def test_density_ncl(self):
print("TEST DENSITY NCL")
sys.stdout.flush()
print("LOAD WAVEFUNCTION")
sys.stdout.flush()
wf = NCLWavefunction.from_directory('noncollinear')
print("FINISHED LOAD WAVEFUNCTION")
sys.stdout.flush()
#wf = wf.desymmetrized_copy()
wf.write_density_realspace(scale = wf.structure.lattice.volume)
wf.write_density_realspace(dim=np.array([40,40,40]), scale = wf.structure.lattice.volume)
tstchg = Chgcar.from_file("AECCAR2").data['total']# / wf.structure.volume
chg = Chgcar.from_file("PYAECCAR").data['total']
reldiff = np.sqrt(np.mean(((chg-tstchg)/tstchg)**2))
newchg = chg-tstchg
Chgcar(Poscar(wf.structure), {'total': newchg}).write_file('DIFFCHGCAR.vasp')
print(np.sum(chg)/40**3, np.sum(tstchg)/40**3)
assert_almost_equal(reldiff, 0, decimal=3)
def test_density(self):
print("TEST DENSITY")
sys.stdout.flush()
wf = Wavefunction.from_directory('nosym')
#wf = wf.desymmetrized_copy()
wf.write_density_realspace(dim=np.array([40,40,40]), scale = wf.structure.lattice.volume)
tstchg = Chgcar.from_file("AECCAR2").data['total']# / wf.structure.volume
chg = Chgcar.from_file("PYAECCAR").data['total']
reldiff = np.sqrt(np.mean(((chg-tstchg)/tstchg)**2))
newchg = chg-tstchg
Chgcar(Poscar(wf.structure), {'total': newchg}).write_file('DIFFCHGCAR.vasp')
print(np.sum(chg)/40**3, np.sum(tstchg)/40**3)
assert_almost_equal(reldiff, 0, decimal=2)
wf = Wavefunction.from_directory('nosym')
res = wf.write_density_realspace(filename="BAND4DENS", bands=4)
#os.remove('PYAECCAR')
print("DENS shape", res.shape)
assert_almost_equal(np.sum(res)*wf.structure.lattice.volume/np.cumprod(res.shape)[-1], 1, 4)
def to_chgcar(self, filename=None):
from pymatgen.io.vasp.inputs import Poscar
from pymatgen.io.vasp.outputs import Chgcar
# From: http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html
# This file contains the total charge density multiplied by the volume
# For spinpolarized calculations, two sets of data can be found in the CHGCAR file.
# The first set contains the total charge density (spin up plus spin down),
# the second one the magnetization density (spin up minus spin down).
# For non collinear calculations the CHGCAR file contains the total charge density
# and the magnetisation density in the x, y and z direction in this order.
myrhor = self.datar * self.structure.volume
data_dict = {"total": myrhor[0]}
if self.nsppol == 2: {"diff": myrhor[0] - myrhor[1]}
if self.nspinor == 2: raise NotImplementedError("pymatgen Chgcar does not implement nspinor == 2")
chgcar = Chgcar(Poscar(self.structure), data_dict)
if filename is not None: chgcar.write_file(filename)
return chgcar
#%%
from pymatgen.io.vasp.outputs import Chgcar
from pymatgen.io.cube import Cube
import os
os.chdir('/home/jinho93/molecule/ddt/cp2k/bulk/asym/t1')
cub = Cube('s1-SPIN_DENSITY-1_0.cube')
cub.NZ
for i in range(cub.NX):
for j in range(cub.NY):
for k in range(cub.NZ):
if i + k > cub.NZ + 2 or i + k < cub.NZ / 2 + 5:
cub.data[i, j, k] = 0
chg = Chgcar(cub.structure, {'total': cub.data})
chg.write_file('NEW_CHGCAR')
# chg = Chgcar(cub.structure, cub.data)
# %%