mirror of
https://github.com/triqs/dft_tools
synced 2024-12-21 11:53:41 +01:00
Restructured the source files
The classes ProjectorShell and ProjectorGroup are now defined in different source files. This makes 'plotools.py' only contain routines that control the data flows, including consistency checks and output.
This commit is contained in:
Oleg E. Peil
parent
b285f37eca
commit
61395b12fa
@ -1,7 +1,6 @@
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import itertools as it
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import numpy as np
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import vasp.atm.c_atm_dos as c_atm_dos
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np.set_printoptions(suppress=True)
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@ -50,39 +49,6 @@ class Projector:
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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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@ -108,481 +74,6 @@ def check_data_consistency(pars, el_struct):
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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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ib_min = 10000000
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ib_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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assert ib1 <= ib2, "No bands inside the window for ik = %s"%(ik)
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ib_win[ik, isp, 0] = ib1
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ib_win[ik, isp, 1] = ib2
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ib_min = min(ib_min, ib1)
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ib_max = max(ib_max, ib2)
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return ib_win, ib_min, ib_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, self.emax = gr_pars['ewindow']
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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, ib_min, ib_max = select_bands(eigvals, self.emin, self.emax)
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self.ib_win = ib_win
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self.ib_min = ib_min
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self.ib_max = ib_max
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self.nb_max = ib_max - ib_min + 1
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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, ib_min, ib_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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# print "ik = ", ik
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# print overl.real
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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_orth[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, nc_flag):
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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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self.nc_flag = nc_flag
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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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self.ndim = self.extract_tmatrices(sh_pars)
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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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# extract_tmatrices
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#
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################################################################################
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def extract_tmatrices(self, sh_pars):
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"""
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Extracts and interprets transformation matrices provided by the
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config-parser.
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There are two relevant options in 'sh_pars':
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'tmatrix' : a transformation matrix applied to all ions in the shell
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'tmatrices': interpreted as a set of transformation matrices for each ion.
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If both of the options are present a warning is issued and 'tmatrices'
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supersedes 'tmatrix'.
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"""
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nion = len(self.ion_list)
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nm = self.lm2 - self.lm1
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if 'tmatrices' in sh_pars:
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if 'tmatrix' in sh_pars:
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mess = "Both TRANSFORM and TRANSFILE are specified, TRANSFORM will be ignored."
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issue_warning(mess)
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raw_matrices = sh_pars['tmatrices']
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nrow, ncol = raw_matrices.shape
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assert nrow%nion == 0, "Number of rows in TRANSFILE must be divisible by the number of ions"
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assert ncol%nm == 0, "Number of columns in TRANSFILE must be divisible by the number of orbitals 2*l + 1"
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nr = nrow / nion
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nsize = ncol / nm
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assert nsize in (1, 2, 4), "Number of columns in TRANSFILE must be divisible by either 1, 2, or 4"
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#
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# Determine the spin-dimension and whether the matrices are real or complex
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#
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# if nsize == 1 or nsize == 2:
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# Matrices (either real or complex) are spin-independent
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# nls_dim = nm
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# if msize == 2:
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# is_complex = True
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# else:
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# is_complex = False
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# elif nsize = 4:
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# Matrices are complex and spin-dependent
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# nls_dim = 2 * nm
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# is_complex = True
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#
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is_complex = nsize > 1
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ns_dim = max(1, nsize / 2)
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# Dimension of the orbital subspace
