forked from djyaron/compreu
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ASEgraphene.py
528 lines (446 loc) · 22.7 KB
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ASEgraphene.py
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# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
from ase import Atoms, Atom
from ase.visualize import view
import numpy as np
from cclib.parser import *
import logging
from scipy.spatial import KDTree
from collections import Counter
import subprocess
import os
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from Tkinter import *
np.set_printoptions(precision=3,suppress=True)
ORCA_filepath = os.getcwd()
def build_sheet(nx, nz, symmetry=0):
nx=nx+1
nz=(nz+1)/2
basic_cell= Atoms('C4',
positions=[[3.11488, 2.50000, 0.71000],
[4.34463, 2.50000, 1.42000],
[4.34463, 2.50000, 2.84000],
[3.11488, 2.50000, 3.55000]],
cell=[[2.45951, 0, 0],
[0, 1, 0],
[0, 0, 4.26]])
atoms=basic_cell.repeat((nx,1,nz))
atoms.pop(basic_cell.get_number_of_atoms()*nz-1)
atoms.pop(0)
if symmetry == 1:
print "Making graphene sheet symmetric"
global to_be_removed
to_be_removed = []
sym_fix_int = nz-1
for i in xrange(2, nz+sym_fix_int, 2):
to_be_removed.append(2*i-2)
to_be_removed.append(2*i-1)
to_be_removed = to_be_removed[::-1]
for entry in to_be_removed:
atoms.pop(entry)
else:
print "Molecule was not made symmetric"
return atoms
def nitrogenate(sheet, position):
symbols = atoms.get_chemical_symbols()
symbols[position] = 'N'
sheet.set_chemical_symbols(symbols)
return position
def print_atoms(atoms):
out=''
for atom in atoms:
atom_str= '{0}\t{1}\t{2}\t{3}\n'.format(atom.symbol, atom.position[0], atom.position[1], atom.position[2])
out=out+atom_str
return out
def make_orca(atoms, filename="filename.inp", charge="0", multiplicity="1", method="am1", geometry_opt=0, output="temp.out", compute_cores=3, convergence_tolerance="default"):
if method == "am1":
if geometry_opt == 0:
parameters1= '{0}\t{1}\t{2}\n\t{3}'.format("%method", "method", method, "end")
elif geometry_opt == 1:
if convergence_tolerance == "default":
parameters1= '{0}\n\t{1}\n\t{2}\n\n{3}\n{4}\n\n{5}\n{6}\n\n'.format("%method method am1", "method OPT", "end", "%SCF MAXITER 300", " end", "%geom MaxIter 250", " end")
else:
parameters1= '{0}\n\t{1}\n\t{2}\n\n{3}\n{4}\n{5}\n\n{6}\n{7}\n\n'.format("%method method am1", "method OPT", "end", "%SCF MAXITER 300", " Convergence " + convergence_tolerance, " end", "%geom MaxIter 250", " end")
elif method == "DFT":
if geometry_opt == 0:
parameters1 = '{0}\t{1}\n'.format("!", "DFT-Energy")
elif geometry_opt == 1:
parameters1= '{0}\t{1}\n'.format("!", "Good-Opt")
out = ''
parameters0 = '{0}\n{1}\n\n'.format("%pal nprocs " + str(compute_cores), " end")
parameters2 ='{0}\t{1}\t{2}\t{3}\n'.format("*", "xyz", charge, multiplicity)
out=out+parameters0+parameters1+parameters2
end_of_atom_coordinates="*"
with open(filename, 'w') as f:
f.write(out)
f.write(print_atoms(atoms))
f.write(end_of_atom_coordinates)
subprocess.call(ORCA_filepath + "/orca/orca "+ filename + " > " + output, shell=True)
return parse(output)
def parse(filename):
myfile = ccopen(filename)
data = myfile.parse()
return data
def make_gaussian(atoms, method="am1", geometry_opt=False, output="temp.chk"):
if method == "am1" and geometry_opt == False:
out = ''
