def test_getParser(self):
"""Test passing of eps keyword argument by getParser function.
"""
pcif = getParser('cif', eps=1e-6)
grph = pcif.parseFile(self.graphiteciffile)
self.assertEqual(8, len(grph))
self.assertTrue(all(a.label.startswith('C1') for a in grph[:2]))
self.assertTrue(all(a.label.startswith('C2') for a in grph[2:]))
pcif2 = getParser('cif')
grph2 = pcif2.parseFile(self.graphiteciffile)
self.assertEqual(4, len(grph2))
return
def _wrapParseMethod(self, method, *args, **kwargs):
"""A helper evaluator method. Try the specified parse method with
each registered structure parser and return the first successful
resul. Structure parsers that match structure file extension are
tried first.
Set format attribute to the detected file format.
Return Structure instance, or raise StructureFormatError.
"""
from diffpy.Structure.Parsers import getParser
ofmts = self._getOrderedFormats()
stru = None
# try all parsers in sequence
parsers_emsgs = []
for fmt in ofmts:
p = getParser(fmt)
try:
pmethod = getattr(p, method)
stru = pmethod(*args, **kwargs)
self.format = fmt
break
except StructureFormatError, err:
parsers_emsgs.append("%s: %s" % (fmt, err))
except NotImplementedError:
pass
def read(self, filename, format='auto'):
"""Load structure from a file, any original data become lost.
filename -- file to be loaded
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
import diffpy.Structure
import diffpy.Structure.Parsers
getParser = diffpy.Structure.Parsers.getParser
p = getParser(format)
new_structure = p.parseFile(filename)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
if not self.title:
import os.path
tailname = os.path.basename(filename)
tailbase = os.path.splitext(tailname)[0]
self.title = tailbase
return p
def read(self, filename, format='auto'):
"""Load structure from a file, any original data become lost.
filename -- file to be loaded
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
import diffpy.Structure
import diffpy.Structure.Parsers
getParser = diffpy.Structure.Parsers.getParser
p = getParser(format)
new_structure = p.parseFile(filename)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
if not self.title:
import os.path
tailname = os.path.basename(filename)
tailbase = os.path.splitext(tailname)[0]
self.title = tailbase
return p
def _wrapParseMethod(self, method, *args, **kwargs):
"""A helper evaluator method. Try the specified parse method with
each registered structure parser and return the first successful
resul. Structure parsers that match structure file extension are
tried first.
Set format attribute to the detected file format.
Return Structure instance, or raise StructureFormatError.
"""
from diffpy.Structure.Parsers import getParser
ofmts = self._getOrderedFormats()
stru = None
# try all parsers in sequence
parsers_emsgs = []
for fmt in ofmts:
p = getParser(fmt)
try:
pmethod = getattr(p, method)
stru = pmethod(*args, **kwargs)
self.format = fmt
break
except StructureFormatError, err:
parsers_emsgs.append("%s: %s" % (fmt, err))
except NotImplementedError:
pass
def parse_cif_upload(content):
content_type, content_string = content.split(',')
decoded = base64.b64decode(content_string)
cif_s = decoded.decode('utf-8')
p = getParser('cif')
struc = p.parse(cif_s)
struc.sg = p.spacegroup
return struc
def writeStr(self, format):
"""return string representation of the structure in specified format
Note: available structure formats can be obtained by:
from Parsers import formats
"""
from diffpy.Structure.Parsers import getParser
p = getParser(format)
s = p.tostring(self)
return s
def writeStr(self, format):
"""return string representation of the structure in specified format
Note: available structure formats can be obtained by:
from Parsers import formats
"""
from diffpy.Structure.Parsers import getParser
p = getParser(format)
s = p.tostring(self)
return s
def loadCif(path):
"""load CIF file from given path to create a Structure instance
"""
if sys.version_info[0] < 3:
from diffpy.Structure.Parsers import getParser
else:
from diffpy.structure.parsers import getParser
p = getParser('cif')
nacl = p.parseFile(path)
nacl.sg = p.spacegroup
return nacl
def loadStructure(filename, fmt='auto'):
"""Load a new structure from a specified file.
filename -- file to be loaded
fmt -- format of the structure file. Must be one of the formats
defined in the Parsers subpackage. When 'auto', all
Parsers are tried in sequence.
Return a new Structure object.
Return PDFFitStructure object for 'pdffit' or 'discus' formats.
"""
from diffpy.Structure.Parsers import getParser
p = getParser(fmt)
rv = p.parseFile(filename)
return rv
def loadStructure(filename, fmt='auto'):
"""Load a new structure from a specified file.
filename -- file to be loaded
fmt -- format of the structure file. Must be one of the formats
defined in the Parsers subpackage. When 'auto', all
Parsers are tried in sequence.
Return a new Structure object.
Return PDFFitStructure object for 'pdffit' or 'discus' formats.
"""
from diffpy.Structure.Parsers import getParser
p = getParser(fmt)
rv = p.parseFile(filename)
return rv
def write(self, filename, format):
"""Save structure to file in the specified format
No return value.