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assert nr%ns_dim == 0, "Number of rows in TRANSFILE is not compatible with the spin dimension"
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ndim = nr / ns_dim
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self.tmatrices = np.zeros((nion, nr, nm * ns_dim), dtype=np.complex128)
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if is_complex:
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raw_matrices = raw_matrices[:, ::2] + raw_matrices[:, 1::2] * 1j
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for io in xrange(nion):
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i1 = io * nr
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i2 = (io + 1) * nr
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self.tmatrices[io, :, :] = raw_matrices[i1:i2, :]
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return ndim
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if 'tmatrix' in sh_pars:
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raw_matrix = sh_pars['tmatrix']
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nrow, ncol = raw_matrix.shape
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assert ncol%nm == 0, "Number of columns in TRANSFORM must be divisible by the number of orbitals 2*l + 1"
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# Only spin-independent matrices are expected here
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nsize = ncol / nm
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assert nsize in (1, 2), "Number of columns in TRANSFORM must be divisible by either 1 or 2"
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is_complex = nsize > 1
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if is_complex:
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matrix = raw_matrix[:, ::2] + raw_matrix[:, 1::2] * 1j
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else:
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matrix = raw_matrix
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ndim = nrow
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self.tmatrices = np.zeros((nion, nrow, nm), dtype=np.complex128)
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for io in xrange(nion):
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self.tmatrices[io, :, :] = raw_matrix
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return ndim
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# If no transformation matrices are provided define a default one
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ns_dim = 2 if self.nc_flag else 1
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ndim = nm * ns_dim
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self.tmatrices = np.zeros((nion, ndim, ndim), dtype=np.complex128)
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for io in xrange(nion):
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self.tmatrices[io, :, :] = np.identity(ndim, dtype=np.complex128)
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return ndim
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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, ib_min, ib_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.ib_min = ib_min
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self.ib_max = ib_max
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nb_max = ib_max - ib_min + 1
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# Set the dimensions of the array
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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_max), 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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ib_win = ib2 - ib1
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self.proj_win[:, isp, ik, :, :ib_win] = self.proj_arr[:, isp, ik, :, ib1:ib2]
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################################################################################
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#
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# density_matrix
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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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overlaps = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
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# self.proj_win = np.zeros((nion, ns, nk, nlm, nb_max), dtype=np.complex128)
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kweights = el_struct.kmesh['kweights']
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occnums = el_struct.ferw
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ib1 = self.ib_min
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ib2 = self.ib_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[io, isp, 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
|
||||
overlaps[isp, io, :, :] += np.dot(proj_k,
|
||||
proj_k.conj().T).real * weight
|
||||
|
||||
# if not symops is None:
|
||||
# occ_mats = symmetrize_matrix_set(occ_mats, symops, ions, perm_map)
|
||||
|
||||
return occ_mats, overlaps
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# density_of_states
|
||||
#
|
||||
################################################################################
|
||||
def density_of_states(self, el_struct, emesh):
|
||||
"""
|
||||
Returns projected DOS for the shell.
|
||||
"""
|
||||
nion, ns, nk, nlm, nbtot = self.proj_win.shape
|
||||
|
||||
# There is a problem with data storage structure of projectors that will
|
||||
# make life more complicated. The problem is that band-indices of projectors
|
||||
# for different k-points do not match because we store 'nb_max' values starting
|
||||
# from 0.
|
||||
nb_max = self.ib_max - self.ib_min + 1
|
||||
ns_band = self.ib_win.shape[1]
|
||||
|
||||
ne = len(emesh)
|
||||
dos = np.zeros((ne, ns, nion, nlm))
|
||||
w_k = np.zeros((nk, nb_max, ns, nion, nlm), dtype=np.complex128)
|
||||
for isp in xrange(ns):
|
||||
for ik in xrange(nk):
|
||||
is_b = min(isp, ns_band)
|
||||
ib1 = self.ib_win[ik, is_b, 0]
|
||||
ib2 = self.ib_win[ik, is_b, 1] + 1
|
||||
for ib_g in xrange(ib1, ib2):
|
||||
for io in xrange(nion):
|
||||
# Note the difference between 'ib' and 'ibn':
|
||||
# 'ib' counts from 0 to 'nb_k - 1'
|
||||
# 'ibn' counts from 'ib1 - ib_min' to 'ib2 - ib_min'
|
||||
ib = ib_g - ib1
|
||||
ibn = ib_g - self.ib_min
|
||||
proj_k = self.proj_win[io, isp, ik, :, ib]
|
||||
w_k[ik, ib, isp, io, :] = proj_k * proj_k.conj()
|
||||
|
||||
# eigv_ef = el_struct.eigvals[ik, ib, isp] - el_struct.efermi
|
||||
itt = el_struct.kmesh['itet'].T
|
||||
# k-indices are starting from 0 in Python
|
||||
itt[1:, :] -= 1
|
||||
for isp in xrange(ns):
|
||||
for ib, eigk in enumerate(el_struct.eigvals[:, self.ib_min:self.ib_max+1, isp].T):
|
||||
for ie, e in enumerate(emesh):
|
||||
eigk_ef = eigk - el_struct.efermi
|
||||
cti = c_atm_dos.dos_weights_3d(eigk_ef, e, itt)
|
||||
for im in xrange(nlm):
|
||||
for io in xrange(nion):
|
||||
dos[ie, isp, io, im] += np.sum((cti * w_k[itt[1:, :], ib, isp, io, im].real).sum(0) * itt[0, :])
|
||||
|
||||
dos *= 2 * el_struct.kmesh['volt']
