Source code for triqs_dft_tools.converters.plovasp.vaspio


################################################################################
#
# 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

log = logging.getLogger('plovasp.vaspio')

[docs] 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 # ################################################################################ ################################################################################
[docs] class VaspData: """ Container class for all VASP data. """
[docs] def __init__(self, vasp_dir, read_all=True, efermi_required=True): self.vasp_dir = vasp_dir 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 # ################################################################################ ################################################################################
[docs] 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 """
[docs] def __init__(self): self.plo = None self.proj_params = None
[docs] 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")
[docs] 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
[docs] 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 # ################################################################################ ################################################################################
[docs] 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 """
[docs] def __init__(self): self.q_cart = None
[docs] 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)
# print # print " Coords:" # for it in range(ntypes): # print " Element:", el_names[it] # print q_at[it] ################################################################################ ################################################################################ # # class Kpoints # ################################################################################ ################################################################################
[docs] 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) """
[docs] def __init__(self): self.kpts = None self.nktot = None self.kwghts = None
# # Reads IBZKPT file #
[docs] 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
# data = { 'nktot': nktot, # 'kpts': kpts, # 'ntet': ntet, # 'itet': itet, # 'volt': volt } # # return data ################################################################################ ################################################################################ # # class Eigenval # ################################################################################ ################################################################################
[docs] class Eigenval: """ Class containing Kohn-Sham-eigenvalues data from VASP (EIGENVAL file). """
[docs] def __init__(self): self.eigs = None self.ferw = None
[docs] 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 # ################################################################################ ################################################################################
[docs] class Doscar: """ Class containing some data from DOSCAR """
[docs] def __init__(self): self.ncdij = None self.efermi = None
[docs] 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 # ################################################################
[docs] 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 })