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Added calculation of density matrices for a shell

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A method 'density_matrix()' for evaluating a density matrix of a given shell
has been added to class ProjectorShell. It requires an ElectronicStructure
object as an input an by default produces a site- and spin-diagonal
part of the density matrix using the Fermi-weights obtained directly from VASP.
Ideally, this density matrix should coincide with the one calculated
within VASP itself (inside the LDA+U module).

Corresponding sanity test has been added, which shows only that the
calculation does not crash. Real numerical tests are needed.
This commit is contained in:
Oleg E. Peil 2015-02-19 21:22:51 +01:00 committed by Michel Ferrero
parent ad6b3ab708
commit 3317371762
5 changed files with 86 additions and 10 deletions
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10
python/converters/vasp/python/elstruct.py
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@ -15,6 +15,7 @@ class ElectronicStructure:
- *efermi* (float) : Fermi level read from DOSCAR
- *proj_raw* (array[complex]) : raw projectors from PLOCAR
- *eigvals* (array[float]) : KS eigenvalues
- *ferw* (array[float]) : Fermi weights from VASP
- *kmesh* (dict) : parameters of the `k`-mesh
- *structure* (dict) : parameters of the crystal structure
- *symmetry* (dict) : paramters of symmetry
@ -29,12 +30,12 @@ class ElectronicStructure:
self.kmesh = {'nktot': self.nktot}
self.kmesh['kpoints'] = vasp_data.kpoints.kpts
self.kmesh['kwights'] = vasp_data.eigenval.kwghts
self.kmesh['kweights'] = vasp_data.eigenval.kwghts
try:
self.kmesh['ntet'] = vasp_data.kpoints.ntet
self.kmesh['itet'] = vasp_data.kpoints.itet
self.kmesh['volt'] = vasp_data.kpoints.volt
except NameError:
except AttributeError:
pass
# Note that one should not subtract this Fermi level from eigenvalues
@ -55,6 +56,11 @@ class ElectronicStructure:
# [see ProjectorGroup.orthogonalization()]
self.proj_raw = vasp_data.plocar.plo.transpose((0, 1, 2, 4, 3))
# In fact, Fermi weights do not depend on ions
# FIXME: restructure the data in PLOCAR to remove the redundant dependency
# of 'ferw' on ions
self.ferw = vasp_data.plocar.ferw[0, :, :, :]
# Check that the number of atoms is the same in PLOCAR and POSCAR
natom_plo = vasp_data.plocar.params['nion']
assert natom_plo == self.natom, "PLOCAR is inconsistent with POSCAR (number of atoms)"

34
python/converters/vasp/python/plotools.py
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@ -1,4 +1,5 @@
import itertools as it
import numpy as np
class Projector:
@ -292,6 +293,39 @@ class ProjectorShell:
ib2_win = ib2 - self.nb_min
self.proj_win[:, isp, ik, :, ib1_win:ib2_win] = self.proj_arr[:, isp, ik, :, ib1:ib2]
################################################################################
#
# select_projectors
#
################################################################################
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)
kweights = el_struct.kmesh['kweights']
occnums = el_struct.ferw
ib1 = self.nb_min
ib2 = self.nb_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[isp, io, ik, ...]
occ_mats[isp, io, :, :] += np.dot(proj_k * occ[ib1:ib2],
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
def generate_ortho_plos(conf_pars, vasp_data):
"""

