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dft_tools/python/triqs_dft_tools/converters/plovasp/vaspio.py
the-hampel 44d791d90d update new vasp h5 interface to new structure
2024-10-23 15:18:27 +02:00

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################################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
# Copyright (C) 2011 by M. Ferrero, O. Parcollet
#
# DFT tools: Copyright (C) 2011 by M. Aichhorn, L. Pourovskii, V. Vildosola
#
# PLOVasp: Copyright (C) 2015 by O. E. Peil
#
# TRIQS is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
r"""
plovasp.vaspio
==============
Input of required VASP data.
Six VASP files are required:
- PROJCAR
- LOCPROJ
- POSCAR
- IBZKPT
- EIGENVAL
- DOSCAR
"""
import logging
import numpy as np
import re
import os
from h5 import HDFArchive
log = logging.getLogger('plovasp.vaspio')
def read_lines(filename):
r"""
Generator of lines for a file
Parameters
----------
filename (str) : name of the file
"""
with open(filename, 'r') as f:
for line in f:
yield line
################################################################################
################################################################################
#
# class VaspData
#
################################################################################
################################################################################
class VaspData:
"""
Container class for all VASP data.
"""
def __init__(self, vasp_dir, read_all=True, efermi_required=True):
self.vasp_dir = vasp_dir
# read from vaspout.h5 if possible
vasph5 = os.path.isfile(os.path.join(vasp_dir, 'vaspout.h5'))
if vasph5:
log.warning("Reading from vaspout.h5")
h5path = os.path.join(vasp_dir, 'vaspout.h5')
self.plocar = h5Plocar(h5path)
self.poscar = h5Poscar(h5path)
self.kpoints = h5Kpoints(h5path)
self.eigenval = h5Eigenval(h5path)
self.doscar = h5Doscar(h5path)
else:
self.plocar = Plocar()
self.poscar = Poscar()
self.kpoints = Kpoints()
self.eigenval = Eigenval()
self.doscar = Doscar()
if read_all:
self.plocar.from_file(vasp_dir)
self.poscar.from_file(vasp_dir)
self.kpoints.from_file(vasp_dir)
try:
self.eigenval.from_file(vasp_dir)
except (IOError, StopIteration):
self.eigenval.eigs = None
self.eigenval.ferw = None
log.warning("Error reading from EIGENVAL, trying LOCPROJ...")
try:
self.doscar.from_file(vasp_dir)
except (IOError, StopIteration):
if efermi_required:
log.warning("Error reading Efermi from DOSCAR, trying LOCPROJ...")
try:
self.plocar.efermi
self.doscar.efermi = self.plocar.efermi
except NameError:
raise Exception("Efermi cannot be read from DOSCAR or LOCPROJ")
else:
# TODO: This a hack. Find out a way to determine ncdij without DOSCAR
log.warning("Error reading Efermi from DOSCAR, taking from config")
self.doscar.ncdij = self.plocar.nspin
##########################
#
# class Plocar
#
##########################
class Plocar:
"""
Class containing raw PLO data from VASP.
Properties:
- *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 __init__(self):
self.plo = None
self.proj_params = None
def from_file(self, vasp_dir='./', plocar_filename='PLOCAR'):
r"""
Reads non-normalized projectors from a binary file ('PLOCAR' by default)
generated by VASP PLO interface.
Parameters
----------
vasp_dir (str) : path to the VASP working directory [default = './']
plocar_filename (str) : filename [default = 'PLOCAR']
"""
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
# self.params, self.plo, self.ferw = c_plocar_io.read_plocar(vasp_dir + plocar_filename)
# self.proj_params, self.plo = self.temp_parser(projcar_filename=vasp_dir + "PROJCAR", locproj_filename=vasp_dir + "LOCPROJ")
self.proj_params, self.plo = self.locproj_parser(locproj_filename=vasp_dir + "LOCPROJ")
def locproj_parser(self, locproj_filename='LOCPROJ'):
r"""
Parses LOCPROJ (for VASP >= 5.4.2) to get VASP projectors.
