def main_nci(args):
"""Build NCI model and dump VMD script and cube files for visualizing NCI with VMD."""
# load molecule
mol = Molecule.from_file(args.fname)
# make cubic grid
if args.cube.endswith('.cube'):
# load cube file
cube = UniformGrid.from_cube(args.cube)
elif len(args.cube.split(',')) == 2:
# make a cubic grid
spacing, extension = [float(item) for item in args.cube.split(',')]
cube = UniformGrid.from_molecule(mol,
spacing=spacing,
extension=extension,
rotate=True)
else:
raise ValueError('Argument cube={0} is not recognized!'.format(
args.cube))
# build NCI model
nci = NCI.from_molecule(mol, grid=cube)
# dump files/scripts for visualizing NCI
nci.generate_scripts(args.output,
isosurf=args.isosurface,
denscut=args.denscut)
# plot reduced density gradient vs. signed density
if args.plot:
nci.generate_plot(args.output, color=args.color)
def main_esp(args):
"""Generate VMD script and cube files for visualizing ESP on electron density iso-surface."""
# load molecule
mol = Molecule.from_file(args.fname)
# make cubic grid
if args.cube.endswith('.cube'):
# load cube file
cube = UniformGrid.from_cube(args.cube)
elif len(args.cube.split(',')) == 2:
# make a cubic grid
spacing, extension = [float(item) for item in args.cube.split(',')]
cube = UniformGrid.from_molecule(mol, spacing=spacing, extension=extension, rotate=True)
else:
raise ValueError('Argument cube={0} is not recognized!'.format(args.cube))
# dump cube files & script for visualization
espname = args.output + '_esp.cube'
rhoname = args.output + '_rho.cube'
vmdname = args.output + '.vmd'
cube.generate_cube(rhoname, mol.compute_density(cube.points))
cube.generate_cube(espname, mol.compute_esp(cube.points))
print_vmd_script_isosurface(vmdname, rhoname, colorfile=espname, isosurf=args.isosurface,
scalemin=args.scalemin, scalemax=args.scalemax)
def main_mot(args):
"""Build MOTBasedTool model and dump VMD script and cube files for visualizing MO."""
# load molecule
mol = Molecule.from_file(args.fname)
# make cubic grid
if args.cube.endswith('.cube'):
# load cube file
cube = UniformGrid.from_cube(args.cube)
elif len(args.cube.split(',')) == 2:
# make a cubic grid
spacing, extension = [float(item) for item in args.cube.split(',')]
cube = UniformGrid.from_molecule(mol, spacing=spacing, extension=extension, rotate=True)
else:
raise ValueError('Argument cube={0} is not recognized!'.format(args.cube))
if args.index is not None:
index = [int(item) for item in args.index.split(',')]
if len(index) == 1:
index = index[0]
else:
index = None
# build MOT model
mot = MOTBasedTool.from_molecule(mol)
# print logging message
logging.info('')
logging.info('Initialized : {0}'.format(mot))
logging.info('# of basis : {0}'.format(mot.nbasis))
logging.info('# of a & b electrons : {0}'.format(mot.nelectrons))
logging.info('')
logging.info('Index of a & b LUMO : {0}'.format(mot.lumo_index))
logging.info('Energy of a & b LUMO : {0}'.format(mot.lumo_energy))
logging.info('')
logging.info('Index of a & b H**O : {0}'.format(mot.homo_index))
logging.info('Energy of a & b H**O : {0}'.format(mot.homo_energy))
logging.info('')
# dump file/script for visualizing MOT
mot.generate_scripts(args.output, spin=args.spin, index=index, grid=cube,
isosurf=args.isosurface)
def main_lol(args):
"""Build LOL model and dump VMD script and cube files for visualizing LOL."""
# load molecule
mol = Molecule.from_file(args.fname)
# make cubic grid
if args.cube.endswith('.cube'):
# load cube file
cube = UniformGrid.from_cube(args.cube)
elif len(args.cube.split(',')) == 2:
# make a cubic grid
spacing, extension = [float(item) for item in args.cube.split(',')]
cube = UniformGrid.from_molecule(mol, spacing=spacing, extension=extension, rotate=True)
else:
raise ValueError('Argument cube={0} is not recognized!'.format(args.cube))
# build LOL model
lol = LOL.from_molecule(mol, grid=cube, trans=args.trans, trans_k=args.trans_k,
trans_a=args.trans_a, denscut=args.denscut)
# dump file/script for visualizing LOL
lol.generate_scripts(args.output, isosurf=args.isosurface)
def main_conceptual_local(args):
"""Build LocalConceptualDFT class and dump a cube file of local descriptor."""
