def setUp(self):
conf_file = _rpath + 'example.cfg'
self.pars = ConfigParameters(conf_file)
self.pars.parse_input()
vasp_data = VaspData(_rpath + 'one_site/')
self.el_struct = ElectronicStructure(vasp_data)
efermi = self.el_struct.efermi
self.eigvals = self.el_struct.eigvals - efermi
struct = self.el_struct.structure
kmesh = self.el_struct.kmesh
self.proj_sh = ProjectorShell(self.pars.shells[0], vasp_data.plocar.plo, vasp_data.plocar.proj_params, kmesh, struct, 0)
self.proj_gr = ProjectorGroup(self.pars.groups[0], [self.proj_sh], self.eigvals)
def setUp(self):
"""
"""
conf_file = _rpath + 'example.cfg'
self.pars = ConfigParameters(conf_file)
self.pars.parse_input()
vasp_data = VaspData(_rpath + 'one_site/')
self.el_struct = ElectronicStructure(vasp_data)
# efermi = vasp_data.doscar.efermi
# eigvals = vasp_data.eigenval.eigs - efermi
efermi = self.el_struct.efermi
eigvals = self.el_struct.eigvals - efermi
emin, emax = self.pars.groups[0]['ewindow']
struct = self.el_struct.structure
kmesh = self.el_struct.kmesh
self.proj_sh = ProjectorShell(self.pars.shells[0],
vasp_data.plocar.plo,
vasp_data.plocar.proj_params, kmesh,
struct, 0)
self.proj_gr = ProjectorGroup(self.pars.groups[0], [self.proj_sh],
eigvals)
ov[iorb, iorb2] = overlap[ispin, ind, ind2]
den_mat_sites.append(dm)
print " Density matrix" + (12 * norb - 12) * " " + "Overlap"
for drow, dov in zip(dm, ov):
out = ''.join(map("{0:12.7f}".format, drow))
out += " "
out += ''.join(map("{0:12.7f}".format, dov))
print out
return den_mat_sites
vasp_dir = './'
# extract density matrices and write them to rotations file -> done
vasp_data = VaspData(vasp_dir, efermi_required=True)
el_struct = ElectronicStructure(vasp_data)
den_mat = calc_density_matrix(el_struct)
rot_file = open('rotations.dat', 'w')
print den_mat
for i, mat in enumerate(den_mat):
mat = mat * 0.5
e_values, e_vectors = np.linalg.eigh(mat)
print e_values
print e_vectors
rot_file.write('# site ' + str(i) + '\n')
rot_file.write(" ".join(str(x) for x in e_vectors[:, 0]) + '\n')
rot_file.write(" ".join(str(x) for x in e_vectors[:, 1]) + '\n')
rot_file.write('\n')
#print np.dot(e_vectors[:,0:2].transpose(),np.dot(mat,e_vectors[:,0:2]))
rot_file.close()