This is a prototype parser that should eventually be written in C for
better performance on large files.
Returns projector parameters (site/orbital indices etc.) and an array
with projectors.
"""
orb_labels = ["s", "py", "pz", "px", "dxy", "dyz", "dz2", "dxz", "dx2-y2",
"fy(3x2-y2)", "fxyz", "fyz2", "fz3", "fxz2", "fz(x2-y2)", "fx(x2-3y2)"]
def lm_to_l_m(lm):
l = int(np.sqrt(lm))
m = lm - l * l
return l, m
# Read the first line of LOCPROJ to get the dimensions
with open(locproj_filename, 'rt') as f:
line = f.readline()
line = line.split("#")[0]
sline = line.split()
self.ncdij, nk, self.nband, nproj = list(map(int, sline[0:4]))
# VASP.6.
self.nspin = self.ncdij if self.ncdij < 4 else 1
log.debug("ISPIN is {}".format(self.nspin))
self.nspin_band = 2 if self.ncdij == 2 else 1
try:
self.efermi = float(sline[4])
except:
log.warning("Error reading Efermi from LOCPROJ, trying DOSCAR...")
plo = np.zeros((nproj, self.nspin, nk, self.nband), dtype=complex)
proj_params = [{} for i in range(nproj)]
iproj_site = 0
is_first_read = True
# VASP.6.
if self.ncdij == 4:
self.nc_flag = 1
self.ncdij = 1
else:
self.nc_flag = 0
log.debug("NC FLAG : {}".format(self.nc_flag))
# First read the header block with orbital labels
line = self.search_for(f, "^ *ISITE")
ip = 0
while line:
sline = line.split(':')
isite = int(sline[1].split()[0])
label = sline[-1].strip()
lm = orb_labels.index(label)
l, m = lm_to_l_m(lm)
# ip_new = iproj_site * norb + il
# ip_prev = (iproj_site - 1) * norb + il
proj_params[ip]['label'] = label
proj_params[ip]['isite'] = isite
proj_params[ip]['l'] = l
if self.nc_flag == True:
if (ip % 2) == 0:
proj_params[ip]['m'] = 2 * m
else:
proj_params[ip]['m'] = 2 * m + 1
else:
proj_params[ip]['m'] = m
ip += 1
line = f.readline().strip()
assert ip == nproj, "Number of projectors in the header is wrong in LOCPROJ"
self.eigs = np.zeros((nk, self.nband, self.nspin_band))
self.ferw = np.zeros((nk, self.nband, self.nspin_band))
patt = re.compile("^orbital")
for ispin in range(self.nspin):
for ik in range(nk):
for ib in range(self.nband):
line = ""
while not line:
line = f.readline().strip()
sline = line.split()
isp_, ik_, ib_ = list(map(int, sline[1:4]))
assert isp_ == ispin + 1 and ik_ == ik + 1 and ib_ == ib + 1, "Inconsistency in reading LOCPROJ"
self.eigs[ik, ib, ispin] = float(sline[4])
self.ferw[ik, ib, ispin] = float(sline[5])
for ip in range(nproj):
line = f.readline()
sline = line.split()
ctmp = complex(float(sline[1]), float(sline[2]))
plo[ip, ispin, ik, ib] = ctmp
print("Read parameters: LOCPROJ")
for il, par in enumerate(proj_params):
print(il, " -> ", par)
return proj_params, plo
def search_for(self, f, patt):
r"""
Reads file 'f' until pattern 'patt' is encountered and returns
the corresponding line.
"""
cpatt = re.compile(patt)
line = "x"
while not re.match(cpatt, line) and line:
line = f.readline()
return line
##########################
#
# class Poscar
#
##########################
class Poscar:
"""
Class containing POSCAR data from VASP.
