mirror of
https://github.com/triqs/dft_tools
synced 2024-11-15 02:23:49 +01:00
be21838e30
The new projector input requires a different approach of selecting the projectors for each shell. Specifically, for each site/orbital index defined for a given shell one has to look for the corresponding input projector (from PROJCAR). Also, small fixes were required to make 'ferw' array index order consistent with what is expected in ProjectorShell. This order might eventually be modified.
638 lines
22 KiB
Python
638 lines
22 KiB
Python
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import itertools as it
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import numpy as np
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# 'simplejson' is supposed to be faster than 'json' in stdlib.
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try:
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import simplejson as json
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except ImportError:
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import json
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class Projector:
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"""
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Class describing a local-orbital projector.
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"""
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def __init__(self, matrix, ib1=1, ib2=None, nion=1):
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self.p_matrix = matrix.astype(np.complex128)
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self.norb, self.nb = matrix.shape
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self.nion = nion
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self.ib1 = ib1 - 1
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if not ib2 is None:
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self.ib2 = ib2 - 1
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else:
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self.ib2 = self.nb - 1
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def project_up(self, mat):
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return np.dot(self.p_matrix.conj().T, np.dot(mat, self.p_matrix))
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def project_down(self, mat):
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assert mat.shape == (self.nb, self.nb), " Matrix must match projector in size"
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return np.dot(self.p_matrix, np.dot(mat, self.p_matrix.conj().T))
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def orthogonalize(self):
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"""
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Orthogonalizes a projector.
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Returns an overlap matrix and its eigenvalues for initial projectors.
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"""
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self.p_matrix, overlap, over_eig = orthogonalize_projector(self.p_matrix)
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return (overlap, over_eig)
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################################################################################
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#
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# orthogonalize_projector_matrix()
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#
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################################################################################
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def orthogonalize_projector_matrix(p_matrix):
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"""
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Orthogonalizes a projector defined by a rectangular matrix `p_matrix`.
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Parameters
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----------
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p_matrix (numpy.array[complex]) : matrix `Nm x Nb`, where `Nm` is
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the number of orbitals, `Nb` number of bands
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Returns
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-------
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Orthogonalized projector matrix, initial overlap matrix and its eigenvalues.
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"""
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# Overlap matrix O_{m m'} = \sum_{v} P_{m v} P^{*}_{v m'}
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overlap = np.dot(p_matrix, p_matrix.conj().T)
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# Calculate [O^{-1/2}]_{m m'}
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eig, eigv = np.linalg.eigh(overlap)
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assert np.all(eig > 0.0), ("Negative eigenvalues of the overlap matrix:"
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"projectors are ill-defined")
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sqrt_eig = np.diag(1.0 / np.sqrt(eig))
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shalf = np.dot(eigv, np.dot(sqrt_eig, eigv.conj().T))
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# Apply \tilde{P}_{m v} = \sum_{m'} [O^{-1/2}]_{m m'} P_{m' v}
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p_ortho = np.dot(shalf, p_matrix)
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return (p_ortho, overlap, eig)
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################################################################################
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# check_data_consistency()
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################################################################################
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def check_data_consistency(pars, el_struct):
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"""
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Check the consistency of the VASP data.
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"""
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# Check that ions inside each shell are of the same sort
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for sh in pars.shells:
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assert max(sh['ion_list']) <= el_struct.natom, "Site index in the projected shell exceeds the number of ions in the structure"
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sorts = set([el_struct.type_of_ion[io] for io in sh['ion_list']])
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assert len(sorts) == 1, "Each projected shell must contain only ions of the same sort"
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# Check that ion and orbital lists in shells match those of projectors
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ion_list = sh['ion_list']
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lshell = sh['lshell']
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for ion in ion_list:
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for par in el_struct.proj_params:
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if par['isite'] - 1 == ion and par['l'] == lshell:
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break
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else:
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errmsg = "Projector for isite = %s, l = %s does not match PROJCAR"%(ion + 1, lshell)
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raise Exception(errmsg)
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################################################################################
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# select_bands()
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################################################################################
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def select_bands(eigvals, emin, emax):
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"""
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Select a subset of bands lying within a given energy window.
