PyPI 官网下载 | pyprocar-3.8.7.tar.gz

import numpy as np import re import logging import matplotlib.pyplot as plt import sys from ..utilsprocar import UtilsProcar class ProcarParser: """Parses a PROCAR file and store it in memory. It only deals with PROCAR files, that means no Fermi energy (UtilsProcar.FermiOutcar can help), and the reciprocal vectors should be supplied (if used, see UtilsProcar class). Members: __init__(self, loglevel): The setup the variables internally, `loglevel` sets the verbosity level ie: `loglevel=logging.DEBUG` for debugging. Its default is `logging.WARNING` readFile(self, procar=None, permissive=False, recLattice=None): The only method of the API it load the file completely. Arguments: `procar=None`: name of the PROCAR file, can be a gzipped file (the extension is no required). The default covers a wide range of obvious alternatives. `permissive=False`: Set to `True` if the PROCAR file has problems reading the Kpoints (stupid Fortran), but in that case the Kpoints mesh will be discarded. Future updates could allow it to handle other formating/corruption issues. `recLattice`=None: Reciprical Vectors, you want to provide them since not all the paths on the BZ are the same. Don't use the other methods beggining with underscores "_" Example: To read a PROCAR or PROCAR.gz file: >>> foo = ProcarParser() >>> foo.readFile() To include the reciprocal vectors, and file name MyFirstPROCAR >>> outcarparser = UtilsProcar() >>> recLat = outcarparser.RecLatOutcar(args.outcar) >>> foo = ProcarParser() >>> foo.readFile("MyFirstPROCAR", recLat=recLat) """ def __init__(self, loglevel=logging.WARNING): # array with k-points, they have the following values # -None: if not parsed (yet) or parsed with a `permissive` flag on # -direct coordinates: if a recLattice was not supplied to the parser # -cartesian coords: if a recLattice was supplied to the parser. # In the later cases, self.kpoints.shape=(self.kpointsCount, 3) self.kpoints = None # Number of kpoints, as given by the KPOINTS header (PROCAR file) self.kpointsCount = None # bands headers present in PROCAR file. # self.bands.shape=(self.kpointsCount,self.bandsCount) self.bands = None # Number of bands. For a spin polarized calculation the number of # bands is double (spin ip + spin down). On this array there is no # distinction between spin up and down self.bandsCount = None #Number of ions+1 the +1 is the 'tot' field, ie: the sum over all atoms self.ionsCount = None self.fileStr = None #the actual file, stored in memory self.spd = None #the atom/orbital projected data self.cspd = None #spd data with the phase self.orbitalName = [ "s", "py", "pz", "px", "dxy", "dyz", "dz2", "dxz", "dx2", "tot" ] self.orbitalCount = None #number of orbitals # number of spin components (blocks of data), 1: non-magnetic non # polarized, 2: spin polarized collinear, 4: non-collinear # spin. # NOTE: before calling to `self._readOrbital` the case '4' # is marked as '1' self.ispin = None self.recLattice = None #reciprocal lattice vectors self.utils = UtilsProcar() self.log = logging.getLogger("ProcarParser") self.log.setLevel(loglevel) self.ch = logging.StreamHandler() self.ch.setFormatter( logging.Formatter("%(name)s::%(levelname)s:" " %(message)s")) self.ch.setLevel(logging.DEBUG) self.log.addHandler(self.ch) #At last, one message to the logger. self.log.debug("Procar instanciated") return @property def nspin(self): """ number of spin, default is 1. """ nspindict = {1: 1, 2: 2, 4: 2, None: 1} return nspindict[self.ispin] @property def spd_orb(self): # indices: ikpt, iband, ispin, iion, iorb # remove indices and total from iorb. return self.spd[:, :, :, 1:-1] def _readKpoints(self, permissive=False): """Reads the k-point headers. A typical k-point line is: k-point 1 : 0.00000000 0.00000000 0.00000000 weight = 0.00003704\n fills self.kpoint[kpointsCount][3] The weights are discarded (are they useful?) """ self.log.debug("readKpoints") if not self.fileStr: log.warning( "You should invoke `procar.readFile()` instead. Returning") return # finding all the K-points headers self.kpoints = re.findall(r"k-point\s+\d+\s*:\s+([-.\d\s]+)", self.fileStr) self.log.debug(str(len(self.kpoints)) + " K-point headers found") self.log.debug("The first match found is: " + str(self.kpoints[0])) # trying to build an array self.kpoints = [x.split() for x in self.kpoints] try: self.kpoints = np.array(self.kpoints, dtype=float) except ValueError: self.log.error("Ill-formatted data:") print('\n'.join([str(x) for x in self.kpoints])) if permissive is True: # Discarding the kpoints list, however I need to set # self.ispin beforehand. if len(self.kpoints) == self.kpointsCount: self.ispin = 1 elif len(self.kpoints) == 2 * self.kpointsCount: self.ispin = 2 else: raise ValueError("Kpoints do not match with ispin=1 or 2.") self.kpoints = None self.log.warning( "K-points list is useless, setting it to `None`") return else: raise ValueError( "Badly formated Kpoints headers, try `--permissive`") # if successful, go on # trying to identify an non-polarized or non-collinear case, a # polarized case or a defective file if len(self.kpoints) != self.kpointsCount: #if they do not match, may means two things a spin polarized #case or a bad file, lets check self.log.debug("Number of kpoints do not match, looking for a " "spin-polarized case") # lets start testing if it is spin polarized, if so, there # should be 2 identical blocks of kpoints. up, down = np.vsplit(self.kpoints, 2) if (up == down).all(): self.log.info("Spin-polarized calculation found") self.ispin = 2 # just keeping one set of kpoints (the other will be # discarded) self.kpoints = up else: self.log.error("Number of K-points do not match! check them.") raise RuntimeError("Bad Kpoints list.") # if ISPIN != 2 setting ISPIN=1 (later for the non-collinear case 1->4) # It is unknown until parsing the projected data else: self.ispin = 1 #checking again, for compatibility, if len(self.kpoints) != self.kpointsCount: raise RuntimeError( "Kpoints number do not match with metadata (header of PROCAR)") self.log.debug(str(self.kpoints)) self.log.info("The kpoints shape is " + str(self.kpoints.shape)) if self.recLattice is not None: self.log.info("Changing to cartesians coordinates") self.kpoints = np.dot(self.kpoints, self.recLattice) self.log.debug("New kpoints: \n" + str(self.k