def generate_scripts(self, fname, isosurf=0.8):
"""Generate VMD scripts & cube file to visualize ELF iso-surface.
Parameters
----------
fname : str
File name used for the generated files.
The VMD script and cube file will be named fname.vmd and fname-elf.cube, respectively.
isosurf : float, optional
Value of ELF iso-surface used in VMD script.
"""
if not isinstance(self._grid, UniformGrid):
raise ValueError('Only possible if argument grid is a cubic grid.')
if self._denstool.density.shape[0] != self._grid.points.shape[0]:
raise ValueError(
'Number of grid points should match number of dens values!')
# dump ELF cube file & generate vmd script
vmdname = fname + '.vmd'
cubname = fname + '-elf.cube'
self._grid.generate_cube(cubname, self.value)
print_vmd_script_isosurface(vmdname,
cubname,
isosurf=isosurf,
representation='Line')
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 generate_scripts(self, fname, spin='a', index=None, isosurf=0.05, grid=None):
"""Generate VMD script(s) and cube file(s) to visualize MO iso-surface of given orbitals.
Parameters
----------
fname : str
A string representing the path to a fname of generated files.
The VMD script and cube file will be named fname_mo{index}.vmd and
fname_mo{index}.cube, respectively.
spin : str, optional
The type of occupied spin orbitals. Choose either 'a' or 'b'.
index : int, optional
Integer representing the index of spin orbital to visualize. Spin orbitals are each
indexed from 1 to :attr:`nbasis`. If None, files for visualizing all orbitals are
generated.
isosurf : float, optional
Value of MO iso-surface used in VMD script.
grid : UniformGrid, optional
Instance of UniformGrid used for computation and generating cube file(s).
If None, a cubic grid is constructed from molecule with spacing=0.2 & extension=5.0.
"""
if spin not in ['a', 'b']:
raise ValueError('Argument spin can only be "a" or "b".')
if index is not None and not isinstance(index, int):
raise ValueError('Argument index is either None or an integer for visualization. '
'Given index={0}'.format(index))
if grid is None:
grid = UniformGrid.from_molecule(self._molecule, spacing=0.2, extension=5.0, rotate=True)
elif not isinstance(grid, UniformGrid):
raise ValueError('Argument grid should be a UniformGrid to generate cube files.')
if index is None:
spin_index = {'a': 0, 'b': 1}
index = range(1, self._molecule.mo.homo_index[spin_index[spin]] + 1)
else:
index = [index]
for mo_index in index:
vmdname = fname + '_mo{0}.vmd'.format(mo_index)
cubname = fname + '_mo{0}.cube'.format(mo_index)
mo_value = self.compute_orbital_expression(grid.points, spin=spin, index=mo_index)
grid.generate_cube(cubname, mo_value)
print_vmd_script_isosurface(vmdname, cubname, isosurf=isosurf, negative=True,
material='BlownGlass')
def generate_scripts(self, fname, isosurf=0.5):
"""Generate VMD scripts & cube file to visualize LOL iso-surface.
Parameters
----------
fname : str
A string representing the path to a fname of generated files.
The VMD script and cube file will be named fname.vmd and fname-lol.cube, respectively.
isosurf : float
Value of LOL iso-surface used in VMD script.
"""
if not isinstance(self._grid, UniformGrid):
raise ValueError("Only possible if argument grid is a cubic grid.")
