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
def toLines(self, stru):
"""Convert Structure stru to a list of lines in PDFfit format.
Return list of strings.
"""
# build the stru_pdffit dictionary initialized from the defaults
# in PDFFitStructure
stru_pdffit = PDFFitStructure().pdffit
if stru.pdffit:
stru_pdffit.update(stru.pdffit)
lines = []
# default values of standard deviations
d_sigxyz = numpy.zeros(3, dtype=float)
d_sigo = 0.0
d_sigU = numpy.zeros((3,3), dtype=float)
# here we can start
l = "title " + stru.title
lines.append( l.strip() )
lines.append( "format pdffit" )
lines.append( "scale %9.6f" % stru_pdffit["scale"] )
lines.append( "sharp %9.6f, %9.6f, %9.6f, %9.6f" % (
stru_pdffit["delta2"],
stru_pdffit["delta1"],
stru_pdffit["sratio"],
stru_pdffit["rcut"]) )
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)
lat = stru.lattice
lines.append( "cell %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" % (
lat.a, lat.b, lat.c, lat.alpha, lat.beta, lat.gamma) )
lines.append( "dcell %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" %
tuple(stru_pdffit["dcell"]) )
lines.append( "ncell %9i, %9i, %9i, %9i" % (1, 1, 1, len(stru)) )
lines.append( "atoms" )
for a in stru:
ad = a.__dict__
lines.append( "%-4s %17.8f %17.8f %17.8f %12.4f" % (
a.element.upper(), a.xyz[0], a.xyz[1], a.xyz[2], a.occupancy) )
sigmas = numpy.concatenate(
( ad.get("sigxyz", d_sigxyz), [ad.get("sigo", d_sigo)] ) )
lines.append( " %18.8f %17.8f %17.8f %12.4f" % tuple(sigmas) )
sigU = ad.get("sigU", d_sigU)
Uii = ( a.U[0][0], a.U[1][1], a.U[2][2] )
Uij = ( a.U[0][1], a.U[0][2], a.U[1][2] )
sigUii = ( sigU[0][0], sigU[1][1], sigU[2][2] )
sigUij = ( sigU[0][1], sigU[0][2], sigU[1][2] )
lines.append( " %18.8f %17.8f %17.8f" % Uii )
lines.append( " %18.8f %17.8f %17.8f" % sigUii )
lines.append( " %18.8f %17.8f %17.8f" % Uij )
lines.append( " %18.8f %17.8f %17.8f" % sigUij )
return lines
def toLines(self, stru):
"""Convert Structure stru to a list of lines in PDFfit format.
Return list of strings.
"""
# build the stru_pdffit dictionary initialized from the defaults
# in PDFFitStructure
stru_pdffit = PDFFitStructure().pdffit
if stru.pdffit:
stru_pdffit.update(stru.pdffit)
lines = []
# default values of standard deviations
d_sigxyz = numpy.zeros(3, dtype=float)
d_sigo = 0.0
d_sigU = numpy.zeros((3, 3), dtype=float)
# here we can start
l = "title " + stru.title
lines.append(l.strip())
lines.append("format pdffit")
lines.append("scale %9.6f" % stru_pdffit["scale"])
lines.append("sharp %9.6f, %9.6f, %9.6f, %9.6f" %
(stru_pdffit["delta2"], stru_pdffit["delta1"],
stru_pdffit["sratio"], stru_pdffit["rcut"]))
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)
lat = stru.lattice
lines.append("cell %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" %
(lat.a, lat.b, lat.c, lat.alpha, lat.beta, lat.gamma))
lines.append("dcell %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" %
tuple(stru_pdffit["dcell"]))
lines.append("ncell %9i, %9i, %9i, %9i" % (1, 1, 1, len(stru)))
lines.append("atoms")
for a in stru:
ad = a.__dict__
lines.append(
"%-4s %17.8f %17.8f %17.8f %12.4f" %
(a.element.upper(), a.xyz[0], a.xyz[1], a.xyz[2], a.occupancy))
sigmas = numpy.concatenate(
(ad.get("sigxyz", d_sigxyz), [ad.get("sigo", d_sigo)]))
lines.append(" %18.8f %17.8f %17.8f %12.4f" % tuple(sigmas))
sigU = ad.get("sigU", d_sigU)
Uii = (a.U[0][0], a.U[1][1], a.U[2][2])
Uij = (a.U[0][1], a.U[0][2], a.U[1][2])
sigUii = (sigU[0][0], sigU[1][1], sigU[2][2])
sigUij = (sigU[0][1], sigU[0][2], sigU[1][2])
lines.append(" %18.8f %17.8f %17.8f" % Uii)
lines.append(" %18.8f %17.8f %17.8f" % sigUii)
lines.append(" %18.8f %17.8f %17.8f" % Uij)
lines.append(" %18.8f %17.8f %17.8f" % sigUij)
return lines