Properties:
- nq (int) : total number of ions
- ntypes ([int]) : number of ion types
- nions (int) : a list of number of ions of each type
- a_brav (numpy.array((3, 3), dtype=float)) : lattice vectors
- kpt_basis (numpy.array((3, 3), dtype=float)) : reciprocal lattice vectors
- q_types ([numpy.array((nions, 3), dtype=float)]) : a list of
arrays each containing fractional coordinates of ions of a given type
"""
def __init__(self):
self.q_cart = None
def from_file(self, vasp_dir='./', poscar_filename='POSCAR'):
r"""
Reads POSCAR and returns a dictionary.
Parameters
----------
vasp_dir (str) : path to the VASP working directory [default = './']
plocar_filename (str) : filename [default = 'POSCAR']
"""
# Convenince local function
def readline_remove_comments():
return next(f).split('!')[0].split('#')[0].strip()
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
f = read_lines(vasp_dir + poscar_filename)
# Comment line
comment = next(f).rstrip()
print(" Found POSCAR, title line: %s" % (comment))
# Read scale
sline = readline_remove_comments()
ascale = float(sline)
# Read lattice vectors
self.a_brav = np.zeros((3, 3))
for ia in range(3):
sline = readline_remove_comments()
self.a_brav[ia, :] = list(map(float, sline.split()))
# Negative scale means that it is a volume scale
if ascale < 0:
vscale = -ascale
vol = np.linalg.det(self.a_brav)
ascale = (vscale / vol) ** (1.0 / 3)
self.a_brav *= ascale
# Depending on the version of VASP there could be
# an extra line with element names
sline = readline_remove_comments()
try:
# Old v4.6 format: no element names
self.nions = list(map(int, sline.split()))
self.el_names = ['El%i' % (i) for i in range(len(self.nions))]
except ValueError:
# New v5.x format: read element names first
self.el_names = sline.split()
sline = readline_remove_comments()
self.nions = list(map(int, sline.split()))
# Set the number of atom sorts (types) and the total
# number of atoms in the unit cell
self.ntypes = len(self.nions)
self.nq = sum(self.nions)
# Check for the line 'Selective dynamics' (and ignore it)
sline = readline_remove_comments()
if sline[0].lower() == 's':
sline = readline_remove_comments()
# Check whether coordinates are cartesian or fractional
cartesian = (sline[0].lower() in 'ck')
# determine reciprocal basis in units of 2*pi
self.kpt_basis = np.linalg.inv(self.a_brav.T)
# Read atomic positions
self.q_types = []
self.type_of_ion = []
for it in range(self.ntypes):
# Array mapping ion index to type
self.type_of_ion += self.nions[it] * [it]
q_at_it = np.zeros((self.nions[it], 3))
for iq in range(self.nions[it]):
sline = readline_remove_comments()
qcoord = list(map(float, sline.split()[:3]))
if cartesian:
qcoord = np.dot(self.kpt_basis, qcoord)
q_at_it[iq, :] = qcoord
self.q_types.append(q_at_it)
print(" Total number of ions:", self.nq)
print(" Number of types:", self.ntypes)
print(" Number of ions for each type:", self.nions)
##########################
#
# class Kpoints
#
##########################
class Kpoints:
"""
Class describing k-points and optionally tetrahedra.
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
be uniform)
"""
def __init__(self):
self.kpts = None
self.nktot = None
self.kwghts = None
#
# Reads IBZKPT file
#
def from_file(self, vasp_dir='./', ibz_filename='IBZKPT'):
r"""
Reads from IBZKPT: k-points and optionally
tetrahedra topology (if present).
