def write_3D(self, bias, file, filetype=None):
"""Write the density as a 3D file.
Units: [e/A^3]"""
self.calculate_ldos(bias)
self.calc.wfs.kd.comm.sum(self.ldos)
ldos = self.gd.collect(self.ldos)
# print "write: integrated =", self.gd.integrate(self.ldos)
if mpi.rank != MASTER:
return
if filetype is None:
# estimate file type from name ending
filetype = file.split('.')[-1]
filetype.lower()
if filetype == 'cube':
write_cube(file, self.calc.get_atoms(), ldos / Bohr**3)
elif filetype == 'plt':
write_plt(file, self.calc.get_atoms(), ldos / Bohr**3)
else:
raise NotImplementedError('unknown file type "' + filetype + '"')
def write_3D(self, bias, file, filetype=None):
"""Write the density as a 3D file.
Units: [e/A^3]"""
self.calculate_ldos(bias)
self.calc.wfs.kpt_comm.sum(self.ldos)
ldos = self.gd.collect(self.ldos)
## print "write: integrated =", self.gd.integrate(self.ldos)
if mpi.rank != MASTER:
return
if filetype is None:
# estimate file type from name ending
filetype = file.split('.')[-1]
filetype.lower()
if filetype == 'cube':
write_cube(file, self.calc.get_atoms(), ldos / Bohr**3)
elif filetype == 'plt':
write_plt(file, self.calc.get_atoms(), ldos / Bohr**3)
else:
raise NotImplementedError('unknown file type "' + filetype + '"')
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)
from __future__ import print_function
from ase.io.plt import write_plt
from gpaw import restart
basename = 'CO'
# load binary file and get calculator
atoms, calc = restart(basename + '.gpw')
# loop over all wfs and write their cube files
nbands = calc.get_number_of_bands()
for band in range(nbands):
wf = calc.get_pseudo_wave_function(band=band)
fname = '{0}_{1}.plt'.format(basename, band)
print('writing wf', band, 'to file', fname)
write_plt(fname, atoms, data=wf)