|
||||
# for isp in xrange(ns):
|
||||
# for ik, weight, occ in it.izip(it.count(), kweights, occnums[isp, :, :]):
|
||||
# for io in xrange(nion):
|
||||
# proj_k = self.proj_win[isp, io, ik, ...]
|
||||
# occ_mats[isp, io, :, :] += np.dot(proj_k * occ[ib1:ib2],
|
||||
# proj_k.conj().T).real * weight
|
||||
# overlaps[isp, io, :, :] += np.dot(proj_k,
|
||||
# proj_k.conj().T).real * weight
|
||||
|
||||
# if not symops is None:
|
||||
# occ_mats = symmetrize_matrix_set(occ_mats, symops, ions, perm_map)
|
||||
|
||||
return dos
|
||||
|
||||
|
||||
|
||||
################################################################################
|
||||
#
|
||||
|
||||
269
python/vasp/proj_group.py
Normal file
269
python/vasp/proj_group.py
Normal file
@ -0,0 +1,269 @@
|
||||
|
||||
import numpy as np
|
||||
|
||||
np.set_printoptions(suppress=True)
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# orthogonalize_projector_matrix()
|
||||
#
|
||||
################################################################################
|
||||
def orthogonalize_projector_matrix(p_matrix):
|
||||
"""
|
||||
Orthogonalizes a projector defined by a rectangular matrix `p_matrix`.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
||||
p_matrix (numpy.array[complex]) : matrix `Nm x Nb`, where `Nm` is
|
||||
the number of orbitals, `Nb` number of bands
|
||||
|
||||
Returns
|
||||
-------
|
||||
|
||||
Orthogonalized projector matrix, initial overlap matrix and its eigenvalues.
|
||||
"""
|
||||
# Overlap matrix O_{m m'} = \sum_{v} P_{m v} P^{*}_{v m'}
|
||||
overlap = np.dot(p_matrix, p_matrix.conj().T)
|
||||
# Calculate [O^{-1/2}]_{m m'}
|
||||
eig, eigv = np.linalg.eigh(overlap)
|
||||
assert np.all(eig > 0.0), ("Negative eigenvalues of the overlap matrix:"
|
||||
"projectors are ill-defined")
|
||||
sqrt_eig = np.diag(1.0 / np.sqrt(eig))
|
||||
shalf = np.dot(eigv, np.dot(sqrt_eig, eigv.conj().T))
|
||||
# Apply \tilde{P}_{m v} = \sum_{m'} [O^{-1/2}]_{m m'} P_{m' v}
|
||||
p_ortho = np.dot(shalf, p_matrix)
|
||||
|
||||
return (p_ortho, overlap, eig)
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# select_bands()
|
||||
#
|
||||
################################################################################
|
||||
def select_bands(eigvals, emin, emax):
|
||||
"""
|
||||
Select a subset of bands lying within a given energy window.
|
||||
The band energies are assumed to be sorted in an ascending order.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
||||
eigvals (numpy.array) : all eigenvalues
|
||||
emin, emax (float) : energy window
|
||||
|
||||
Returns
|
||||
-------
|
||||
|
||||
ib_win, nb_min, nb_max :
|
||||
"""
|
||||
# Sanity check
|
||||
if emin > eigvals.max() or emax < eigvals.min():
|
||||
raise Exception("Energy window does not overlap with the band structure")
|
||||
|
||||
nk, nband, ns_band = eigvals.shape
|
||||
ib_win = np.zeros((nk, ns_band, 2), dtype=np.int32)
|
||||
|
||||
ib_min = 10000000
|
||||
ib_max = 0
|
||||
for isp in xrange(ns_band):
|
||||
for ik in xrange(nk):
|
||||
for ib in xrange(nband):
|
||||
en = eigvals[ik, ib, isp]
|
||||
if en >= emin:
|
||||
break
|
||||
ib1 = ib
|
||||
for ib in xrange(ib1, nband):
|
||||
en = eigvals[ik, ib, isp]
|
||||
if en > emax:
|
||||
break
|
||||
else:
|
||||
# If we reached the last band add 1 to get the correct bound
|
||||
ib += 1
|
||||
ib2 = ib - 1
|
||||
|
||||
assert ib1 <= ib2, "No bands inside the window for ik = %s"%(ik)
|
||||
|
||||
ib_win[ik, isp, 0] = ib1
|
||||
ib_win[ik, isp, 1] = ib2
|
||||
|
||||
ib_min = min(ib_min, ib1)
|
||||
ib_max = max(ib_max, ib2)
|
||||
|
||||
return ib_win, ib_min, ib_max
|
||||
|
||||
################################################################################
|
||||
################################################################################
|
||||
#
|
||||
# class ProjectorGroup
|
||||
#
|
||||
################################################################################
|
||||
################################################################################
|
||||
class ProjectorGroup:
|
||||
"""
|
||||
Container of projectors defined within a certain energy window.
|
||||
|
||||
The constructor selects a subset of projectors according to
|
||||
the parameters from the config-file (passed in `pars`).