Parameters
----------
vasp_dir (str) : path to the VASP working directory [default = './']
plocar_filename (str) : filename [default = 'IBZKPT']
"""
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
ibz_file = read_lines(vasp_dir + ibz_filename)
# Skip comment line
line = next(ibz_file)
# Number of k-points
line = next(ibz_file)
self.nktot = int(line.strip().split()[0])
print()
print(" {0:>26} {1:d}".format("Total number of k-points:", self.nktot))
self.kpts = np.zeros((self.nktot, 3))
self.kwghts = np.zeros((self.nktot))
# Skip comment line
line = next(ibz_file)
for ik in range(self.nktot):
line = next(ibz_file)
sline = line.strip().split()
self.kpts[ik, :] = list(map(float, sline[:3]))
self.kwghts[ik] = float(sline[3])
self.kwghts /= self.nktot
# Attempt to read tetrahedra
# Skip comment line ("Tetrahedra")
try:
line = next(ibz_file)
# Number of tetrahedra and volume = 1/(6*nkx*nky*nkz)
line = next(ibz_file)
sline = line.split()
self.ntet = int(sline[0])
self.volt = float(sline[1])
print(" {0:>26} {1:d}".format("Total number of tetrahedra:", self.ntet))
# Traditionally, itet[it, 0] contains multiplicity
self.itet = np.zeros((self.ntet, 5), dtype=int)
for it in range(self.ntet):
line = next(ibz_file)
self.itet[it, :] = list(map(int, line.split()[:5]))
except StopIteration as ValueError:
print(" No tetrahedron data found in %s. Skipping..." % (ibz_filename))
self.ntet = 0
##########################
#
# class Eigenval
#
##########################
class Eigenval:
"""
Class containing Kohn-Sham-eigenvalues data from VASP (EIGENVAL file).
"""
def __init__(self):
self.eigs = None
self.ferw = None
def from_file(self, vasp_dir='./', eig_filename='EIGENVAL'):
"""
Reads eigenvalues from EIGENVAL. Note that the file also
contains k-points with weights. They are also stored and
then used to check the consistency of files read.
"""
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
f = read_lines(vasp_dir + eig_filename)
# First line: only the first and the last number out of four
# are used; these are 'nions' and 'ispin'
sline = next(f).split()
self.nq = int(sline[0])
self.ispin = int(sline[3])
# Second line: cell volume and lengths of lattice vectors (skip)
sline = next(f)
# Third line: temperature (skip)
sline = next(f)
# Fourth and fifth line: useless
sline = next(f)
sline = next(f)
# Sixth line: NELECT, NKTOT, NBTOT
sline = next(f).split()
self.nelect = int(sline[0])
self.nktot = int(sline[1])
self.nband = int(sline[2])
# Set of eigenvalues and k-points
self.kpts = np.zeros((self.nktot, 3))
self.kwghts = np.zeros((self.nktot,))
self.eigs = np.zeros((self.nktot, self.nband, self.ispin))
self.ferw = np.zeros((self.nktot, self.nband, self.ispin))
for ik in range(self.nktot):
sline = next(f) # Empty line
sline = next(f) # k-point info
tmp = list(map(float, sline.split()))
self.kpts[ik, :] = tmp[:3]
self.kwghts[ik] = tmp[3]
for ib in range(self.nband):
sline = next(f).split()
tmp = list(map(float, sline))
assert len(tmp) == 2 * self.ispin + 1, "EIGENVAL file is incorrect (probably from old versions of VASP)"
self.eigs[ik, ib, :] = tmp[1:self.ispin + 1]
self.ferw[ik, ib, :] = tmp[self.ispin + 1:]
##########################
#
# class Doscar
#
##########################
class Doscar:
"""
Class containing some data from DOSCAR
"""
def __init__(self):
self.ncdij = None
self.efermi = None
def from_file(self, vasp_dir='./', dos_filename='DOSCAR'):
"""
Reads only E_Fermi from DOSCAR.
"""
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
f = read_lines(vasp_dir + dos_filename)
# First line: NION, NION, JOBPAR, NCDIJ
sline = next(f).split()
# Skip next 4 lines
for _ in range(4):
sline = next(f)
# Sixth line: EMAX, EMIN, NEDOS, EFERMI, 1.0
sline = next(f).split()
self.efermi = float(sline[3])
# TODO: implement output of SYMMCAR in VASP and read it here
##########################
#
# Reads SYMMCAR
#
##########################
def read_symmcar(vasp_dir, symm_filename='SYMMCAR'):
"""
Reads SYMMCAR.