# load the first molecule
mol = Molecule.from_file(args.file_wfn[0])
# make cubic grid
if args.cube.endswith('.cube'):
# load cube file
cube = UniformGrid.from_cube(args.cube)
elif len(args.cube.split(',')) == 2:
# make a cubic grid
spacing, threshold = [float(item) for item in args.cube.split(',')]
cube = UniformGrid.from_molecule(mol, spacing, threshold)
else:
raise ValueError('Argument cube={0} is not recognized!'.format(
args.cube))
# build global tool
model = LocalConceptualDFT.from_file(args.file_wfn, args.model,
cube.points)
# check whether local property exists
if not hasattr(model, args.prop):
raise ValueError('The {0} local conceptual DFT class does not contain '
'{1} attribute.'.format(args.model, args.prop))
if callable(getattr(model, args.prop)):
raise ValueError(
'The {0} argument is a method, please provide an attribute of '
'{1} local conceptual DFT.'.format(args.prop, args.model))
# name of files
cubefile = '{0}.cube'.format(args.output_name)
vmdfile = '{0}.vmd'.format(args.output_name)
# dump cube file of local property
cube.generate_cube(cubefile, getattr(model, args.prop))
# generate VMD scripts for visualizing iso-surface with VMD
print_vmd_script_isosurface(vmdfile, cubefile, isosurf=args.isosurface)
r"""
===================================================
EX1: ESP from wave-function file & user-defied cube
===================================================
Compute ESP and visualize it on electron density iso-surface for SCl2.
"""
from chemtools import UniformGrid, Molecule, print_vmd_script_isosurface
# 1. Build Molecule
fname = 'scl2'
mol = Molecule.from_file(fname + '.fchk')
cub = UniformGrid.from_molecule(mol, spacing=1.0, extension=5.0)
# 2. Generate cube files: fname_esp.cube & fname_rho.cube
espname = fname + '_esp.cube'
rhoname = fname + '_rho.cube'
cub.generate_cube(rhoname, mol.compute_density(cub.points))
cub.generate_cube(espname, mol.compute_esp(cub.points))
# 3. Generate vmd script: fname.vmd
# To visualize the iso-surface, use command: $ vmd -e fname.vmd
print_vmd_script_isosurface(fname + '.vmd',
rhoname,
r"""
============================================
EX3: LOL from Molecule and user-defined cube
============================================
Compute LOL and visualize it for formamide, using the inverse hyperbolic transformation.
"""
from chemtools import LOL, UniformGrid, Molecule
# 1. Build Molecule, UnifromGrid and LOL model
mol = Molecule.from_file('formamide_q+0.fchk')
cub = UniformGrid.from_molecule(mol, spacing=0.1, extension=2.0)
lol = LOL.from_molecule(mol, grid=cub, trans='inverse_hyperbolic', trans_k=1, trans_a=1)
# 2. Generate cube file(s) and script for visualizing LOL
# Files generated are chonh2-lol.cube & chonh2.vmd
# To visualize the iso-surface, use command: $ vmd -e chonh2.vmd
lol.generate_scripts('chonh2', isosurf=0.55)
# DISCARD BELOW:
# the code below is for displaying the LOL image on the website, you should remove it
# when running the script on your machine.
from tools.rug import plot_existing_image
plot_existing_image('lol055_chonh2_hyperbolic.jpg')
r"""
============================================
EX3: NCI from Molecule and user-defined cube
============================================
Compute NCI and visualize it for formic acid dimer.
"""
from chemtools import NCI, UniformGrid, Molecule
# 1. Build UniformGrid and NCI model
mol = Molecule.from_file('formic_acid_dimer.fchk')
cub = UniformGrid.from_molecule(mol, spacing=0.1, extension=0.5)
nci = NCI.from_molecule(mol, grid=cub)
# 2. Generate plot, cube file(s) and script for visualizing NCI
# Files generated are formic_acid_dimer-dens.cube, formic_acid_dimer-grad.cube,
# & formic_acid_dimer.vmd
# To visualize the iso-surface, use command: $ vmd -e formic_acid_dimer.vmd
# nci.generate_plot('formic_acid_dimer', denslim=(-0.15, 0.15))
nci.generate_scripts('formic_acid_dimer')
# DISCARD BELOW:
# the code below is for displaying the NCI image on the website, you should remove it
# when running the script on your machine.
from tools.rug import plot_existing_image
plot_existing_image('nci_formic_acid_dimer.jpg')
Compute ELF and visualize spherically averaged ELF for Kr atom
using 'rational' & 'hyperbolic' transformations.