|
||||
|
||||
Parameters:
|
||||
|
||||
- gr_pars (dict) : group parameters from the config-file
|
||||
- shells ([ProjectorShell]) : array of ProjectorShell objects
|
||||
- eigvals (numpy.array) : array of KS eigenvalues
|
||||
|
||||
"""
|
||||
def __init__(self, gr_pars, shells, eigvals, ferw):
|
||||
"""
|
||||
Constructor
|
||||
"""
|
||||
self.emin, self.emax = gr_pars['ewindow']
|
||||
self.ishells = gr_pars['shells']
|
||||
self.ortho = gr_pars['normalize']
|
||||
self.normion = gr_pars['normion']
|
||||
|
||||
self.shells = shells
|
||||
|
||||
# Determine the minimum and maximum band numbers
|
||||
ib_win, ib_min, ib_max = select_bands(eigvals, self.emin, self.emax)
|
||||
self.ib_win = ib_win
|
||||
self.ib_min = ib_min
|
||||
self.ib_max = ib_max
|
||||
self.nb_max = ib_max - ib_min + 1
|
||||
|
||||
# Select projectors within the energy window
|
||||
for ish in self.ishells:
|
||||
shell = self.shells[ish]
|
||||
shell.select_projectors(ib_win, ib_min, ib_max)
|
||||
|
||||
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# nelect_window
|
||||
#
|
||||
################################################################################
|
||||
def nelect_window(self, el_struct):
|
||||
"""
|
||||
Determines the total number of electrons within the window.
|
||||
"""
|
||||
self.nelect = 0
|
||||
nk, ns_band, _ = self.ib_win.shape
|
||||
rspin = 2.0 if ns_band == 1 else 1.0
|
||||
for isp in xrange(ns_band):
|
||||
for ik in xrange(nk):
|
||||
ib1 = self.ib_win[ik, isp, 0]
|
||||
ib2 = self.ib_win[ik, isp, 1]
|
||||
occ = el_struct.ferw[isp, ik, ib1:ib2]
|
||||
kwght = el_struct.kmesh['kweights'][ik]
|
||||
self.nelect += occ.sum() * kwght * rspin
|
||||
|
||||
return self.nelect
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# orthogonalize
|
||||
#
|
||||
################################################################################
|
||||
def orthogonalize(self):
|
||||
"""
|
||||
Orthogonalize a group of projectors.
|
||||
|
||||
There are two options for orthogonalizing projectors:
|
||||
1. one ensures orthogonality on each site (NORMION = True);
|
||||
2. one ensures orthogonality for subsets of sites (NORMION = False),
|
||||
as, e.g., in cluster calculations.
|
||||
|
||||
In order to handle various cases the strategy is first to build a
|
||||
mapping that selects appropriate blocks of raw projectors, forms a
|
||||
matrix consisting of these blocks, orthogonalize the matrix, and use
|
||||
the mapping again to write the orthogonalized projectors back to the
|
||||
projector arrays. Note that the blocks can comprise several projector arrays
|
||||
contained in different projector shells.
|
||||
|
||||
Mapping is defined as a list of 'block_maps' corresponding to subsets
|
||||
of projectors to be orthogonalized. Each subset corresponds to a subset of sites
|
||||
and spans all orbital indices. defined by 'bl_map' as
|
||||
|
||||
bl_map = [((i1_start, i1_end), (i1_shell, i1_ion)),
|
||||
((i2_start, i2_end), (i2_shell, i2_ion)),
|
||||
...],
|
||||
|
||||
where `iX_start`, `iX_end` is the range of indices of the block matrix
|
||||
(in Python convention `iX_end = iX_last + 1`, with `iX_last` being the last index
|
||||
of the range),
|
||||
`iX_shell` and `iX_ion` the shell and site indices. The length of the range
|
||||
should be consistent with 'nlm' dimensions of a corresponding shell, i.e.,
|
||||
`iX_end - iX_start = nlm[iX_shell]`.
|
||||
|
||||
Consider particular cases:
|
||||
1. Orthogonality is ensured on each site (NORMION = True).
|
||||
For each site 'ion' we have the following mapping:
|
||||
|
||||
block_maps = [bl_map[ion] for ion in xrange(shell.nion)
|
||||
for shell in shells]
|
||||
|
||||
bl_map = [((i1_start, i1_end), (i1_shell, ion)),
|
||||
((i2_start, i2_end), (i2_shell, ion)),
|
||||
...],
|
||||
|
||||
2. Orthogonality is ensured on all sites within the group (NORMION = True).
|
||||
The mapping:
|
||||
|
||||
block_maps = [bl_map]
|
||||
|
||||
bl_map = [((i1_start, i1_end), (i1_shell, i1_shell.ion1)),
|
||||
((i1_start, i1_end), (i1_shell, i1_shell.ion2)),
|
||||
...