parameters0 = '{0}\n{1}\n{2}'.format("%mem=48MB", "%chk=/scratch/", output)
def daves_super_saturate(atoms):
pos = atoms.get_positions()
tree = KDTree(atoms.get_positions())
list_tree = list(tree.query_pairs(1.430))
bondedTo = [ [] for i in xrange(len(atoms))]
for bond in list_tree:
bondedTo[bond[0]].append(bond[1])
bondedTo[bond[1]].append(bond[0])
Zs = atoms. get_atomic_numbers()
# figure out what needs a hydrogen atom
for iatom in xrange(len(atoms)):
nbonds = len( bondedTo[iatom] )
Z = Zs[iatom]
if (Z,nbonds) == (6,2):
print "we should add H to atom ", iatom
r0 = pos[iatom, :]
bond1 = pos[ bondedTo[iatom][0] , : ] - r0
bond2 = pos[ bondedTo[iatom][1], :] -r0
rH = -(bond1 + bond2)
rH = 1.09 * rH / np.linalg.norm(rH)
atoms.append(Atom('H', r0+rH ))
def find_edge_atoms(atoms):
edge_atoms = []
pos = atoms.get_positions()
tree = KDTree(atoms.get_positions())
list_tree = list(tree.query_pairs(1.430))
bondedTo = [ [] for i in xrange(len(atoms))]
for bond in list_tree:
bondedTo[bond[0]].append(bond[1])
bondedTo[bond[1]].append(bond[0])
Zs = atoms. get_atomic_numbers()
# figure out what needs a hydrogen atom
for iatom in xrange(len(atoms)):
nbonds = len( bondedTo[iatom] )
Z = Zs[iatom]
if (Z,nbonds) == (6,2):
edge_atoms.append(iatom)
return edge_atoms
def calc_edge_nitrogens(nx="1", nz="1", method="am1", optimize_geometry=0, make_symmetric=0, sub_all_zigzag=0):
if make_symmetric == 1:
print "atoms sheet at start of calc is symmetric"
atoms = build_sheet(nx, nz, symmetry=1)
symmetry_folder_string = "_symmetric"
##set parameter for multiplicity of 2 here##########
else:
atoms = build_sheet(nx, nz, symmetry=0)
symmetry_folder_string = "_asymmetric"
no_hydrogen = atoms.get_positions()
no_hydrogen_count = atoms.get_number_of_atoms()
daves_super_saturate(atoms)
os.popen("mkdir " + ORCA_filepath + "/%dx%dsheet%s" % (nx, nz, symmetry_folder_string))
os.chdir(ORCA_filepath + "/%dx%dsheet%s" % (nx, nz, symmetry_folder_string))
data = make_orca(atoms, filename="%dx%dgraphene.inp" % (nx, nz), multiplicity="1", method=method, geometry_opt=optimize_geometry, output= ORCA_filepath + "/%dx%dsheet%s/orca_%dx%dsheet.out" % (nx, nz, symmetry_folder_string, nx, nz))
moenergies_array = data.moenergies[0]
##Writes carbon only sheet energy values
with open("%dx%d_edge_results.txt" % (nx, nz), 'w') as r:
r.write("%dx%d Graphene Sheet -- No Nitrogens\n" % (nx, nz))
r.write("Total SCF energy in eV:\t")
r.write(str(data.scfenergies))
r.write("\nMolecular orbital energy of HOMO in eV:\t")
r.write(str(moenergies_array[data.homos]))
r.write("\nMolecular orbital energy of LUMO in eV:\t")
r.write(str(moenergies_array[data.homos+1]))
##Pattern for describing zig-zag edge atom positions. Creates edge_carbon_index array based on nx & nz parameters
addition = [0]
multiplication = []
edge_carbon_index =[]
for number in xrange(0, 2*nx):
addition.append(number)
for number in xrange(2, 2*(nx+2), 2):
multiplication.append(number)
multiplication.append(number)
for value in xrange(0, len(addition)):
edge_carbon_index.append(nz*multiplication[value]+addition[value])
edge_carbon_index.pop(1)
if make_symmetric == 1:
edge_carbon_index[:] = [x-len(to_be_removed) for x in edge_carbon_index]
else:
pass
##setup arrays for color map that will be utilized in draw_colormap function later
x_pos, y_pos, scf_energy, HOMO_energy, LUMO_energy = (np.array([]) for i in range(5))
