write_ndx(path='.')
def md_files(job):
import mbuild as mb
import foyer
water = create_spce_water()
water.name = "SOL"
pore = mb.recipes.GraphenePoreSolvent(
pore_width=1.0,
pore_length=1.0,
pore_depth=1.1,
n_sheets=1,
slit_pore_dim=2,
solvent=water,
n_solvent=job.sp.nwater,
x_bulk=0,
)
ff = foyer.Forcefield(get_ff("pore-spce.xml"))
pore.translate([0, 0.3325, 0])
water = mb.Compound()
gph = mb.Compound()
for child in pore.children:
if child.name == "SOL":
water.add(mb.clone(child))
else:
gph.add(mb.clone(child))
typed_water = ff.apply(water, residues="SOL", combining_rule="lorentz")
typed_gph = ff.apply(gph, combining_rule="lorentz")
typed_pore = typed_gph + typed_water
typed_pore.box[1] = 20
with job:
import os
import glob
import numpy as np
import unyt as u
import mbuild as mb
from cp2kmdpy.molecule_optimization import (
Molecule_optimization,
) # for single molecule optimization
from cp2kmdpy.md import MD # for running MD
from cp2kmdpy import runners
import setter
typed_pore.save("init.mol2", overwrite=True)
temperature = job.sp.T * u.K
# Defining the molecule we want to simulate
graphene_water = mb.load("init.mol2")
molecule = graphene_water
box = mb.box.Box(lengths=[0.9824, 2, 1.0635])
q = MD(
molecules=[molecule],
box=box,
cutoff=650,
functional="BLYP",
basis_set={
"C": "DZVP-MOLOPT-SR-GTH",
"H": "DZVP-MOLOPT-SR-GTH",
"O": "DZVP-MOLOPT-SR-GTH",
},
periodicity="XYZ",
n_molecules=[1],
traj_type="PDB",
seed=1,
project_name="carbon_water",
initial_coordinate_filename="init.mol2",
fixed_list="1..80",
)
q.temperature = temperature
q.ensemble = "NVT"
q.simulation_time = 1000 * u.ps
# Initializing q
q.md_initialization()
# generating input files
setter.md_files(q)
job.doc.input_filename = q.input_filename
job.doc.output_filename = q.output_filename
job.doc.restart_filename = q.project_name + "-1.restart"