|
||||
((i2_start, i2_end), (i2_shell, i2_shell.ion1)),
|
||||
((i2_start, i2_end), (i2_shell, i2_shell.ion2)),
|
||||
...],
|
||||
|
||||
"""
|
||||
# Quick exit if no normalization is requested
|
||||
if not self.ortho:
|
||||
return
|
||||
|
||||
# TODO: add the case of 'normion = True'
|
||||
assert not self.normion, "'NORMION = True' is not yet implemented"
|
||||
|
||||
# Determine the dimension of the projector matrix
|
||||
# and map the blocks to the big matrix
|
||||
i1_bl = 0
|
||||
bl_map = [{} for ish in self.ishells]
|
||||
for ish in self.ishells:
|
||||
_shell = self.shells[ish]
|
||||
nion, ns, nk, nlm, nb_max = _shell.proj_win.shape
|
||||
bmat_bl = [] # indices corresponding to a big block matrix
|
||||
for ion in xrange(nion):
|
||||
i2_bl = i1_bl + nlm
|
||||
bmat_bl.append((i1_bl, i2_bl))
|
||||
i1_bl = i2_bl
|
||||
bl_map[ish]['bmat_blocks'] = bmat_bl
|
||||
|
||||
ndim = i2_bl
|
||||
p_mat = np.zeros((ndim, nb_max), dtype=np.complex128)
|
||||
for isp in xrange(ns):
|
||||
for ik in xrange(nk):
|
||||
nb = self.ib_win[ik, isp, 1] - self.ib_win[ik, isp, 0] + 1
|
||||
# Combine all projectors of the group to one block projector
|
||||
for ish in self.ishells:
|
||||
shell = self.shells[ish]
|
||||
blocks = bl_map[ish]['bmat_blocks']
|
||||
for ion in xrange(nion):
|
||||
i1, i2 = blocks[ion]
|
||||
p_mat[i1:i2, :nb] = shell.proj_win[ion, isp, ik, :nlm, :nb]
|
||||
# Now orthogonalize the obtained block projector
|
||||
p_orth, overl, eig = orthogonalize_projector_matrix(p_mat)
|
||||
# print "ik = ", ik
|
||||
# print overl.real
|
||||
# Distribute back projectors in the same order
|
||||
for ish in self.ishells:
|
||||
shell = self.shells[ish]
|
||||
blocks = bl_map[ish]['bmat_blocks']
|
||||
for ion in xrange(nion):
|
||||
i1, i2 = blocks[ion]
|
||||
shell.proj_win[ion, isp, ik, :nlm, :nb] = p_orth[i1:i2, :nb]
|
||||
|
||||
|
||||
|
||||
314
python/vasp/proj_shell.py
Normal file
314
python/vasp/proj_shell.py
Normal file
@ -0,0 +1,314 @@
|
||||
|
||||
import itertools as it
|
||||
import numpy as np
|
||||
import vasp.atm.c_atm_dos as c_atm_dos
|
||||
|
||||
np.set_printoptions(suppress=True)
|
||||
|
||||
def issue_warning(message):
|
||||
"""
|
||||
Issues a warning.
|
||||
"""
|
||||
print
|
||||
print " !!! WARNING !!!: " + message
|
||||
print
|
||||
|
||||
################################################################################
|
||||
################################################################################
|
||||
#
|
||||
# class ProjectorShell
|
||||
#
|
||||
################################################################################
|
||||
################################################################################
|
||||
class ProjectorShell:
|
||||
"""
|
||||
Container of projectors related to a specific shell.
|
||||
|
||||
The constructor pre-selects a subset of projectors according to
|
||||
the shell parameters passed from the config-file.