x_pos = np.append(x_pos, no_hydrogen[:,0])
y_pos = np.append(y_pos, no_hydrogen[:,2])
all_carbon_scf = data.scfenergies
##Writes energy values associated with single nitrogen substitions into energy arrays
nitrogenated_x_pos, nitrogenated_y_pos, nitrogenated_scf, nitrogenated_HOMO, nitrogenated_LUMO = (np.array([]) for i in range(5))
for index_number in edge_carbon_index:
if make_symmetric == 1:
print "nitrogenate make atoms sheet is symmetric"
atoms = build_sheet(nx, nz, symmetry=1)
else:
atoms = build_sheet(nx, nz, symmetry=0)
nitrogenate(atoms, index_number)
daves_super_saturate(atoms)
data = make_orca(atoms, filename = "%dx%dsheetN%d" % (nx, nz, index_number), multiplicity="1", method=method, geometry_opt=optimize_geometry, output=ORCA_filepath + "/%dx%dsheet%s/orca_%dx%dsheet.out" % (nx, nz, symmetry_folder_string, nx, nz))
moenergies_array = data.moenergies[0]
##Segregate all carbon energies from substituted nitrogen energies within all pertaining arrays
##X & Y position array segregation
nitrogenated_x_pos = np.append(nitrogenated_x_pos, x_pos[index_number])
nitrogenated_y_pos = np.append(nitrogenated_y_pos, y_pos[index_number])
##Energies arrays segregation
nitrogenated_scf = np.append(nitrogenated_scf, (data.scfenergies-all_carbon_scf))
nitrogenated_HOMO = np.append(nitrogenated_HOMO, moenergies_array[data.homos])
nitrogenated_LUMO = np.append(nitrogenated_LUMO, moenergies_array[data.homos+1])
##Writes nitrogen substition energies into results text file
with open("%dx%d_edge_results.txt" % (nx, nz), 'a+') as e:
moenergies_array = data.moenergies[0]
e.write("\n\n%dx%dsheetN%d\n" % (nx, nz, index_number))
e.write("Total SCF energy in eV:\t")
e.write(str(data.scfenergies))
e.write("\nMolecular orbital energy of HOMO in eV:\t")
e.write(str(moenergies_array[data.homos]))
e.write("\nMolecular orbital energy of LUMO in eV:\t")
e.write(str(moenergies_array[data.homos+1]))
##Creates colormaps
cm = plt.get_cmap("hot")
title_list =["SCF_Energy_Map", "HOMO_Energy_Map", "LUMO_Energy_Map"]
energy_list = [nitrogenated_scf, nitrogenated_HOMO, nitrogenated_LUMO]
plt.xlabel("Atom X Position on Sheet")
plt.ylabel("Atom Z Position on Sheet")
fig = plt.figure()
ax = fig.add_subplot(111)
for i in xrange(3):
fig = plt.figure()
ax = fig.add_subplot(111)
plt.xlabel("Atom X Position on Sheet")
plt.ylabel("Atom Z Position on Sheet")
plt.title(title_list[i])
plt.axis('equal')
#COLOR = (energy_list[i]-energy_list[i].min())/(energy_list[i].max()-energy_list[i].min())
COLOR = energy_list[i]
ax.scatter(x_pos, y_pos, c="0.5", s=100, marker='o', edgecolors='none')
p = ax.scatter(nitrogenated_x_pos, nitrogenated_y_pos, c=COLOR, s=100, marker='o', edgecolors='none', label="something")
cbar = plt.colorbar(p)
cbar.set_label("Energy in eV")
plt.savefig(title_list[i]+".png")
plt.clf()
def nitrogenate_all_zig_zag(nx_min, nx_max, nz_min, nz_max, method="am1", optimize_geometry=0, make_symmetric=0, saturate_nitrogens=0):
all_N_SCF_energy_list, all_N_HOMO_energy_list, all_N_LUMO_energy_list = (np.array([]) for dummy_var in xrange(3))
pltylabel_list = "SCF Energy", "HOMO Energy", "LUMO Energy"
sheet_dimensions, sheet_count = ([] for dummy_var in xrange(2))
for nx in xrange(nx_min, nx_max+1, 2):
for nz in xrange(nz_min, nz_max+1, 2):
if make_symmetric == 1:
atoms = build_sheet(nx, nz, symmetry=1)
