def notestDetermineWavefunctionRange(self):
density_file = join(test_folder, 'Rho.grid.nc')
rho, r, dh_cell = readNCDensity(density_file)
rho = rho.sum(axis=0)
r = determineWaveFunctionRange(
rho=rho,
r=r,
density_range=(-3.5, -2.5),
point_density=6,
)
X, Y, Z = r
self.assertArraysEqual((X.min(), X.max()), (-3.8654757894093597, 3.8654757894093597), 5)
self.assertArraysEqual((Y.min(), Y.max()), (-1.86849, 1.86849), 5)
self.assertArraysEqual((Z.min(), Z.max()), (1.40626, 4.92191), 5)
def prepareDenchar(label='./siesta', density_range=(-3.5, -2.5)):
folder = os.path.dirname(label)
nc_filename = join(folder, 'Rho.grid.nc')
rho, r, dh_cell = readNCDensity(nc_filename)
rho = rho.sum(axis=0)
X, Y, Z = determineWaveFunctionRange(
rho=rho,
r=r,
point_density=5,
density_range=density_range,
)
span = np.array([
[X.min(), X.max()],
[Y.min(), Y.max()],
[Z.min(), Z.max()],
])
d_input = makeDencharInput(
span=span,
shape=X.shape,
main_file='siesta.fdf',
plot_wavefunctions=False,
plot_charge=True,
)
with open('denchar_charge.fdf', 'w') as f:
f.write(d_input)
d_input = makeDencharInput(
span=span,
shape=X.shape,
main_file='siesta.fdf',
plot_wavefunctions=True,
plot_charge=False,
)
with open('denchar_wf.fdf', 'w') as f:
f.write(d_input)
cmd = 'denchar < denchar_charge.fdf &> TMP.out'
p = subprocess.Popen(cmd, shell=True)
p.wait()