|
||||
|
||||
Parameters:
|
||||
|
||||
- sh_pars (dict) : shell parameters from the config-file
|
||||
- proj_raw (numpy.array) : array of raw projectors
|
||||
|
||||
"""
|
||||
def __init__(self, sh_pars, proj_raw, proj_params, nc_flag):
|
||||
self.lorb = sh_pars['lshell']
|
||||
self.ion_list = sh_pars['ion_list']
|
||||
self.user_index = sh_pars['user_index']
|
||||
self.nc_flag = nc_flag
|
||||
# try:
|
||||
# self.tmatrix = sh_pars['tmatrix']
|
||||
# except KeyError:
|
||||
# self.tmatrix = None
|
||||
|
||||
self.lm1 = self.lorb**2
|
||||
self.lm2 = (self.lorb+1)**2
|
||||
|
||||
self.ndim = self.extract_tmatrices(sh_pars)
|
||||
# if self.tmatrix is None:
|
||||
# self.ndim = self.lm2 - self.lm1
|
||||
# else:
|
||||
## TODO: generalize this to a tmatrix for every ion
|
||||
# self.ndim = self.tmatrix.shape[0]
|
||||
|
||||
# Pre-select a subset of projectors (this should be an array view => no memory is wasted)
|
||||
# !!! This sucks but I have to change the order of 'ib' and 'ilm' indices here
|
||||
# This should perhaps be done right after the projector array is read from PLOCAR
|
||||
# self.proj_arr = proj_raw[self.ion_list, :, :, :, self.lm1:self.lm2].transpose((0, 1, 2, 4, 3))
|
||||
# We want to select projectors from 'proj_raw' and form an array
|
||||
# self.proj_arr[nion, ns, nk, nlm, nb]
|
||||
# TODO: think of a smart way of copying the selected projectors
|
||||
# perhaps, by redesigning slightly the structure of 'proj_arr' and 'proj_win'
|
||||
# or by storing only a mapping between site/orbitals and indices of 'proj_raw'
|
||||
# iproj_l = []
|
||||
nion = len(self.ion_list)
|
||||
nlm = self.lm2 - self.lm1
|
||||
_, ns, nk, nb = proj_raw.shape
|
||||
self.proj_arr = np.zeros((nion, ns, nk, nlm, nb), dtype=np.complex128)
|
||||
for io, ion in enumerate(self.ion_list):
|
||||
for m in xrange(nlm):
|
||||
# Here we search for the index of the projector with the given isite/l/m indices
|
||||
for ip, par in enumerate(proj_params):
|
||||
if par['isite'] - 1 == ion and par['l'] == self.lorb and par['m'] == m:
|
||||
# iproj_l.append(ip)
|
||||
self.proj_arr[io, :, :, m, :] = proj_raw[ip, :, :, :]
|
||||
break
|
||||
|
||||
# self.proj_arr = proj_raw[iproj_l, :, :, :].transpose((1, 2, 0, 3))
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# extract_tmatrices
|
||||
#
|
||||
################################################################################
|
||||
def extract_tmatrices(self, sh_pars):
|
||||
"""
|
||||
Extracts and interprets transformation matrices provided by the
|
||||
config-parser.
|
||||
There are two relevant options in 'sh_pars':
|
||||
|
||||
'tmatrix' : a transformation matrix applied to all ions in the shell
|
||||
'tmatrices': interpreted as a set of transformation matrices for each ion.
|
||||
|
||||
If both of the options are present a warning is issued and 'tmatrices'
|
||||
supersedes 'tmatrix'.
|
||||
"""
|
||||
nion = len(self.ion_list)
|
||||
nm = self.lm2 - self.lm1
|
||||
|
||||
if 'tmatrices' in sh_pars:
|
||||
if 'tmatrix' in sh_pars:
|
||||
mess = "Both TRANSFORM and TRANSFILE are specified, TRANSFORM will be ignored."
|
||||
issue_warning(mess)
|
||||
|
||||
raw_matrices = sh_pars['tmatrices']
|
||||
nrow, ncol = raw_matrices.shape
|
||||
|
||||
assert nrow%nion == 0, "Number of rows in TRANSFILE must be divisible by the number of ions"
|
||||
assert ncol%nm == 0, "Number of columns in TRANSFILE must be divisible by the number of orbitals 2*l + 1"
|
||||
|
||||
nr = nrow / nion
|
||||
nsize = ncol / nm
|
||||
assert nsize in (1, 2, 4), "Number of columns in TRANSFILE must be divisible by either 1, 2, or 4"
|
||||
#
|
||||
# Determine the spin-dimension and whether the matrices are real or complex
|
||||
#
|
||||
# if nsize == 1 or nsize == 2:
|
||||
# Matrices (either real or complex) are spin-independent
|
||||
# nls_dim = nm
|
||||
# if msize == 2:
|
||||
# is_complex = True
|
||||
# else:
|
||||
# is_complex = False
|
||||
# elif nsize = 4:
|
||||
# Matrices are complex and spin-dependent
|
||||
# nls_dim = 2 * nm
|
||||
# is_complex = True
|
||||
#
|
||||
is_complex = nsize > 1
|
||||
ns_dim = max(1, nsize / 2)
|
||||
|
||||
# Dimension of the orbital subspace
|
||||
assert nr%ns_dim == 0, "Number of rows in TRANSFILE is not compatible with the spin dimension"
|
||||
ndim = nr / ns_dim
|
||||
|
||||
