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_mot(args):
"""Build MOTBasedTool model and dump VMD script and cube files for visualizing MO."""
if args.info:
mol = Molecule.from_file(args.fname)
else:
mol, cube = load_molecule_and_grid(args.fname, args.cube)
hia, hib = np.array(mol.homo_index) - 1
lia, lib = np.array(mol.lumo_index) - 1
ea, eb = mol.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.mo.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
index = args.index
if index is not None:
index = [int(item) for item in index.split(",")]
if len(index) == 1:
index = index[0]
# build model
mot = OrbPart.from_molecule(mol)
# dump files for visualization
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)
def main_lol(args):
"""Build LOL model and dump VMD script and cube files for visualizing LOL."""
# load molecule & cubic grid
mol, cube = load_molecule_and_grid(args.fname, args.cube)
# build 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 files for visualization
output = args.output
if output is None:
output = args.fname.split(".")[0]
lol.generate_scripts(output, isosurf=args.isosurface)
def main_esp(args):
"""Generate VMD script and cube files for visualizing ESP on electron density iso-surface."""
# load molecule & cubic grid
mol, cube = load_molecule_and_grid(args.fname, args.cube)
# dump files for visualization
output = args.output
if output is None:
output = args.fname.split(".")[0]
espname = output + "_esp.cube"
rhoname = output + "_dens.cube"
vmdname = 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_nci(args):
"""Build NCI model and dump VMD script and cube files for visualizing NCI with VMD."""
# load molecule & cubic grid
mol, cube = load_molecule_and_grid(args.fname, args.cube)
# build model
nci = NCI.from_molecule(mol, grid=cube)
# dump files for visualization
output = args.output
if output is None:
output = args.fname.split(".")[0]
nci.generate_scripts(output, isosurf=args.isosurface, denscut=args.denscut)
# plot reduced density gradient vs. signed density
if args.plot:
nci.generate_plot(output, color=args.color)