symmetry_folder_string = "_symmetric"
addition = [0]
multiplication = []
edge_carbon_index =[]
for number in xrange(0, 2*nx):
addition.append(number)
for number in xrange(2, 2*(nx+2), 2):
multiplication.append(number)
multiplication.append(number)
for value in xrange(0, len(addition)):
edge_carbon_index.append(nz*multiplication[value]+addition[value])
edge_carbon_index.pop(1)
edge_carbon_index[:] = [x-len(to_be_removed) for x in edge_carbon_index]
elif make_symmetric == 0:
atoms = build_sheet(nx, nz, symmetry=0)
symmetry_folder_string = "_asymmetric"
if saturate_nitrogens == 1:
for edge_carbon in edge_carbon_index:
symbols = atoms.get_chemical_symbols()
symbols[edge_carbon] = 'N'
atoms.set_chemical_symbols(symbols)
pos = atoms.get_positions()
tree = KDTree(atoms.get_positions())
list_tree = list(tree.query_pairs(1.430))
bondedTo = [[] for i in xrange(len(atoms))]
for bond in list_tree:
bondedTo[bond[0]].append(bond[1])
bondedTo[bond[1]].append(bond[0])
Zs = atoms.get_atomic_numbers()
for iatom in xrange(len(atoms)):
nbonds = len(bondedTo[iatom])
Z = Zs[iatom]
if (Z,nbonds) == (7,2):
r0 = pos[iatom]
bond1 = pos[ bondedTo[iatom][0]] - r0
bond2 = pos[ bondedTo[iatom][1]] -r0
rH = -(bond1 + bond2)
rH = 1.09 * rH / np.linalg.norm(rH)
atoms.append(Atom('H', r0+rH ))
daves_super_saturate(atoms)
elif saturate_nitrogens == 0:
daves_super_saturate(atoms)
#view(atoms, viewer="avogadro")
os.popen("mkdir " + ORCA_filepath + "/all_N_zigzag")
os.chdir(ORCA_filepath + "/all_N_zigzag")
if (nx>4 and nx<6) and (nz>4 and nz<6):
data = make_orca(atoms, filename="nitrogenated_%dx%dgraphene.inp" % (nx, nz), multiplicity="1", method=method, geometry_opt=optimize_geometry, output= ORCA_filepath + "/all_N_zigzag/orca%s_nitrogenated_%dx%dsheet.out" % (symmetry_folder_string, nx, nz), convergence_tolerance="Medium")
if nx>6:
data = make_orca(atoms, filename="nitrogenated_%dx%dgraphene.inp" % (nx, nz), multiplicity="1", method=method, geometry_opt=optimize_geometry, output= ORCA_filepath + "/all_N_zigzag/orca%s_nitrogenated_%dx%dsheet.out" % (symmetry_folder_string, nx, nz), convergence_tolerance="Loose")
else:
data = make_orca(atoms, filename="nitrogenated_%dx%dgraphene.inp" % (nx, nz), multiplicity="1", method=method, geometry_opt=optimize_geometry, output= ORCA_filepath + "/all_N_zigzag/orca%s_nitrogenated_%dx%dsheet.out" % (symmetry_folder_string, nx, nz))
moenergies_array = data.moenergies[0]
all_N_SCF_energy_list = np.append(all_N_SCF_energy_list, int(data.scfenergies))
all_N_HOMO_energy_list = np.append(all_N_HOMO_energy_list, moenergies_array[data.homos])
all_N_LUMO_energy_list = np.append(all_N_LUMO_energy_list, moenergies_array[data.homos+1])
sheet_dimensions.append("%sx%s" % (nx, nz))
with open("nitrogenated_edge_results.txt", 'a+') as e:
e.write("\n##########################\n")
e.write("Nitrogenated %dx%d sheet\n" % (nx, nz))
e.write("##########################\n")
e.write("Total SCF energy in eV:\t")
e.write(str(data.scfenergies))
e.write("\nMolecular orbital energy of HOMO in eV:\t")
e.write(str(moenergies_array[data.homos]))
e.write("\nMolecular orbital energy of LUMO in eV:\t")
e.write(str(moenergies_array[data.homos+1]))
for dimension in xrange(0, len(sheet_dimensions)):
sheet_count.append(dimension)
sheet_count = [x+0.2 for x in sheet_count]
for y in xrange(0, 3):