self.tmatrices = np.zeros((nion, nr, nm * ns_dim), dtype=np.complex128)
|
||||
|
||||
if is_complex:
|
||||
raw_matrices = raw_matrices[:, ::2] + raw_matrices[:, 1::2] * 1j
|
||||
|
||||
for io in xrange(nion):
|
||||
i1 = io * nr
|
||||
i2 = (io + 1) * nr
|
||||
self.tmatrices[io, :, :] = raw_matrices[i1:i2, :]
|
||||
|
||||
return ndim
|
||||
|
||||
if 'tmatrix' in sh_pars:
|
||||
raw_matrix = sh_pars['tmatrix']
|
||||
nrow, ncol = raw_matrix.shape
|
||||
|
||||
assert ncol%nm == 0, "Number of columns in TRANSFORM must be divisible by the number of orbitals 2*l + 1"
|
||||
|
||||
# Only spin-independent matrices are expected here
|
||||
nsize = ncol / nm
|
||||
assert nsize in (1, 2), "Number of columns in TRANSFORM must be divisible by either 1 or 2"
|
||||
|
||||
is_complex = nsize > 1
|
||||
if is_complex:
|
||||
matrix = raw_matrix[:, ::2] + raw_matrix[:, 1::2] * 1j
|
||||
else:
|
||||
matrix = raw_matrix
|
||||
|
||||
ndim = nrow
|
||||
|
||||
self.tmatrices = np.zeros((nion, nrow, nm), dtype=np.complex128)
|
||||
for io in xrange(nion):
|
||||
self.tmatrices[io, :, :] = raw_matrix
|
||||
|
||||
return ndim
|
||||
|
||||
# If no transformation matrices are provided define a default one
|
||||
ns_dim = 2 if self.nc_flag else 1
|
||||
ndim = nm * ns_dim
|
||||
|
||||
self.tmatrices = np.zeros((nion, ndim, ndim), dtype=np.complex128)
|
||||
for io in xrange(nion):
|
||||
self.tmatrices[io, :, :] = np.identity(ndim, dtype=np.complex128)
|
||||
|
||||
return ndim
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# select_projectors
|
||||
#
|
||||
################################################################################
|
||||
def select_projectors(self, ib_win, ib_min, ib_max):
|
||||
"""
|
||||
Selects a subset of projectors corresponding to a given energy window.
|
||||
"""
|
||||
self.ib_win = ib_win
|
||||
self.ib_min = ib_min
|
||||
self.ib_max = ib_max
|
||||
nb_max = ib_max - ib_min + 1
|
||||
|
||||
# Set the dimensions of the array
|
||||
nion, ns, nk, nlm, nbtot = self.proj_arr.shape
|
||||
# !!! Note that the order of the two last indices is different !!!
|
||||
self.proj_win = np.zeros((nion, ns, nk, nlm, nb_max), dtype=np.complex128)
|
||||
|
||||
# Select projectors for a given energy window
|
||||
ns_band = self.ib_win.shape[1]
|
||||
for isp in xrange(ns):
|
||||
for ik in xrange(nk):
|
||||
# TODO: for non-collinear case something else should be done here
|
||||
is_b = min(isp, ns_band)
|
||||
ib1 = self.ib_win[ik, is_b, 0]
|
||||
ib2 = self.ib_win[ik, is_b, 1] + 1
|
||||
ib_win = ib2 - ib1
|
||||
self.proj_win[:, isp, ik, :, :ib_win] = self.proj_arr[:, isp, ik, :, ib1:ib2]
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# density_matrix
|
||||
#
|
||||
################################################################################
|
||||
def density_matrix(self, el_struct, site_diag=True, spin_diag=True):
|
||||
"""
|
||||
Returns occupation matrix/matrices for the shell.
|
||||
"""
|
||||
nion, ns, nk, nlm, nbtot = self.proj_win.shape
|
||||
|
||||
assert site_diag, "site_diag = False is not implemented"
|
||||
assert spin_diag, "spin_diag = False is not implemented"
|
||||
|
||||
occ_mats = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
|
||||
overlaps = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
|
||||
|
||||
# self.proj_win = np.zeros((nion, ns, nk, nlm, nb_max), dtype=np.complex128)
|
||||
kweights = el_struct.kmesh['kweights']
|
||||
occnums = el_struct.ferw
|
||||
ib1 = self.ib_min
|
||||
ib2 = self.ib_max + 1
|
||||
for isp in xrange(ns):
|
||||
for ik, weight, occ in it.izip(it.count(), kweights, occnums[isp, :, :]):
|
||||
for io in xrange(nion):
|
||||
proj_k = self.proj_win[io, isp, ik, ...]
|
||||
occ_mats[isp, io, :, :] += np.dot(proj_k * occ[ib1:ib2],
|
||||
proj_k.conj().T).real * weight
|
||||
overlaps[isp, io, :, :] += np.dot(proj_k,
|
||||
proj_k.conj().T).real * weight
|
||||
|
||||
# if not symops is None:
|
||||
# occ_mats = symmetrize_matrix_set(occ_mats, symops, ions, perm_map)
|
||||
|
||||
return occ_mats, overlaps
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# density_of_states
|
||||
#
|
||||
################################################################################
|
||||
def density_of_states(self, el_struct, emesh):
|
||||
"""
|
||||
Returns projected DOS for the shell.
