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)
Compute dual descriptor on a cubic grid based on the quadratic energy model using
frontier molecular orbital (FMO) approach, and generate visualization scripts.
"""
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
np.array([
[2.27823914e00, 4.13899085e-07, 3.12033662e-07],
[1.01154892e-02, 1.09802629e-07, -6.99333116e-07],
[-1.09577141e00, 1.77311416e00, 1.42544321e-07],
]),
0.1,
6,
)
# 2. Build a quadratic energy models using FMO approach
# path to molecule's fchk file
file_path = "ch2o_q+0.fchk"
# build a quadratic global conceptual DFT tool
tool = LocalConceptualDFT.from_file(file_path,
model="quadratic",
points=xyz.reshape(-1, 3))
# 3. Evaluate quadratic Fukui function on the grid points.
ff_quad = tool.fukui_function.reshape(xyz.shape[:2])
# 4. Plot 2D-contour plots of quadratic Fukui function.
# sample contour lines
levels = np.array([0.001 * n * n for n in range(500)])
# plot contours of quadratic Fukui function
plt.contour(xyz[:, :, 0], xyz[:, :, 1], ff_quad, levels)
# plot atomic centers
x_atoms, y_atoms = tool.coordinates[:, 0], tool.coordinates[:, 1]
from chemtools import LocalConceptualDFT, UniformGrid, print_vmd_script_isosurface
file_path = ['ch2o_q+0.fchk', 'ch2o_q+1.fchk', 'ch2o_q-1.fchk']
# 1. Make cubic grid for plotting Fukui function.
# The cubic grid points are spaced by 0.2 a.u. & extending 5.0 a.u. on each side.
# All 3 molecules have the same geometry (they just differ in the number of electrons
# and multiplicity), so the cubic grid based on the first molecule works for all.
cube = UniformGrid.from_file(file_path[0], spacing=0.2, extension=5.0)
# 2. Build linear energy model for Formaldehyde using finite difference (FD) approach.
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',