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_conceptual_local(args):
"""Build LocalConceptualDFT class and dump a cube file of local descriptor."""
# load molecule & cubic grid
mol, cube = load_molecule_and_grid(args.fname, args.cube)
# build model
model = LocalConceptualDFT.from_molecule(args.fname, 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
cubfname = "{0}.cube".format(args.output)
vmdfname = "{0}.vmd".format(args.output)
# dump cube file of local property
cube.generate_cube(cubfname, getattr(model, args.prop))
# generate VMD scripts for visualizing iso-surface with VMD
print_vmd_script_isosurface(vmdfname,
cubfname,
isosurf=args.isosurface,
material="BlownGlass")
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)
"""
from chemtools import LocalConceptualDFT, UniformGrid, print_vmd_script_isosurface
# 1. Make cubic grid for plotting dual descriptor.
# The cubic grid points are spaced by 0.2 a.u. & extending 5.0 a.u. on each side.
file_path = 'ch2o_q+0.fchk'
cube = UniformGrid.from_file(file_path, spacing=0.2, extension=5.0)
# 2. Build quadratic energy model for Formaldehyde using FMO approach.
tool = LocalConceptualDFT.from_file(file_path, model='quadratic', points=cube.points)
# 3. Dump dual descriptor evaluated on cubic grid.
cube.generate_cube('coh2_dual_fmo.cube', tool.dual_descriptor)
# 4. Generate VMD scripts to plot dual-descriptor iso-surface.
# To visualize the iso-surface, use command: $ vmd -e coh2_dual_fmo.vmd
print_vmd_script_isosurface('coh2_dual_fmo.vmd', 'coh2_dual_fmo.cube', isosurf=0.005,
scalemin=-0.005, scalemax=0.005, colorscheme=[0, 1], negative=True)
# DISCARD BELOW:
# the code below is for displaying the dual descriptor 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('ch2o_dual_fmo.jpg')
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,
colorfile=espname,
isosurf=0.002,
scalemin=-0.02,
scalemax=0.04)
# 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('esp_scl2.png')
tool = LocalConceptualDFT.from_file(file_path,
model='linear',
points=cube.points)
# 3. Dump Fukui functions (f+, f- and f0) evaluated on cubic grid.
cube.generate_cube('coh2_ffp_fd.cube', tool.ff_plus)
cube.generate_cube('coh2_ff0_fd.cube', tool.ff_zero)
cube.generate_cube('coh2_ffm_fd.cube', tool.ff_minus)
# 4. Generate VMD scripts to plot dual-descriptor iso-surface.
# To visualize the iso-surface, use command: $ vmd -e coh2_ffp_fd.vmd
print_vmd_script_isosurface('coh2_ffp_fd.vmd',
'coh2_ffp_fd.cube',
isosurf=0.005)
print_vmd_script_isosurface('coh2_ff0_fd.vmd',
'coh2_ff0_fd.cube',
isosurf=0.005)
print_vmd_script_isosurface('coh2_ffm_fd.vmd',
'coh2_ffm_fd.cube',
isosurf=0.005,
negative=True,
colorscheme=[0, 1])
# DISCARD BELOW:
# the code below is for displaying the ff image on the website, you should remove it
# when running the script on your machine.
from tools.rug import plot_existing_image
fname = 'dichloropyridine26_q+0'
mol = Molecule.from_file(fname + '.fchk')
cub = UniformGrid.from_molecule(mol, spacing=1.0, spacing=1.0, extension=5.0)
orb = DFTBasedTool.from_molecule(mol, cub.points)
# 2. Generate cube files: fname_esp.cube & fname_rho.cube
lip_a, lip_b = orb.average_local_ionization_energy
lipname = fname + '_lip.cube'
rhoname = fname + '_rho.cube'
cub.generate_cube(rhoname, mol.compute_density(cub.points))
cub.generate_cube(lipname, lip_a + lip_b)
# 3. Generate vmd script: fname.vmd
# To visualize the iso-surface, use command: $ vmd -e fname.vmd
print_vmd_script_isosurface(fname + '.vmd', rhoname, colorfile=lipname, isosurf=0.002,
scalemin=-1.0, scalemax=mol.homo_energy[0])
# 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('esp_scl2.png')
file_path = 'ch2o_q+0.fchk'
# 1. Make a Cubic grid for plotting Fukui functions.
# The cubic grid points are spaced by 0.2 a.u. & extending 5.0 a.u. on each side.
cube = UniformGrid.from_file(file_path, spacing=0.2, extension=5.0)
# 2. Build linear energy model for Formaldehyde using frontier molecular orbital (FMO) theory.
tool = LocalConceptualDFT.from_file(file_path, model='linear', points=cube.points)
# 3. Dump Fukui functions (f+, f- and f0) evaluated on cubic grid.
cube.generate_cube('coh2_ffm_fmo.cube', tool.ff_minus)
cube.generate_cube('coh2_ffp_fmo.cube', tool.ff_plus)
cube.generate_cube('coh2_ff0_fmo.cube', tool.ff_zero)
# 4. Generate VMD scripts to plot Fukui function iso-surface.
# To visualize the iso-surface, use command: $ vmd -e coh2_ffp_fmo.vmd
print_vmd_script_isosurface('coh2_ffp_fmo.vmd', 'coh2_ffp_fmo.cube', isosurf=0.005)
print_vmd_script_isosurface('coh2_ff0_fmo.vmd', 'coh2_ff0_fmo.cube', isosurf=0.005)
print_vmd_script_isosurface('coh2_ffm_fmo.vmd', 'coh2_ffm_fmo.cube', isosurf=0.005)
# DISCARD BELOW:
# the code below is for displaying the ff 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('ch2o-ff_fmo.jpg')