|
||||
"""
|
||||
nion, ns, nk, nlm, nbtot = self.proj_win.shape
|
||||
|
||||
# There is a problem with data storage structure of projectors that will
|
||||
# make life more complicated. The problem is that band-indices of projectors
|
||||
# for different k-points do not match because we store 'nb_max' values starting
|
||||
# from 0.
|
||||
nb_max = self.ib_max - self.ib_min + 1
|
||||
ns_band = self.ib_win.shape[1]
|
||||
|
||||
ne = len(emesh)
|
||||
dos = np.zeros((ne, ns, nion, nlm))
|
||||
w_k = np.zeros((nk, nb_max, ns, nion, nlm), dtype=np.complex128)
|
||||
for isp in xrange(ns):
|
||||
for ik in xrange(nk):
|
||||
is_b = min(isp, ns_band)
|
||||
ib1 = self.ib_win[ik, is_b, 0]
|
||||
ib2 = self.ib_win[ik, is_b, 1] + 1
|
||||
for ib_g in xrange(ib1, ib2):
|
||||
for io in xrange(nion):
|
||||
# Note the difference between 'ib' and 'ibn':
|
||||
# 'ib' counts from 0 to 'nb_k - 1'
|
||||
# 'ibn' counts from 'ib1 - ib_min' to 'ib2 - ib_min'
|
||||
ib = ib_g - ib1
|
||||
ibn = ib_g - self.ib_min
|
||||
proj_k = self.proj_win[io, isp, ik, :, ib]
|
||||
w_k[ik, ib, isp, io, :] = proj_k * proj_k.conj()
|
||||
|
||||
# eigv_ef = el_struct.eigvals[ik, ib, isp] - el_struct.efermi
|
||||
itt = el_struct.kmesh['itet'].T
|
||||
# k-indices are starting from 0 in Python
|
||||
itt[1:, :] -= 1
|
||||
for isp in xrange(ns):
|
||||
for ib, eigk in enumerate(el_struct.eigvals[:, self.ib_min:self.ib_max+1, isp].T):
|
||||
for ie, e in enumerate(emesh):
|
||||
eigk_ef = eigk - el_struct.efermi
|
||||
cti = c_atm_dos.dos_weights_3d(eigk_ef, e, itt)
|
||||
for im in xrange(nlm):
|
||||
for io in xrange(nion):
|
||||
dos[ie, isp, io, im] += np.sum((cti * w_k[itt[1:, :], ib, isp, io, im].real).sum(0) * itt[0, :])
|
||||
|
||||
dos *= 2 * el_struct.kmesh['volt']
|
||||
# for isp in xrange(ns):
|
||||
# for ik, weight, occ in it.izip(it.count(), kweights, occnums[isp, :, :]):
|
||||
# for io in xrange(nion):
|
||||
# proj_k = self.proj_win[isp, io, ik, ...]
|
||||
# occ_mats[isp, io, :, :] += np.dot(proj_k * occ[ib1:ib2],
|
||||
# proj_k.conj().T).real * weight
|
||||
# overlaps[isp, io, :, :] += np.dot(proj_k,
|
||||
# proj_k.conj().T).real * weight
|
||||
|
||||
# if not symops is None:
|
||||
# occ_mats = symmetrize_matrix_set(occ_mats, symops, ions, perm_map)
|
||||
|
||||
return dos
|
||||
|
||||
|
||||
|
||||
@ -236,13 +236,13 @@ class TestParseFileTmatrix(arraytest.ArrayTestCase):
|
||||
[ -3.80200000e-04, 0.00000000e+00, 6.04452000e-02, -1.00000000e-07, -9.98171400e-01],
|
||||
[ -5.14500000e-04, -0.00000000e+00, -9.98171400e-01, 0.00000000e+00, -6.04450000e-02]])
|
||||
|
||||
res = self.cpars.parse_file_tmatrix('tmatrix_file.dat')
|
||||
res = self.cpars.parse_file_tmatrix(_rpath + 'tmatrix_file.dat')
|
||||
self.assertEqual(res, expected)
|
||||
|
||||
# Scenario 2
|
||||
def test_wrong_file(self):
|
||||
with self.assertRaises(ValueError):
|
||||
self.cpars.parse_file_tmatrix('test1.cfg')
|
||||
self.cpars.parse_file_tmatrix(_rpath + 'test1.cfg')
|
||||
|
||||
################################################################################
|
||||
#
|
||||
|
||||
Loading…
Reference in New Issue
Block a user