pltylist = all_N_SCF_energy_list, all_N_HOMO_energy_list, all_N_LUMO_energy_list
rectangles = plt.bar(np.arange(all_N_SCF_energy_list.size), pltylist[y], 0.4, alpha=0.4, color='b')
plt.title("%s vs Sheet Dimensions" % pltylabel_list[y])
plt.ylabel(pltylabel_list[y])
plt.xticks(sheet_count, sheet_dimensions)
plt.xlabel("Sheet Dimension")
plt.savefig("%s.png" % pltylabel_list[y])
plt.clf()
###Tkinter Section Below
################################################################################################################
################################################################################################################
#Requires 'hovering cursor' tooltip for all major components
root = Tk()
root.title("Graphene Nitrogenator")
Label(root, text="GUI for Nitrogenated Graphene Energy Calculations").pack()
class sheet_param:
def __init__(self, master):
global horizon_sheet_variable
horizon_sheet_variable = StringVar()
global vertical_sheet_variable
vertical_sheet_variable = StringVar()
param_frame = Frame(master)
Label(param_frame, text="horizontal").grid(row=1, column=1)
Label(param_frame, text="vertical").grid(row=1, column=3)
Label(param_frame, text="Sheet Dimensions").grid(row=2, sticky=E)
Label(param_frame, text="x").grid(row=2, column=2)
Entry(param_frame, width=2, textvariable=horizon_sheet_variable).grid(row=2, column=1)
Entry(param_frame, width=2, textvariable=vertical_sheet_variable).grid(row=2, column=3)
param_frame.pack()
class checkbox:
def __init__(self,master):
self.cbox_frame = Frame(master)
self.cbox_frame.pack()
def symtrc_cbox(self):
global symmetry_var
symmetry_var = IntVar()
Checkbutton(self.cbox_frame, text="Make molecule symmetric", variable=symmetry_var).pack(anchor=W)
def unsaturate_cbox(self):
global unsat_var
unsat_var = IntVar()
Checkbutton(self.cbox_frame, text="Leave molecule unsaturated", variable=unsat_var, onvalue=1, offvalue=0).pack(anchor=W)
#unsat_var_string = str(unsat_var.get())
def opt_geo_cbox(self):
opt_geo_var = IntVar()
Checkbutton(self.cbox_frame, text="Optimize Geometry", variable=opt_geo_var, onvalue=1, offvalue=0).pack(anchor=W)
global selected_geometry_opt
selected_geometry_opt = int(opt_geo_var.get())
def nitrogenate_all_cbox(self):
global N_all_cbox_var
N_all_cbox_var = IntVar()
Checkbutton(self.cbox_frame, text="Nitrogenate all zig-zag positions", variable=N_all_cbox_var, onvalue=1, offvalue=0).pack(anchor=W)
#can't seem to get checkboxes to align
class drop_list:
def __init__(self, master):
self.drop_list_frame = Frame(master)
self.drop_list_frame.pack()
self.method_var = StringVar()
self.calculator_var = StringVar()
def calc_combobox(self):
self.calculator_var.set("ORCA")
OptionMenu(self.drop_list_frame, self.calculator_var, "ORCA", "NWChem", "Gaussian").grid(row=0, column=1)
Label(self.drop_list_frame, text="Calculator").grid(row=0, sticky=E)
global selected_calculator
selected_calculator = str(self.calculator_var.get())
def calc_method(self):
self.method_var.set("am1")
OptionMenu(self.drop_list_frame, self.method_var, "am1", "DFT").grid(row=1, column=1)
Label(self.drop_list_frame, text="Method").grid(row=1, sticky=E)
global selected_calc_method
selected_calc_method = str(self.method_var.get())
class button:
def __init__(self, master):
self.button_frame = Frame(master)
self.button_frame.pack(expand="yes")