"""
import numpy as np
import matplotlib.pyplot as plt
from chemtools import Molecule, ELF
from horton import AtomicGrid
# 1. Build Molecule, AtomicGrid and ELF model
mol = Molecule.from_file('atom_kr.fchk')
grid = AtomicGrid(mol.numbers[0], mol.pseudo_numbers[0], mol.coordinates[0],
agspec='exp:0.005:10.0:200:194', random_rotate=False)
elf_r = ELF.from_molecule(mol, grid=grid, trans='rational', trans_k=2, trans_a=1)
elf_h = ELF.from_molecule(mol, grid=grid, trans='hyperbolic', trans_k=1, trans_a=1)
# 2. Compute spherically-averaged density ($4.0 \pi r^2 \rho$) & ELF
elf_r = grid.get_spherical_average(elf_r.value)
elf_h = grid.get_spherical_average(elf_h.value)
dens = grid.get_spherical_average(mol.compute_density(points=grid.points))
dens *= (4.0 * np.pi * grid.rgrid.radii**2)
# 3. Plot ElF and (scaled) radially weighted density versus radius
def main_mot(args):
"""Build MOTBasedTool model and dump VMD script and cube files for visualizing MO."""
# load molecule
mol = Molecule.from_file(args.fname)
hia, hib = np.array(mol.homo_index) - 1
lia, lib = np.array(mol.lumo_index) - 1
ea, eb = mol.orbital_energy
print('')
print('File: {0}'.format(args.fname))
# print('Charge : % 5f' % np.sum(mol.numbers) - np.sum(ne))
# print('Multiplicity: % 5d' % np.max(ne) - np.min(ne) + 1)
print('')
print('Atomic number and coordinates:')
for index, num in enumerate(mol.numbers):
coord = mol.coordinates[index, :]
print('% 2i %10.6f %10.6f %10.6f' %
(num, coord[0], coord[1], coord[2]))
print('')
print('Information on alpha & beta electrons:')
print('# electrons : % 3.3f % 3.3f' % mol.nelectrons)
print('H**O index : % 3d % 5d' % mol.homo_index)
print('')
print('LUMO+2 index : %10.6f %10.6f' % (ea[lia + 2], eb[lib + 2]))
print('LUMO+1 energy: %10.6f %10.6f' % (ea[lia + 1], eb[lib + 1]))
print('LUMO energy: %10.6f %10.6f' % mol.lumo_energy)
print('H**O energy: %10.6f %10.6f' % mol.homo_energy)
print('H**O-1 energy: %10.6f %10.6f' % (ea[hia - 1], eb[hib - 1]))
print('H**O-2 energy: %10.6f %10.6f' % (ea[hia - 2], eb[hib - 2]))
print('')
if args.info:
return
# make cubic grid
if args.cube.endswith('.cube'):
# load cube file
cube = UniformGrid.from_cube(args.cube)
elif len(args.cube.split(',')) == 2:
# make a cubic grid
spacing, extension = [float(item) for item in args.cube.split(',')]
cube = UniformGrid.from_molecule(mol,
spacing=spacing,
extension=extension,
rotate=True)
else:
raise ValueError('Argument cube={0} is not recognized!'.format(
args.cube))
if args.index is not None:
index = [int(item) for item in args.index.split(',')]
if len(index) == 1:
index = index[0]
else:
index = None
# build MOT model
mot = MOTBasedTool.from_molecule(mol)
# print logging message
# logging.info('')
# logging.info('Initialized : {0}'.format(mot))
# logging.info('# of basis : {0}'.format(mot.nbasis))
# logging.info('# of a & b electrons : {0}'.format(mot.nelectrons))
# logging.info('')
# logging.info('Index of a & b LUMO : {0}'.format(mot.lumo_index))
# logging.info('Energy of a & b LUMO : {0}'.format(mot.lumo_energy))
# logging.info('')
# logging.info('Index of a & b H**O : {0}'.format(mot.homo_index))
# logging.info('Energy of a & b H**O : {0}'.format(mot.homo_energy))
# logging.info('')
# dump file/script for visualizing MOT
if args.output is None:
args.output = args.fname.rsplit('.')[0]
mot.generate_scripts(args.output,
spin=args.spin,
index=index,
grid=cube,
isosurf=args.isosurface)
r"""
=================================
EX1: Topology of Electron Density
=================================
Compute critical points and visualize it for cyclobutadiene.
"""
from chemtools import Molecule, UniformGrid, TopologicalTool
# 1. Build Topology model
mol = Molecule.from_file('c4h4.fchk')
cub = UniformGrid.from_molecule(mol, spacing=0.1, extension=0.1, rotate=False)
top = TopologicalTool.from_molecule(mol, points=cub.points)
# 2. Generate vmd script: fname.vmd
# To visualize the iso-surface, use command: $ vmd -e fname.vmd
top.generate_scripts('c4h4.vmd')
# DISCARD BELOW:
# the code below is for displaying the ELF image on the website, you should remove it
# when running the script on your machine.
from tools.rug import plot_existing_image
plot_existing_image('top_c4h4.jpg')