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The band energies are assumed to be sorted in an ascending order.
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Parameters
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----------
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eigvals (numpy.array) : all eigenvalues
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emin, emax (float) : energy window
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Returns
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-------
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ib_win, nb_min, nb_max :
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"""
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# Sanity check
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if emin > eigvals.max() or emax < eigvals.min():
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raise Exception("Energy window does not overlap with the band structure")
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nk, nband, ns_band = eigvals.shape
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ib_win = np.zeros((nk, ns_band, 2), dtype=np.int32)
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nb_min = 10000000
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nb_max = 0
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for isp in xrange(ns_band):
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for ik in xrange(nk):
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for ib in xrange(nband):
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en = eigvals[ik, ib, isp]
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if en >= emin:
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break
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ib1 = ib
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for ib in xrange(ib1, nband):
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en = eigvals[ik, ib, isp]
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if en > emax:
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break
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else:
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# If we reached the last band add 1 to get the correct bound
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ib += 1
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ib2 = ib - 1
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ib_win[ik, isp, 0] = ib1
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ib_win[ik, isp, 1] = ib2
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nb_min = min(nb_min, ib1)
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nb_max = max(nb_max, ib2)
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return ib_win, nb_min, nb_max
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################################################################################
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################################################################################
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#
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# class ProjectorGroup
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#
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################################################################################
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################################################################################
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class ProjectorGroup:
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"""
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Container of projectors defined within a certain energy window.
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The constructor selects a subset of projectors according to
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the parameters from the config-file (passed in `pars`).
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Parameters:
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- gr_pars (dict) : group parameters from the config-file
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- shells ([ProjectorShell]) : array of ProjectorShell objects
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- eigvals (numpy.array) : array of KS eigenvalues
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"""
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def __init__(self, gr_pars, shells, eigvals, ferw):
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"""
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Constructor
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"""
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self.emin = gr_pars['emin']
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self.emax = gr_pars['emax']
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self.ishells = gr_pars['shells']
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self.ortho = gr_pars['normalize']
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self.normion = gr_pars['normion']
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self.shells = shells
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# Determine the minimum and maximum band numbers
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ib_win, nb_min, nb_max = select_bands(eigvals, self.emin, self.emax)
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self.ib_win = ib_win
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self.nb_min = nb_min
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self.nb_max = nb_max
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# Select projectors within the energy window
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for ish in self.ishells:
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shell = self.shells[ish]
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shell.select_projectors(ib_win, nb_min, nb_max)
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################################################################################
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#
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# nelect_window
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#
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################################################################################
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def nelect_window(self, el_struct):
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"""
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Determines the total number of electrons within the window.
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"""
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self.nelect = 0
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nk, ns_band, _ = self.ib_win.shape
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rspin = 2.0 if ns_band == 1 else 1.0
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for isp in xrange(ns_band):
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for ik in xrange(nk):
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ib1 = self.ib_win[ik, isp, 0]
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ib2 = self.ib_win[ik, isp, 1]
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occ = el_struct.ferw[isp, ik, ib1:ib2]
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kwght = el_struct.kmesh['kweights'][ik]
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self.nelect += occ.sum() * kwght * rspin
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return self.nelect
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################################################################################
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#
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# orthogonalize
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#
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################################################################################
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def orthogonalize(self):
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"""
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Orthogonalize a group of projectors.
