import numpy as np class ElectronicStructure: """ Class containing electronic structure data. **Parameters:** - *natom* (int) : total number of atoms - *nktot* (int) : total number of `k`-points - *nband* (int) : total number of bands - *nspin* (int) : spin-polarization - *nc_flag* (True/False) : non-collinearity flag - *efermi* (float) : Fermi level read from DOSCAR - *proj_raw* (array[complex]) : raw projectors from PLOCAR - *eigvals* (array[float]) : KS eigenvalues - *ferw* (array[float]) : Fermi weights from VASP - *kmesh* (dict) : parameters of the `k`-mesh - *structure* (dict) : parameters of the crystal structure - *symmetry* (dict) : paramters of symmetry When the object is created a simple consistency check of the data coming from different VASP files is performed. """ def __init__(self, vasp_data): self.natom = vasp_data.poscar.nq self.type_of_ion = vasp_data.poscar.type_of_ion self.nktot = vasp_data.kpoints.nktot self.kmesh = {'nktot': self.nktot} self.kmesh['kpoints'] = vasp_data.kpoints.kpts self.kmesh['kweights'] = vasp_data.eigenval.kwghts try: self.kmesh['ntet'] = vasp_data.kpoints.ntet self.kmesh['itet'] = vasp_data.kpoints.itet self.kmesh['volt'] = vasp_data.kpoints.volt except AttributeError: pass # Note that one should not subtract this Fermi level from eigenvalues # here because the true Fermi level might be provided by conf-file # (for instance, for spaghetti calculations) self.efermi = vasp_data.doscar.efermi # Note that the number of spin-components of projectors might be different from those # of bands in case of non-collinear calculations self.nspin = vasp_data.eigenval.ispin self.nc_flag = vasp_data.doscar.ncdij == 4 self.nband = vasp_data.eigenval.nband self.eigvals = vasp_data.eigenval.eigs # For later use it is more convenient to use a different order of indices # [see ProjectorGroup.orthogonalization()] self.proj_raw = vasp_data.plocar.plo self.proj_params = vasp_data.plocar.proj_params self.ferw = vasp_data.eigenval.ferw.transpose((2, 0, 1)) # Not needed any more since PROJCAR contains projectors only for a subset of sites # Check that the number of atoms is the same in PLOCAR and POSCAR # natom_plo = vasp_data.plocar.params['nion'] # assert natom_plo == self.natom, "PLOCAR is inconsistent with POSCAR (number of atoms)" # Check that the number of k-points is the same in all files _, ns_plo, nk_plo, nb_plo = vasp_data.plocar.plo.shape assert nk_plo == self.nktot, "PLOCAR is inconsistent with IBZKPT (number of k-points)" nk_eig = vasp_data.eigenval.nktot assert nk_eig == self.nktot, "PLOCAR is inconsistent with EIGENVAL (number of k-points)" # Check that the number of band is the same in PROJCAR and EIGENVAL assert nb_plo == self.nband, "PLOCAR is inconsistent with EIGENVAL (number of bands)" def debug_density_matrix(self): """ Calculate and output the density and overlap matrix out of projectors defined in el_struct. """ plo = self.proj_raw nproj, ns, nk, nb = plo.shape ions = list(set([param['isite'] for param in self.proj_params])) nions = len(ions) norb = nproj / nions den_mat = np.zeros((ns, nproj, nproj), dtype=np.float64) overlap = np.zeros((ns, nproj, nproj), dtype=np.float64) # ov_min = np.ones((ns, nproj, nproj), dtype=np.float64) * 100.0 # ov_max = np.zeros((ns, nproj, nproj), dtype=np.float64) for ispin in xrange(ns): for ik in xrange(nk): kweight = self.kmesh['kweights'][ik] occ = self.ferw[ispin, ik, :] den_mat[ispin, :, :] += np.dot(plo[:, ispin, ik, :] * occ, plo[:, ispin, ik, :].T.conj()).real * kweight ov = np.dot(plo[:, ispin, ik, :], plo[:, ispin, ik, :].T.conj()).real overlap[ispin, :, :] += ov * kweight # ov_max = np.maximum(ov, ov_max) # ov_min = np.minimum(ov, ov_min) # Output only the site-diagonal parts of the matrices for ispin in xrange(ns): print print " Spin:", ispin + 1 for io, ion in enumerate(ions): print " Site:", ion iorb_inds = [(ip, param['m']) for ip, param in enumerate(self.proj_params) if param['isite'] == ion] norb = len(iorb_inds) dm = np.zeros((norb, norb)) ov = np.zeros((norb, norb)) for ind, iorb in iorb_inds: for ind2, iorb2 in iorb_inds: dm[iorb, iorb2] = den_mat[ispin, ind, ind2] ov[iorb, iorb2] = overlap[ispin, ind, ind2] 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