14
python/converters/vasp/python/vaspio.py
View File

@ -54,7 +54,9 @@ class Plocar:
Properties
----------
plo (numpy.array((nion, ns, nk, nb, nlmmax))) : raw projectors
- *plo* (numpy.array((nion, ns, nk, nb, nlmmax))) : raw projectors
- *params* (dict) : parameters read from PLOCAR
- *ferw* (array(nion, ns, nk, nb)) : Fermi weights from VASP
"""
def from_file(self, vasp_dir='./', plocar_filename='PLOCAR'):
@ -206,11 +208,11 @@ class Kpoints:
Properties
----------
nktot (int) : total number of k-points in the IBZ
kpts (numpy.array((nktot, 3), dtype=float)) : k-point vectors (fractional coordinates)
ntet (int) : total number of k-point tetrahedra
itet (numpy.array((ntet, 5), dtype=float) : array of tetrahedra
volt (float) : volume of a tetrahedron (the k-grid is assumed to
- nktot (int) : total number of k-points in the IBZ
- kpts (numpy.array((nktot, 3), dtype=float)) : k-point vectors (fractional coordinates)
- ntet (int) : total number of k-point tetrahedra
- itet (numpy.array((ntet, 5), dtype=float) : array of tetrahedra
- volt (float) : volume of a tetrahedron (the k-grid is assumed to
be uniform)
"""
#

8
python/converters/vasp/test/plotools/test_projgroups.py
View File

@ -46,7 +46,9 @@ class TestProjectorGroup(mytest.MyTestCase):
ib1 = self.proj_gr.ib_win[ik, 0, 0]
ib2 = self.proj_gr.ib_win[ik, 0, 1]
f.write("%i %i\n"%(ib1, ib2))
for ib in xrange(ib2 - self.proj_gr.nb_min + 1):
ib1w = ib1 - self.proj_gr.nb_min
ib2w = ib2 - self.proj_gr.nb_min + 1
for ib in xrange(ib1w, ib2w):
for ilm in xrange(nlm):
p = self.proj_gr.shells[0].proj_win[ion, isp, ik, ilm, ib]
f.write("%5i %s\n"%(ilm+1, p))
@ -65,7 +67,9 @@ class TestProjectorGroup(mytest.MyTestCase):
ib1 = self.proj_gr.ib_win[ik, 0, 0]
ib2 = self.proj_gr.ib_win[ik, 0, 1]
f.write("%i %i\n"%(ib1, ib2))
for ib in xrange(ib2 - self.proj_gr.nb_min + 1):
ib1w = ib1 - self.proj_gr.nb_min
ib2w = ib2 - self.proj_gr.nb_min + 1
for ib in xrange(ib1w, ib2w):
for ilm in xrange(nlm):
p = self.proj_gr.shells[0].proj_win[ion, isp, ik, ilm, ib]
f.write("%5i %s\n"%(ilm+1, p))

30
python/converters/vasp/test/plotools/test_projshells.py
View File

@ -1,6 +1,7 @@
import numpy as np
import vaspio
import elstruct
from inpconf import ConfigParameters
from plotools import select_bands, ProjectorShell
import mytest
@ -18,6 +19,7 @@ class TestProjectorShell(mytest.MyTestCase):
Scenarios:
- compare output for a correct input
- test density matrix
"""
# Scenario 1
def test_example(self):
@ -54,3 +56,31 @@ class TestProjectorShell(mytest.MyTestCase):
expected_file = 'projshells.out'
self.assertFileEqual(testout, expected_file)
# Scenario 2
def test_dens_mat(self):
conf_file = 'example.cfg'
pars = ConfigParameters(conf_file)
pars.parse_input()
vasp_data = vaspio.VaspData('./')
el_struct = elstruct.ElectronicStructure(vasp_data)
efermi = el_struct.efermi
eigvals = el_struct.eigvals - efermi
emin = pars.groups[0]['emin']
emax = pars.groups[0]['emax']
ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax)
proj_sh = ProjectorShell(pars.shells[0], vasp_data.plocar.plo)
proj_sh.select_projectors(ib_win, nb_min, nb_max)
dens_mat = proj_sh.density_matrix(el_struct)
print dens_mat
testout = 'densmat.out.test'
with open(testout, 'wt') as f:
f.write("density matrix: %s\n"%(dens_mat))
expected_file = 'densmat.out'
self.assertFileEqual(testout, expected_file)