"""
# Shorthand for simple parsing
def extract_int_par(parname):
return int(re.findall(parname + '\s*=\s*(\d+)', line)[-1])
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
symmcar_exist = False
sym_file = read_lines(vasp_dir + symm_filename)
line = next(sym_file)
nrot = extract_int_par('NROT')
line = next(sym_file)
ntrans = extract_int_par('NPCELL')
# Lmax
line = next(sym_file)
lmax = extract_int_par('LMAX')
mmax = 2 * lmax + 1
# Nion
line = next(sym_file)
nion = extract_int_par('NION')
print(" {0:>26} {1:d}".format("Number of rotations:", nrot))
print(" {0:>26} {1:d}".format("Number of translations:", ntrans))
print(" {0:>26} {1:d}".format("Number of ions:", nion))
print(" {0:>26} {1:d}".format("L_max:", lmax))
rot_mats = np.zeros((nrot, lmax + 1, mmax, mmax))
rot_map = np.zeros((nrot, ntrans, nion), dtype=int)
for irot in range(nrot):
# Empty line
line = next(sym_file)
# IROT index (skip it)
line = next(sym_file)
# ISYMOP matrix (can be also skipped)
line = next(sym_file)
line = next(sym_file)
line = next(sym_file)
# Skip comment " Permutation map..."
line = next(sym_file)
# Permutations (in chunks of 20 indices per line)
for it in range(ntrans):
for ibl in range((nion - 1) // 20 + 1):
i1 = ibl * 20
i2 = (ibl + 1) * 20
line = next(sym_file)
rot_map[irot, it, i1:i2] = list(map(int, line.split()))
for l in range(lmax + 1):
mmax = 2 * l + 1
# Comment: "L = ..."
line = next(sym_file)
for m in range(mmax):
line = next(sym_file)
rot_mats[irot, l, m, :mmax] = list(map(float, line.split()[:mmax]))
data.update({'nrot': nrot, 'ntrans': ntrans,
'lmax': lmax, 'nion': nion,
'sym_rots': rot_mats, 'perm_map': rot_map})
class h5Poscar:
def __init__(self, h5path):
# self.q_cart = None
with HDFArchive(h5path, 'a') as archive:
struct = archive['results/positions']
ascale = struct['scale']
self.a_brav = struct['lattice_vectors']
self.nions = struct['number_ion_types']
self.el_names = struct['ion_types']
direct = struct['direct_coordinates']
qcoord = struct['position_ions']
if ascale < 0:
vscale = -ascale
vol = np.linalg.det(self.a_brav)
ascale = (vscale / vol) ** (1.0 / 3)
self.a_brav *= ascale
# determine reciprocal basis in units of 2*pi
self.kpt_basis = np.linalg.inv(self.a_brav.T)
# Set the number of atom sorts (types) and the total
# number of atoms in the unit cell
self.ntypes = len(self.nions)
self.nq = sum(self.nions)
# Read atomic positions
self.q_types = []
self.type_of_ion = []
for it in range(self.ntypes):
# Array mapping ion index to type
self.type_of_ion += self.nions[it] * [it]
q_at_it = np.zeros((self.nions[it], 3))
for iq in range(self.nions[it]):
if not direct:
qcoord = np.dot(self.kpt_basis, qcoord[iq + it])
q_at_it[iq, :] = qcoord[iq + it]
self.q_types.append(q_at_it)
print(" Total number of ions:", self.nq)
print(" Number of types:", self.ntypes)
print(" Number of ions for each type:", self.nions)
class h5Kpoints:
def __init__(self, h5path):
# h5path = './vasptriqs.h5'
with HDFArchive(h5path, 'a') as archive:
kpoints = archive['results/electron_eigenvalues']
self.nktot = kpoints['kpoints']
self.kpts = kpoints['kpoint_coords']
self.kwghts = kpoints['kpoints_symmetry_weight']
try:
self.ntet = kpoints['num_tetrahedra']
self.vtet = kpoints['volume_weight_tetrahedra']
self.itet = kpoints['coordinate_id_tetrahedra']
except KeyError:
print(" No tetrahedron data found in vasptriqs.h5. Skipping...")