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"""
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# Quick exit if no normalization is requested
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if not self.ortho:
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return
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# TODO: add the case of 'normion = True'
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assert not self.normion, "'NORMION = True' is not yet implemented"
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# Determine the dimension of the projector matrix
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# and map the blocks to the big matrix
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i1_bl = 0
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bl_map = [{} for ish in self.ishells]
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for ish in self.ishells:
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_shell = self.shells[ish]
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nion, ns, nk, nlm, nb_max = _shell.proj_win.shape
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bmat_bl = [] # indices corresponding to a big block matrix
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for ion in xrange(nion):
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i2_bl = i1_bl + nlm
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bmat_bl.append((i1_bl, i2_bl))
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i1_bl = i2_bl
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bl_map[ish]['bmat_blocks'] = bmat_bl
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ndim = i2_bl
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p_mat = np.zeros((ndim, nb_max), dtype=np.complex128)
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for isp in xrange(ns):
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for ik in xrange(nk):
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nb = self.ib_win[ik, isp, 1] - self.ib_win[ik, isp, 0] + 1
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# Combine all projectors of the group to one block projector
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for ish in self.ishells:
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shell = self.shells[ish]
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blocks = bl_map[ish]['bmat_blocks']
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for ion in xrange(nion):
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i1, i2 = blocks[ion]
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p_mat[i1:i2, :nb] = shell.proj_win[ion, isp, ik, :nlm, :nb]
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# Now orthogonalize the obtained block projector
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p_orth, overl, eig = orthogonalize_projector_matrix(p_mat)
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# Distribute back projectors in the same order
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for ish in self.ishells:
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shell = self.shells[ish]
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blocks = bl_map[ish]['bmat_blocks']
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for ion in xrange(nion):
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i1, i2 = blocks[ion]
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shell.proj_win[ion, isp, ik, :nlm, :nb] = p_mat[i1:i2, :nb]
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################################################################################
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################################################################################
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#
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# class ProjectorShell
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#
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################################################################################
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################################################################################
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class ProjectorShell:
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"""
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Container of projectors related to a specific shell.
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The constructor pre-selects a subset of projectors according to
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the shell parameters passed from the config-file.
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Parameters:
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- sh_pars (dict) : shell parameters from the config-file
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- proj_raw (numpy.array) : array of raw projectors
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"""
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def __init__(self, sh_pars, proj_raw, proj_params):
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self.lorb = sh_pars['lshell']
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self.ion_list = sh_pars['ion_list']
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self.user_index = sh_pars['user_index']
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try:
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self.tmatrix = sh_pars['tmatrix']
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except KeyError:
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self.tmatrix = None
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self.lm1 = self.lorb**2
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self.lm2 = (self.lorb+1)**2
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if self.tmatrix is None:
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self.ndim = self.lm2 - self.lm1
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else:
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# TODO: generalize this to a tmatrix for every ion
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self.ndim = self.tmatrix.shape[0]
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# Pre-select a subset of projectors (this should be an array view => no memory is wasted)
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# !!! This sucks but I have to change the order of 'ib' and 'ilm' indices here
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# This should perhaps be done right after the projector array is read from PLOCAR
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# self.proj_arr = proj_raw[self.ion_list, :, :, :, self.lm1:self.lm2].transpose((0, 1, 2, 4, 3))
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# We want to select projectors from 'proj_raw' and form an array
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# self.proj_arr[nion, ns, nk, nlm, nb]
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# TODO: think of a smart way of copying the selected projectors
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# perhaps, by redesigning slightly the structure of 'proj_arr' and 'proj_win'
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# or by storing only a mapping between site/orbitals and indices of 'proj_raw'
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# iproj_l = []
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nion = len(self.ion_list)
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nlm = self.lm2 - self.lm1
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_, ns, nk, nb = proj_raw.shape
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self.proj_arr = np.zeros((nion, ns, nk, nlm, nb), dtype=np.complex128)
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for io, ion in enumerate(self.ion_list):
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for m in xrange(nlm):
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# Here we search for the index of the projector with the given isite/l/m indices
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for ip, par in enumerate(proj_params):
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if par['isite'] - 1 == ion and par['l'] == self.lorb and par['m'] == m:
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# iproj_l.append(ip)
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self.proj_arr[io, :, :, m, :] = proj_raw[ip, :, :, :]
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break
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# self.proj_arr = proj_raw[iproj_l, :, :, :].transpose((1, 2, 0, 3))
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################################################################################
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#
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# select_projectors
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#
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################################################################################
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def select_projectors(self, ib_win, nb_min, nb_max):
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"""
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Selects a subset of projectors corresponding to a given energy window.
