import numpy as np
import makegraphitics as mg
vdw_defs = {1: 90, 2: 91}
R = 15
GO_separation = 10 # approx 1 nm in experiment (with water!)
oxidiser = mg.reactors.Oxidiser(ratio=2.5,
video_xyz=20,
new_island_freq=1e14,
method="rf")
for i in range(3):
motif = mg.molecules.Hexagon_Graphene(R)
new_layer = mg.Crystal(motif, [1, 1, 1])
new_layer = oxidiser.react(new_layer)
new_layer.coords = new_layer.coords + np.array((0, 0, i * GO_separation))
if i == 0:
sim = new_layer
else:
sim = mg.Combine(sim, new_layer)
mg.Parameterise(sim, new_layer.vdw_defs)
name = "GO_stack"
output = mg.Writer(sim, name)
output.write_xyz(name + ".xyz")
output.write_lammps(name + ".data")
import makegraphitics as mg
flake_radius = 25
layout = [1, 1, 1] # make a 1x1x1 array of flakes
motif = mg.molecules.Hexagon_Graphene(flake_radius)
flake = mg.Crystal(motif, layout)
oxidiser = mg.reactors.Oxidiser(
ratio=2.5, video_xyz=20, new_island_freq=1e14, method="rf"
)
flake = oxidiser.react(flake)
mg.Parameterise(flake)
name = "graphene"
output = mg.Writer(flake, name)
output.write_xyz(name + ".xyz")
output.write_lammps(name + ".data")
from math import pi, cos
import makegraphitics as mg
config = yaml.load(open("config.yaml"), Loader=yaml.FullLoader)
forcefield = "OPLS"
x_length = 20
y_length = 20
# calculate array of unit cells to make sheet
# unit cell is the orthorombic unit cell of graphene
unit_cell_x = 2.0 * config[forcefield]["CC"] * cos(pi / 6.0)
unit_cell_y = 3.0 * config[forcefield]["CC"]
x_cells = int(x_length / unit_cell_x)
y_cells = int(y_length / unit_cell_y)
layout = [x_cells, y_cells, 1] # make an array of unit cells with this dimension
motif = mg.molecules.Graphene(forcefield=forcefield)
sheet = mg.Crystal(motif, layout)
oxidiser = mg.reactors.Oxidiser(
ratio=2.5, video_xyz=20, new_island_freq=1e14, method="rf"
)
sheet = oxidiser.react(sheet)
mg.Parameterise(sheet, sheet.vdw_defs)
name = "GO_sheet"
output = mg.Writer(sheet, name)
output.write_xyz(name + ".xyz")
output.write_lammps(name + ".data")
config = yaml.load(open("config.yaml"), Loader=yaml.FullLoader)
forcefield = "OPLS"
x_length = 20
y_length = 20
layers = 10
# calculate array of unit cells to make sheet
# unit cell is the orthorombic unit cell of graphene
unit_cell_x = 2.0 * config[forcefield]["CC"] * cos(pi / 6.0)
unit_cell_y = 3.0 * config[forcefield]["CC"]
x_cells = int(x_length / unit_cell_x)
y_cells = int(y_length / unit_cell_y)
layout = [
x_cells,
y_cells,
int(layers / 2),
] # make an array of unit cells with this dimension
motif = mg.molecules.Graphite()
graphite = mg.Crystal(motif, layout)
vdw_defs = {1: 90}
mg.Parameterise(graphite, vdw_defs)
name = "graphite"
output = mg.Writer(graphite, name)
output.write_xyz(name + ".xyz")
output.write_lammps(name + ".data")
import yaml
from math import cos, pi
import makegraphitics as mg
config = yaml.load(open("config.yaml"), Loader=yaml.FullLoader)
forcefield = "OPLS"
x_length = 20
y_length = 20
# calculate array of unit cells to make sheet
# unit cell is the orthorombic unit cell of graphene
unit_cell_x = 2.0 * config[forcefield]["CC"] * cos(pi / 6.0)
unit_cell_y = 3.0 * config[forcefield]["CC"]
x_cells = int(x_length / unit_cell_x)
y_cells = int(y_length / unit_cell_y)
layout = [x_cells, y_cells, 1] # make an array of unit cells with this dimension
motif = mg.molecules.Graphene()
graphene = mg.Crystal(motif, layout)
vdw_defs = {1: 90}
mg.Parameterise(graphene, vdw_defs)
name = "graphene"
output = mg.Writer(graphene, name)
output.write_xyz(name + ".xyz")
output.write_lammps(name + ".data")
config = yaml.load(open("config.yaml"), Loader=yaml.FullLoader)
graphite = mg.molecules.Graphite()
bulk = mg.Crystal(graphite, [122, 71, 2])
molecule1 = mg.molecules.Hexagon_Graphene(50)
flake1 = mg.Crystal(molecule1, [1, 1, 1])
# make flake carbons different to bulk
# for atom in range(molecule.natoms):
# if flake.atom_labels[atom] == 1:
# flake.atom_labels[atom] = 3
flake1.coords = flake1.coords + np.array((
20 * 2 * (3**0.5) * config[forcefield]["CC"],
72 * config[forcefield]["CC"],
3.7 + (4) * config[forcefield]["layer_gap"],
))
bulk.coords = bulk.coords + np.array((0, 0, 3.7))
bulk.vdw_defs = {1: 90}
flake1.vdw_defs = {1: 90, 2: 91}
sim = mg.Combine(bulk, flake1)
sim.box_dimensions[2] = 30
# output = Shifter(sim,'lammps')
# output.rotate(180,1)
output = mg.Writer(sim, "flake on graphite")
output.write_xyz("graphene.xyz")
output.write_lammps("flake.data")
import makegraphitics as mg
flake_radius = 25
layout = [1, 1, 1] # make a 1x1x1 array of flakes
motif = mg.molecules.Hexagon_Graphene(flake_radius)
flake = mg.Crystal(motif, layout)
oxidiser = mg.reactors.Oxidiser(ratio=2.5,
new_island_freq=1e14,
method="rf",
carboxyl_charged_ratio=0.5,
counterion="Ca"
#counterion="Na"
)
flake = oxidiser.react(flake)
mg.Parameterise(flake)
flake.validate()
out = mg.Writer(flake)
out.write_xyz()