def test_cube(self):
"""Does the cube file written out for electron density on a Cartesian grid match
expected values?
"""
data, logfile = getdatafile(Psi4, "basicPsi4-1.2.1", ["water_mp2.out"])
# Reference values were calculated using cubegen method in Psi4.
# First six rows are information about the coordinates of the grid and comments.
tmp = []
with open(os.path.dirname(os.path.realpath(__file__)) + "/water_mp2.cube") as f:
lines = f.readlines()
for line in lines[6 : len(lines)]:
tmp.extend(line.split())
tmp = numpy.asanyarray(tmp, dtype=float)
refcube = numpy.resize(tmp, (13, 13, 13))
# Values for the grid below are constructed to match Psi4 cube file.
vol = volume.Volume(
(-1.587532, -1.587532, -1.356299),
(1.58754, 1.58754, 1.81877),
(0.26458860545, 0.26458860545, 0.26458860545),
)
density = volume.electrondensity(data, vol, [data.mocoeffs[0][: data.homos[0]]])
assert_allclose(density.data, refcube, atol=0.5, rtol=0.1)
def test_roundtrip_cube(self):
"""Write a cube file and then read it back. Check if the volume object contains
identical information on each grid point"""
data, logfile = getdatafile(Psi4, "basicPsi4-1.2.1", ["water_mp2.out"])
vol = volume.Volume((-1, -1, -1), (1, 1, 1), (0.4, 0.4, 0.4))
density = volume.electrondensity(data, vol, [data.mocoeffs[0][: data.homos[0]]])
density.writeascube("coarsewater.cube")
density_recovered = volume.read_from_cube("coarsewater.cube")
assert_allclose(density.data, density_recovered.data, rtol=0.05)
def test_density(self):
"""Does the volume occupied by the combined electron density integrate
to the correct value?
"""
data_basis, _ = getdatafile(Gaussian, "basicGaussian09", ["dvb_sp.out"])
data_sp, _ = getdatafile(Gaussian, "basicGaussian09", ["dvb_sp.out"])
vol = volume.Volume((-3.0, -6.0, -2.0), (3.0, 6.0, 2.0), (0.25, 0.25, 0.25))
frontierorbs = [data_sp.mocoeffs[0][(data_sp.homos[0] - 3) : (data_sp.homos[0] + 1)]]
density = volume.electrondensity(data_sp, vol, frontierorbs)
integral = density.integrate()
self.assertTrue(abs(integral - 8.00) < 1e-2)
print("Combined Density of 4 Frontier orbitals=", integral)
def test_density(self):
"""Does the volume occupied by the combined electron density integrate
to the correct value?
"""
data_basis, _ = getdatafile(Gaussian, "basicGaussian03", ["dvb_sp_basis.log"])
data_sp, _ = getdatafile(Gaussian, "basicGaussian03", ["dvb_sp.out"])
vol = volume.Volume((-3.0, -6.0, -2.0), (3.0, 6.0, 2.0), (0.25, 0.25, 0.25))
frontierorbs = [data_sp.mocoeffs[0][(data_sp.homos[0] - 3):(data_sp.homos[0] + 1)]]
density = volume.electrondensity(data_sp.atomcoords[0],
frontierorbs, data_basis.gbasis, vol)
integral = density.integrate()
self.assertTrue(abs(integral - 8.00) < 1e-2)
print("Combined Density of 4 Frontier orbitals=", integral)
def main():
args = _parse_args()
log_file = ccopen(args.quantum_chemical_file)
data = log_file.parse()
me = MolecularExtent(data, args.radius)
me.calculate_extent(args.index)
volume = Volume(me.lower_limit,
me.upper_limit,
spacing=(args.spacing, args.spacing, args.spacing))
slice_end = data.homos[args.spinidx] + 1
print('density of molecular orbitals [0..%d] H**O=%d' %
(slice_end, data.homos[args.spinidx]))
density = electrondensity(data.atomcoords[args.index],
data.mocoeffs[args.spinidx][0:slice_end],
data.gbasis, volume)
print('integral', density.integrate(), density.integrate_square())
if args.output is not None:
density.writeascube(args.output + '.cube')