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"""
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self.ib_win = ib_win
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self.nb_min = nb_min
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self.nb_max = nb_max
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# Set the dimensions of the array
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nb_win = self.nb_max - self.nb_min + 1
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nion, ns, nk, nlm, nbtot = self.proj_arr.shape
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# !!! Note that the order of the two last indices is different !!!
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self.proj_win = np.zeros((nion, ns, nk, nlm, nb_win), dtype=np.complex128)
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# Select projectors for a given energy window
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ns_band = self.ib_win.shape[1]
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for isp in xrange(ns):
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for ik in xrange(nk):
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# TODO: for non-collinear case something else should be done here
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is_b = min(isp, ns_band)
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ib1 = self.ib_win[ik, is_b, 0]
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ib2 = self.ib_win[ik, is_b, 1] + 1
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ib1_win = ib1 - self.nb_min
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ib2_win = ib2 - self.nb_min
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self.proj_win[:, isp, ik, :, ib1_win:ib2_win] = self.proj_arr[:, isp, ik, :, ib1:ib2]
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################################################################################
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#
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# select_projectors
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#
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################################################################################
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def density_matrix(self, el_struct, site_diag=True, spin_diag=True):
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"""
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Returns occupation matrix/matrices for the shell.
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"""
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nion, ns, nk, nlm, nbtot = self.proj_win.shape
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assert site_diag, "site_diag = False is not implemented"
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assert spin_diag, "spin_diag = False is not implemented"
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occ_mats = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
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kweights = el_struct.kmesh['kweights']
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occnums = el_struct.ferw
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ib1 = self.nb_min
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ib2 = self.nb_max + 1
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for isp in xrange(ns):
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for ik, weight, occ in it.izip(it.count(), kweights, occnums[isp, :, :]):
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for io in xrange(nion):
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proj_k = self.proj_win[isp, io, ik, ...]
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occ_mats[isp, io, :, :] += np.dot(proj_k * occ[ib1:ib2],
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proj_k.conj().T).real * weight
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# if not symops is None:
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# occ_mats = symmetrize_matrix_set(occ_mats, symops, ions, perm_map)
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return occ_mats
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################################################################################
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#
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# generate_plo()
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#
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################################################################################
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def generate_plo(conf_pars, el_struct):
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"""
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Parameters
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----------
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conf_pars (dict) : dictionary of input parameters (from conf-file)
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el_struct : ElectronicStructure object
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"""
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check_data_consistency(conf_pars, el_struct)
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proj_raw = el_struct.proj_raw
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try:
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efermi = conf_pars.general['efermi']
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except (KeyError, AttributeError):
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efermi = el_struct.efermi
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# eigvals(nktot, nband, ispin) are defined with respect to the Fermi level
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eigvals = el_struct.eigvals - efermi
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pshells = []
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for sh_par in conf_pars.shells:
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pshells.append(ProjectorShell(sh_par, proj_raw, el_struct.proj_params))
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pgroups = []
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for gr_par in conf_pars.groups:
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pgroup = ProjectorGroup(gr_par, pshells, eigvals, el_struct.ferw)
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# pgroup.orthogonalize()
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pgroups.append(pgroup)
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return pshells, pgroups
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# TODO: k-points with weights should be stored once and for all
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################################################################################
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#
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# kpoints_output
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#
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################################################################################
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def kpoints_output(basename, el_struct):
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"""
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Outputs k-point data into a text file.