def bottom_buttons(self):
Button(self.button_frame, text="Calculate", command=gui_calculate).grid(row=0, column=3)
Button(self.button_frame, text="View in Avogadro", command=gui_view).grid(row=0, column=0)
def test_button(self):
Button(self.button_frame, text="Test Button", command=gui_nitrogenate_all).grid(row=1)
def print_var(self):
string = str(horizon_sheet_variable.get())
print string
def build_param_frame(master):
lbl_bld_frame = LabelFrame(master, text="Graphene Builder Parameters", padx=5, pady =5)
lbl_bld_frame.pack(expand="yes")
sheet_param(lbl_bld_frame)
checkbox(lbl_bld_frame).symtrc_cbox()
checkbox(lbl_bld_frame).unsaturate_cbox()
checkbox(lbl_bld_frame).nitrogenate_all_cbox()
def calc_param_frame(master):
lbl_calc_frame = LabelFrame(master, text="Calculation Parameters", padx=5, pady=5)
lbl_calc_frame.pack(expand="yes")
#drop_list(lbl_calc_frame).calc_combobox()
drop_list(lbl_calc_frame).calc_method()
checkbox(lbl_calc_frame).opt_geo_cbox()
def gui_view():
horizontal_dimension = int(horizon_sheet_variable.get())
vertical_dimension = int(vertical_sheet_variable.get())
symmetry_int = int(symmetry_var.get())
atoms = build_sheet(horizontal_dimension, vertical_dimension, symmetry=symmetry_int)
unsat_int = int(unsat_var.get())
if unsat_int==0:
daves_super_saturate(atoms)
elif unsat_int==1:
pass
view(atoms, viewer="avogadro")
def gui_calculate():
horizontal_dimension = int(horizon_sheet_variable.get())
vertical_dimension = int(vertical_sheet_variable.get())
symmetry_int = int(symmetry_var.get())
global atoms
atoms = build_sheet(horizontal_dimension, vertical_dimension, symmetry=symmetry_int)
# global unsat_int
# unsat_int = int(unsat_var.get())
if N_all_cbox_var==0:
calc_edge_nitrogens(horizontal_dimension, vertical_dimension, method=selected_calc_method, optimize_geometry=selected_geometry_opt, make_symmetric=symmetry_int)
elif N_all_cbox_var==1:
nitrogenate_all_zig_zag(horizontal_dimension, vertical_dimension, method=selected_calc_method, optimize_geometry=selected_geometry_opt, make_symmetric=symmetry_int)
def gui_nitrogenate_all():
horizontal_dimension = int(horizon_sheet_variable.get())
vertical_dimension = int(vertical_sheet_variable.get())
symmetry_int = int(symmetry_var.get())
global atoms
atoms = build_sheet(horizontal_dimension, vertical_dimension, symmetry=symmetry_int)
global unsat_int
unsat_int = int(unsat_var.get())
nitrogenate_all_zig_zag(horizontal_dimension, vertical_dimension, method=selected_calc_method, optimize_geometry=selected_geometry_opt, make_symmetric=symmetry_int)
nitrogenate_all_zig_zag(7,7,3,7, optimize_geometry=1, make_symmetric=1, saturate_nitrogens=1)
#saturated_nitrogenate_all_zig_zag(nx_min=6, nx_max=6, nz_min=6, nz_max=6, method="am1", optimize_geometry=0, make_symmetric=1)
#build_param_frame(root)
#calc_param_frame(root)
#button(root).bottom_buttons()
#button(root).test_button()
#root.mainloop()
#atoms = build_sheet(3, 3, symmetry=1)
#nitrogenate(atoms, 34)
#daves_super_saturate(atoms)
#view(atoms, viewer="avogadro")
#calc_edge_nitrogens(3, 3, method="am1", optimize_geometry=False, make_symmetric=1)
#print data.atomcharges
#############################################Concurrent Bug List##########################################################
#asymmetric molecules are viewed as symmetric in .png energy map files for 3x3 sheet