def read_3D(self, file, filetype=None):
"""Read the density from a 3D file"""
if filetype is None:
# estimate file type from name ending
filetype = file.split('.')[-1]
filetype.lower()
if filetype == 'plt':
data, cell = read_plt(file)
pbc_c = [True, True, True]
N_c = np.array(data.shape)
for c in range(3):
if N_c[c] % 2 == 1:
pbc_c[c] = False
N_c[c] += 1
self.gd = GridDescriptor(N_c, cell.diagonal() / Bohr, pbc_c)
self.offset_c = [int(not a) for a in self.gd.pbc_c]
else:
raise NotImplementedError('unknown file type "' + filetype + '"')
self.file = file
self.ldos = np.array(data * Bohr**3, np.float)
def read_3D(self, file, filetype=None):
"""Read the density from a 3D file"""
if filetype is None:
# estimate file type from name ending
filetype = file.split('.')[-1]
filetype.lower()
if filetype == 'plt':
data, cell = read_plt(file)
pbc_c = [True, True, True]
N_c = np.array(data.shape)
for c in range(3):
if N_c[c] % 2 == 1:
pbc_c[c] = False
N_c[c] += 1
self.gd = GridDescriptor(N_c, cell.diagonal() / Bohr, pbc_c)
self.offset_c = [int(not a) for a in self.gd.pbc_c]
else:
raise NotImplementedError('unknown file type "' + filetype + '"')
self.file = file
self.ldos = np.array(data * Bohr ** 3, np.float)
H2.rotate(57, [1, 1, 1])
fname = 'H2.gpw'
if (not load) or (not os.path.exists(fname)):
calc = GPAW(xc='PBE', nbands=2, spinpol=False, txt=txt)
H2.set_calculator(calc)
H2.get_potential_energy()
if load:
calc.write(fname, 'all')
else:
calc = GPAW(fname, txt=txt)
calc.initialize_wave_functions()
fname = 'aed.plt'
cell = calc.get_atoms().get_cell()
# aed = calc.get_all_electron_density(1, pad=False)
aed = calc.get_pseudo_density(1, pad=False)
# aed = calc.wfs.gd.collect(aed)
if mpi.size == 1:
data_org = [aed, cell]
write_plt(fname, calc.get_atoms(), aed)
# check if read arrays match the written ones
data = read_plt(fname)
for d, do in zip(data, data_org):
dd2 = (d - do)**2
norm = dd2.sum()
print(norm)
assert(norm < 1e-10)
fname = 'H2.gpw'
if (not load) or (not os.path.exists(fname)):
calc = GPAW(xc='PBE', nbands=2, spinpol=False, txt=txt)
H2.set_calculator(calc)
H2.get_potential_energy()
if load:
calc.write(fname, 'all')
else:
calc = GPAW(fname, txt=txt)
calc.initialize_wave_functions()
import gpaw.mpi as mpi
fname = 'aed.plt'
cell = calc.get_atoms().get_cell()
#aed = calc.get_all_electron_density(1, pad=False)
aed = calc.get_pseudo_density(1, pad=False)
#aed = calc.wfs.gd.collect(aed)
if mpi.size == 1:
data_org = [aed, cell]
write_plt(fname, calc.get_atoms(), aed)
# check if read arrays match the written ones
data = read_plt(fname)
for d, do in zip(data, data_org):
dd2 = (d - do)**2
norm = dd2.sum()
print(norm)
assert(norm < 1e-10)