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"""
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kmesh = el_struct.kmesh
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fname = basename + '.kpoints'
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with open(fname, 'wt') as f:
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f.write("# Number of k-points: nktot\n")
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nktot = kmesh['nktot']
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f.write("%i\n"%(nktot))
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# TODO: add the output of reciprocal lattice vectors
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f.write("# List of k-points with weights\n")
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for ik in xrange(nktot):
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kx, ky, kz = kmesh['kpoints'][ik, :]
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kwght = kmesh['kweights'][ik]
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f.write("%15.10f%15.10f%15.10f%20.10f\n"%(kx, ky, kz, kwght))
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# Check if there are tetrahedra defined and if they are, output them
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try:
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ntet = kmesh['ntet']
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volt = kmesh['volt']
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f.write("\n# Number of tetrahedra and volume: ntet, volt\n")
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f.write("%i %s\n"%(ntet, volt))
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f.write("# List of tetrahedra: imult, ik1, ..., ik4\n")
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for it in xrange(ntet):
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f.write(' '.join(map("{0:d}".format, *kmesh['itet'][it, :])) + '\n')
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except KeyError:
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pass
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################################################################################
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#
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# ctrl_output
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#
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################################################################################
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def ctrl_output(conf_pars, el_struct, ng):
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"""
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Outputs a ctrl-file.
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"""
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ctrl_fname = conf_pars.general['basename'] + '.ctrl'
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head_dict = {}
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|
|
# TODO: Add output of tetrahedra
|
|
# Construct the header dictionary
|
|
head_dict['ngroups'] = ng
|
|
head_dict['nk'] = el_struct.kmesh['nktot']
|
|
head_dict['ns'] = el_struct.nspin
|
|
head_dict['nc_flag'] = 1 if el_struct.nc_flag else 0
|
|
# head_dict['efermi'] = conf_pars.general['efermi'] # We probably don't need Efermi
|
|
|
|
header = json.dumps(head_dict, indent=4, separators=(',', ': '))
|
|
|
|
print " Storing ctrl-file..."
|
|
with open(ctrl_fname, 'wt') as f:
|
|
f.write(header + "\n")
|
|
f.write("#END OF HEADER\n")
|
|
|
|
f.write("# k-points and weights\n")
|
|
labels = ['kx', 'ky', 'kz', 'kweight']
|
|
out = "".join(map(lambda s: s.center(15), labels))
|
|
f.write("#" + out + "\n")
|
|
for ik, kp in enumerate(el_struct.kmesh['kpoints']):
|
|
tmp1 = "".join(map("{0:15.10f}".format, kp))
|
|
out = tmp1 + "{0:16.10f}".format(el_struct.kmesh['kweights'][ik])
|
|
f.write(out + "\n")
|
|
|
|
|
|
################################################################################
|
|
#
|
|
# plo_output
|
|
#
|
|
################################################################################
|
|
def plo_output(conf_pars, el_struct, pshells, pgroups):
|
|
"""
|
|
Outputs PLO groups into text files.
|
|
|
|
Filenames are defined by <basename> that is passed from config-file.
|
|
All necessary general parameters are stored in a file '<basename>.ctrl'.
|
|
|
|
Each group is stored in a '<basename>.plog<Ng>' file. The format is the
|
|
following:
|
|
|
|
# Energy window: emin, emax
|
|
ib_min, ib_max
|
|
nelect
|
|
# Eigenvalues
|
|
isp, ik1, kx, ky, kz, kweight
|
|
ib1, ib2
|
|
eig1
|
|
eig2
|
|
...
|
|
eigN
|
|
ik2, kx, ky, kz, kweight
|
|
...
|
|
|
|
# Projected shells
|
|
Nshells
|
|
# Shells: <shell indices>
|
|
# Shell <1>
|
|
Shell 1
|
|
ndim
|
|
# complex arrays: plo(ns, nion, ndim, nb)
|
|
...
|
|
# Shells: <shell indices>
|
|
# Shell <2>
|
|
Shell 2
|
|
...