# dump LOL cube files
fname_vmd = fname + '.vmd'
fname_lol = fname + '-lol.cube'
self._grid.generate_cube(fname_lol, self.value)
# write VMD script for visualization
print_vmd_script_isosurface(fname_vmd, fname_lol, isosurf=isosurf, representation='Line')
def test_print_vmd_script_isosurface():
with tmpdir(
'chemtools.utils.test.test_base.test_vmd_script_isosurface') as dn:
fname = '%s/%s' % (dn, 'test.vmd')
vmd.print_vmd_script_isosurface(fname, 'iso.cube')
with open(fname, 'r') as content_file:
assert content_file.read() == \
(header +
'# load new molecule\n'
'mol new iso.cube type cube first 0 last -1 step 1 filebonds 1 autobonds 1 '
'waitfor all\n'
'#\n'
'# representation of the atoms\n'
'mol representation CPK 1.000000 0.300000 118.000000 131.000000\n'
'mol delrep 0 top\n'
'mol color Element\n'
'mol selection {{all}}\n'
'mol material Opaque\n'
'mol addrep top\n'
'#\n'
'# add representation of the surface\n'
'mol representation Isosurface 0.50000 0 0 0 1 1\n'
'mol color ColorID 0\n'
'mol selection {all}\n'
'mol material Opaque\n'
'mol addrep top\n'
'mol selupdate 1 top 0\n'
'mol colupdate 1 top 0\n'
'mol scaleminmax top 1 -0.050000 0.050000\n'
'mol smoothrep top 1 0\n'
'mol drawframes top 1 {now}\n'
'color scale method RGB\n'
'color Display Background silver\n'
'#\n')
vmd.print_vmd_script_isosurface(fname,
'iso.cube',
colorfile='col.cube',
isosurf=0.6,
material='Transparent',
scalemin=-0.06,
scalemax=0.08)
with open(fname, 'r') as content_file:
assert content_file.read() == \
(header +
'# load new molecule\n'
'mol new col.cube type cube first 0 last -1 step 1 filebonds 1 autobonds 1 '
'waitfor all\n'
'mol addfile iso.cube type cube first 0 last -1 step 1 filebonds 1 autobonds 1 '
'waitfor all\n'
'#\n'
'# representation of the atoms\n'
'mol representation CPK 1.000000 0.300000 118.000000 131.000000\n'
'mol delrep 0 top\n'
'mol color Element\n'
'mol selection {{all}}\n'
'mol material Opaque\n'
'mol addrep top\n'
'#\n'
'# add representation of the surface\n'
'mol representation Isosurface 0.60000 1 0 0 1 1\n'
'mol color Volume 0\n'
'mol selection {all}\n'
'mol material Transparent\n'
'mol addrep top\n'
'mol selupdate 1 top 0\n'
'mol colupdate 1 top 0\n'
'mol scaleminmax top 1 -0.060000 0.080000\n'
'mol smoothrep top 1 0\n'
'mol drawframes top 1 {now}\n'
'color scale method RGB\n'
'color Display Background silver\n'
'#\n')
vmd.print_vmd_script_isosurface(fname,
'iso.cube',
colorscheme=[0, 1],
negative=True)
with open(fname, 'r') as content_file:
assert content_file.read() == \
(header +
'# load new molecule\n'
'mol new iso.cube type cube first 0 last -1 step 1 filebonds 1 autobonds 1 '
'waitfor all\n'
'#\n'
'# representation of the atoms\n'
'mol representation CPK 1.000000 0.300000 118.000000 131.000000\n'
'mol delrep 0 top\n'
'mol color Element\n'
'mol selection {{all}}\n'
'mol material Opaque\n'
'mol addrep top\n'
'#\n'
'# add representation of the surface\n'
'mol representation Isosurface 0.50000 0 0 0 1 1\n'
'mol color ColorID 0\n'
'mol selection {all}\n'
'mol material Opaque\n'
'mol addrep top\n'
'mol selupdate 1 top 0\n'
'mol colupdate 1 top 0\n'
'mol scaleminmax top 1 -0.050000 0.050000\n'
'mol smoothrep top 1 0\n'
'mol drawframes top 1 {now}\n'
'color scale method RGB\n'
'color Display Background silver\n'
'#\n'
'# add representation of the surface\n'
'mol representation Isosurface -0.50000 0 0 0 1 1\n'
'mol color ColorID 1\n'
'mol selection {all}\n'
'mol material Opaque\n'
'mol addrep top\n'
'mol selupdate 1 top 0\n'
'mol colupdate 1 top 0\n'
'mol scaleminmax top 1 -0.050000 0.050000\n'
'mol smoothrep top 1 0\n'
'mol drawframes top 1 {now}\n'
'color scale method RGB\n'
'color Display Background silver\n'
'#\n')