self.ntet = 0
print()
print(" {0:>26} {1:d}".format("Total number of k-points:", self.nktot))
print(" {0:>26} {1:d}".format("Total number of tetrahedra:", self.ntet))
class h5Eigenval:
def __init__(self, h5path):
with HDFArchive(h5path, 'a') as archive:
self.eigs = archive['results/electron_eigenvalues']['eigenvalues']
self.ferw = archive['results/electron_eigenvalues']['fermiweights']
# TODO Change the format in VASP to have [kpoints, bands, spin]
self.eigs = np.transpose(self.eigs, (1, 2, 0))
self.ferw = np.transpose(self.ferw, (1, 2, 0))
class h5Doscar:
def __init__(self, h5path):
with HDFArchive(h5path, 'a') as archive:
self.efermi = archive['results/electron_dos']['efermi']
class h5Plocar():
def __init__(self, h5path):
with HDFArchive(h5path, 'a') as archive:
plo = np.array(archive['results/locproj']['data'])
self.nc_flag = int(archive['results/locproj/parameters']['lnoncollinear'])
self.nproj = plo.shape[0]
self.ncdij = plo.shape[1]
nk = plo.shape[2]
self.nband = plo.shape[3]
self.nspin = self.ncdij if self.ncdij < 4 else 1
self.nspin_band = 2 if self.ncdij == 2 else 1
log.debug("ISPIN is {}".format(self.nspin))
log.debug("NC FLAG : {}".format(self.nc_flag))
# self.proj_params, self.plo = self.locproj_parser(locproj_filename=vasp_dir + "LOCPROJ")
orb_labels = ["s", "py", "pz", "px", "dxy", "dyz", "dz2", "dxz", "dx2-y2",
"fy(3x2-y2)", "fxyz", "fyz2", "fz3", "fxz2", "fz(x2-y2)", "fx(x2-3y2)"]
self.plo = np.zeros((self.nproj, self.nspin, nk, self.nband), dtype=complex)
for proj in range(self.nproj):
for spin in range(self.nspin):
for kpt in range(nk):
for band in range(self.nband):
real_plo = plo[proj, spin, kpt, band, 0] # Real part
imag_plo = plo[proj, spin, kpt, band, 1] # Imaginary part
self.plo[proj, spin, kpt, band] = complex(real_plo, imag_plo)
def lm_to_l_m(lm):
l = int(np.sqrt(lm))
m = lm - l * l
return l, m
self.proj_params = [{} for i in range(self.nproj)]
with HDFArchive(h5path, 'a') as archive:
for it in range(self.nproj):
projectors = archive['results/locproj']['parameters']
self.proj_params[it]['label'] = projectors['ang_type'][it]
self.proj_params[it]['isite'] = projectors['site'][it]
self.proj_params[it]['coord'] = projectors['coordinates'][it]
for it in range(self.nproj):
lm = orb_labels.index(self.proj_params[it]['label'].strip())
l, m = lm_to_l_m(lm)
self.proj_params[it]['l'] = l
if self.nc_flag == True:
if (it % 2) == 0:
self.proj_params[it]['m'] = 2 * m
else:
self.proj_params[it]['m'] = 2 * m + 1
else:
self.proj_params[it]['m'] = m
# assert ip == nproj, "Number of projectors in the header is wrong in LOCPROJ"
print("Read parameters: LOCPROJ")
for il, par in enumerate(self.proj_params):
print(il, " -> ", par)
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