|
|
|
|
"""
|
|
for ig, pgroup in enumerate(pgroups):
|
|
plo_fname = conf_pars.general['basename'] + '.pg%i'%(ig + 1)
|
|
print " Storing PLO-group file '%s'..."%(plo_fname)
|
|
head_dict = {}
|
|
|
|
head_dict['ewindow'] = (pgroup.emin, pgroup.emax)
|
|
head_dict['nb_max'] = pgroup.nb_max
|
|
|
|
# Number of electrons within the window
|
|
head_dict['nelect'] = pgroup.nelect_window(el_struct)
|
|
print " Density within window:", head_dict['nelect']
|
|
|
|
head_shells = []
|
|
for ish in pgroup.ishells:
|
|
shell = pgroup.shells[ish]
|
|
sh_dict = {}
|
|
sh_dict['shell_index'] = ish
|
|
sh_dict['lorb'] = shell.lorb
|
|
sh_dict['ndim'] = shell.ndim
|
|
# Convert ion indices from the internal representation (starting from 0)
|
|
# to conventional VASP representation (starting from 1)
|
|
ion_output = [io + 1 for io in shell.ion_list]
|
|
sh_dict['ion_list'] = ion_output
|
|
sh_dict['ion_sort'] = el_struct.type_of_ion[shell.ion_list[0]]
|
|
|
|
# TODO: add the output of transformation matrices
|
|
|
|
head_shells.append(sh_dict)
|
|
|
|
head_dict['shells'] = head_shells
|
|
|
|
header = json.dumps(head_dict, indent=4, separators=(',', ': '))
|
|
|
|
with open(plo_fname, 'wt') as f:
|
|
f.write(header + "\n")
|
|
f.write("#END OF HEADER\n")
|
|
|
|
# Eigenvalues within the window
|
|
f.write("# Eigenvalues within the energy window: %s, %s\n"%(pgroup.emin, pgroup.emax))
|
|
nk, nband, ns_band = el_struct.eigvals.shape
|
|
for isp in xrange(ns_band):
|
|
f.write("# is = %i\n"%(isp + 1))
|
|
for ik in xrange(nk):
|
|
ib1, ib2 = pgroup.ib_win[ik, isp, 0], pgroup.ib_win[ik, isp, 1]
|
|
f.write(" %i %i\n"%(ib1, ib2))
|
|
for ib in xrange(ib1, ib2 + 1):
|
|
f.write("%15.7f\n"%(el_struct.eigvals[ik, ib, isp]))
|
|
|
|
# Projected shells
|
|
f.write("# Projected shells\n")
|
|
f.write("# Shells: %s\n"%(pgroup.ishells))
|
|
for ish in pgroup.ishells:
|
|
shell = pgroup.shells[ish]
|
|
f.write("# Shell %i\n"%(ish))
|
|
|
|
nion, ns, nk, nlm, nb = shell.proj_win.shape
|
|
for isp in xrange(ns):
|
|
f.write("# is = %i\n"%(isp + 1))
|
|
for ik in xrange(nk):
|
|
f.write("# ik = %i\n"%(ik + 1))
|
|
for ion in xrange(nion):
|
|
for ilm in xrange(nlm):
|
|
ib1, ib2 = pgroup.ib_win[ik, isp, 0], pgroup.ib_win[ik, isp, 1]
|
|
ib1_win = ib1 - shell.nb_min
|
|
ib2_win = ib2 - shell.nb_min
|
|
for ib in xrange(ib1_win, ib2_win + 1):
|
|
p = shell.proj_win[ion, isp, ik, ilm, ib]
|
|
f.write("{0:16.10f}{1:16.10f}\n".format(p.real, p.imag))
|
|
f.write("\n")
|
|
|
|
|
|
################################################################################
|
|
#
|
|
# output_as_text
|
|
#
|
|
################################################################################
|
|
def output_as_text(pars, el_struct, pshells, pgroups):
|
|
"""
|
|
Output all information necessary for the converter as text files.
|
|
"""
|
|
ctrl_output(pars, el_struct, len(pgroups))
|
|
plo_output(pars, el_struct, pshells, pgroups)
|
|
|