class P_discus(StructureParser):
"""Parser for DISCUS structure format. The parser chokes
on molecule and generator records.
"""
def __init__(self):
StructureParser.__init__(self)
self.format = "discus"
# helper variables
self.nl = None
self.lines = None
self.line = None
self.stru = None
self.ignored_lines = []
self.cell_read = False
self.ncell_read = False
return
def parseLines(self, lines):
"""Parse list of lines in DISCUS format.
Return PDFFitStructure instance or raise StructureFormatError.
"""
self.lines = lines
ilines = self._linesIterator()
self.stru = PDFFitStructure()
record_parsers = {
"cell" : self._parse_cell,
"format" : self._parse_format,
"generator" : self._parse_not_implemented,
"molecule" : self._parse_not_implemented,
"ncell" : self._parse_ncell,
"spcgr" : self._parse_spcgr,
"symmetry" : self._parse_not_implemented,
"title" : self._parse_title,
"shape" : self._parse_shape,
}
try:
# parse header
for self.line in ilines:
words = self.line.split()
if not words or words[0][0] == '#': continue
if words[0] == 'atoms': break
rp = record_parsers.get(words[0], self._parse_unknown_record)
rp(words)
# check if cell has been defined
if not self.cell_read:
emsg = "%d: unit cell not defined" % self.nl
raise StructureFormatError(emsg)
# parse atoms
for self.line in ilines:
words = self.line.replace(',', ' ').split()
if not words or words[0][0] == '#': continue
self._parse_atom(words)
# self consistency check
exp_natoms = reduce(lambda x,y : x*y, self.stru.pdffit['ncell'])
# only check if ncell record exists
if self.ncell_read and exp_natoms != len(self.stru):
emsg = 'Expected %d atoms, read %d.' % \
(exp_natoms, len(self.stru))
raise StructureFormatError(emsg)
# take care of superlattice
if self.stru.pdffit['ncell'][:3] != [1,1,1]:
latpars = list(self.stru.lattice.abcABG())
superlatpars = [ latpars[i]*self.stru.pdffit['ncell'][i]
for i in range(3) ] + latpars[3:]
superlattice = Lattice(*superlatpars)
self.stru.placeInLattice(superlattice)
self.stru.pdffit['ncell'] = [1, 1, 1, exp_natoms]
except (ValueError, IndexError):
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: file is not in DISCUS format" % self.nl
raise StructureFormatError, emsg, exc_traceback
return self.stru
# End of parseLines
def toLines(self, stru):
"""Convert Structure stru to a list of lines in DISCUS format.
Return list of strings.
"""
self.stru = stru
# if necessary, convert self.stru to PDFFitStructure
if not isinstance(stru, PDFFitStructure):
self.stru = PDFFitStructure(stru)
# build the stru_pdffit dictionary initialized from the defaults
# in PDFFitStructure
stru_pdffit = PDFFitStructure().pdffit
if stru.pdffit:
stru_pdffit.update(stru.pdffit)
# here we can start
self.lines = lines = []
lines.append( "title " + self.stru.title.strip() )
lines.append( "spcgr " + stru_pdffit["spcgr"] )
if stru_pdffit.get('spdiameter', 0.0) > 0.0:
line = 'shape sphere, %g' % stru_pdffit['spdiameter']
lines.append(line)
if stru_pdffit.get('stepcut', 0.0) > 0.0:
line = 'shape stepcut, %g' % stru_pdffit['stepcut']
lines.append(line)
lines.append( "cell %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" %
self.stru.lattice.abcABG() )
lines.append( "ncell %9i, %9i, %9i, %9i" % (1, 1, 1, len(self.stru)) )
lines.append( "atoms" )
for a in self.stru:
lines.append( "%-4s %17.8f %17.8f %17.8f %12.4f" % (
a.element.upper(), a.xyz[0], a.xyz[1], a.xyz[2], a.Bisoequiv))
return lines
# End of toLines
def _linesIterator(self):
"""Iterator over self.lines, which increments self.nl
"""
# ignore trailing empty lines
stop = len(self.lines)
while stop > 0 and self.lines[stop-1].strip() == "":
stop -= 1
self.nl = 0
# read header of PDFFit file
for self.line in self.lines[:stop]:
self.nl += 1
yield self.line
# end of _linesIterator
def _parse_cell(self, words):
"""Process the cell record from DISCUS structure file.
"""
# split again on spaces or commas
words = self.line.replace(',', ' ').split()
latpars = [ float(w) for w in words[1:7] ]
try:
self.stru.lattice.setLatPar(*latpars)
except ZeroDivisionError:
emsg = "%d: Invalid lattice parameters - zero cell volume" % \
self.nl
raise StructureFormatError(emsg)
self.cell_read = True
return
def _parse_format(self, words):
"""Process the format record from DISCUS structure file.
"""
if words[1] == 'pdffit':
emsg = "%d: file is not in DISCUS format" % self.nl
raise StructureFormatError(emsg)
return
def _parse_ncell(self, words):
"""Process the ncell record from DISCUS structure file.
"""
# split again on spaces or commas
words = self.line.replace(',', ' ').split()
self.stru.pdffit['ncell'] = [ int(w) for w in words[1:5] ]
self.ncell_read = True
return
def _parse_spcgr(self, words):
"""Process the spcgr record from DISCUS structure file.
"""
self.stru.pdffit['spcgr'] = ''.join(words[1:])
return
def _parse_title(self, words):
"""Process the title record from DISCUS structure file.
"""
self.stru.title = self.line.lstrip()[5:].strip()
return
def _parse_shape(self, words):
"""Process the shape record from DISCUS structure file.
"""
# strip away any commas
linefixed = " ".join(words).replace(',', ' ')
wordsfixed = linefixed.split()
shapetype = wordsfixed[1]
if shapetype == 'sphere':
self.stru.pdffit['spdiameter'] = float(words[2])
elif shapetype == 'stepcut':
self.stru.pdffit['stepcut'] = float(words[2])
else:
emsg = 'Invalid type of particle shape correction %r' % shapetype
raise StructureFormatError, emsg
return
def _parse_atom(self, words):
"""Process atom records in DISCUS structure file.
"""
element = words[0][0:1].upper() + words[0][1:].lower()
xyz = [float(w) for w in words[1:4]]
Biso = float(words[4])
self.stru.addNewAtom(element, xyz)
a = self.stru.getLastAtom()
a.Bisoequiv = Biso
return
def _parse_unknown_record(self, words):
"""Process unknown record in DISCUS structure file.
Silently ignores the line and adds it to self.ignored_lines
Raises StructureFormatError.
"""
self.ignored_lines.append(self.line)
return
def _parse_not_implemented(self, words):
"""Process the unimplemented records from DISCUS structure file.
Raises NotImplementedError.
"""
emsg = "%d: reading of DISCUS record %r is not implemented." % \
(self.nl, words[0])
raise NotImplementedError(emsg)