Note: available structure formats can be obtained by:
from Parsers import formats
"""
from diffpy.Structure.Parsers import getParser
p = getParser(format)
p.filename = filename
s = p.tostring(self)
f = open(filename, 'wb')
f.write(s)
f.close()
return
def write(self, filename, format):
"""Save structure to file in the specified format
No return value.
Note: available structure formats can be obtained by:
from Parsers import formats
"""
from diffpy.Structure.Parsers import getParser
p = getParser(format)
p.filename = filename
s = p.tostring(self)
f = open(filename, 'wb')
f.write(s)
f.close()
return
def _loadStructure(path, sample):
"load crystal structure from path and save info in `sample`"
ext = os.path.splitext(path)[-1][1:]
from diffpy.Structure.Parsers import getParser
p = getParser(ext)
sample.atomic_structure = structure = p.parseFile(path)
assert not hasattr(sample, 'chemical_formula')
assert not hasattr(sample, 'lattice')
atoms = [atom.element for atom in structure]
from collections import Counter
atoms_counter = Counter(atoms)
sample.chemical_formula = ''.join('%s%s' % (a, n) for a,n in atoms_counter.items())
class Lattice: pass
lattice = sample.lattice = Lattice()
sl = structure.lattice
lattice.constants = sl.a, sl.b, sl.c, sl.alpha, sl.beta, sl.gamma
lattice.basis_vectors = sl.base
return sample
def readStr(self, s, format='auto'):
"""Load structure from a string, any original data become lost.
s -- string with structure definition
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process input string. This
can be inspected for information related to particular format.
"""
from diffpy.Structure.Parsers import getParser
p = getParser(format)
new_structure = p.parse(s)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
return p
def readStr(self, s, format='auto'):
"""Load structure from a string, any original data become lost.
s -- string with structure definition
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process input string. This
can be inspected for information related to particular format.
"""
from diffpy.Structure.Parsers import getParser
p = getParser(format)
new_structure = p.parse(s)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
return p
def exportStru(self, filename, format='cif', stype='diffpy'):
'''
Save structure to file in the specified format
:param filename: str, name of the file
:param stype: str, the type of stru file to export
:return: None
Note: available structure formats can be obtained by:
from Parsers import formats
'''
from diffpy.Structure.Parsers import getParser
p = getParser(format)
p.filename = filename
stru = self.convertStru(stype)
s = p.tostring(stru)
f = open(filename, 'wb')
f.write(s)
f.close()
return
def slice(crystal, phonon, start, end, npts, cartesian, outhist, eaxis):
"Given phonon data in IDF format, compute slice of SQE data along a specific reciprocal space direction"
# phonon is the path to a directory with IDF phonon data
# read phonon data
from mccomponents.sample.phonon import periodicdispersion_fromidf as pd
import mcni, numpy as np
disp = pd(phonon)
# and construct a proxy to the c++ data object
import mccomponents.homogeneous_scatterer as mh
cdisp = mh.scattererEngine(disp)
# create Q array
start = np.array(start)
end = np.array(end)
step = (end - start) / npts
Qs = start + step * np.arange(0, npts, 1.)[:, np.newaxis]
# Qs: cartesian, hkls: miller indexes
import os
reci_basis = recibasis_fromQgridinfo(os.path.join(phonon, 'Qgridinfo'))
inv_reci_basis = np.linalg.inv(reci_basis)
if cartesian:
hkls = np.dot(Qs, inv_reci_basis)
# these vectors will be used later in method Qtox
start = np.dot(start, inv_reci_basis)
step = np.dot(step, inv_reci_basis)
end = np.dot(end, inv_reci_basis)
else:
hkls = Qs
Qs = np.dot(hkls, reci_basis)
# gather energies and polarizations
nQ = len(Qs)
nbr = disp.dispersion.nBranches
natoms = disp.dispersion.nAtoms
# energies
Es = [cdisp.energy(br, mcni.vector3(*Q)) for Q in Qs for br in range(nbr)]
Es = np.array(Es)
Es.shape = nQ, nbr
# polarizations
pols = [
np.array(cdisp.polarization(br, atom, mcni.vector3(*Q))) for Q in Qs
for br in range(nbr) for atom in range(natoms)
]
pols = np.array(pols)
pols.shape = nQ, nbr, natoms, 3
# get atom positions from crystal structure file
from diffpy.Structure.Parsers import getParser
parser = getParser(os.path.splitext(crystal)[-1][1:])
structure = parser.parseFile(crystal)
atom_positions = [atom.xyz for atom in structure]
# create "events" for later histogramming process to construct slice
events = computeEvents(hkls, Es, pols, atom_positions, reci_basis)
# for x axis of the histogram (along Q)
maxx = np.linalg.norm(end - start)
xaxis = 0, maxx, maxx / npts
# Eaxis = 0, np.max(Es) * 1.1, 1.
Eaxis = eaxis
# functor to convert hkl to "x" value
from distutils.version import LooseVersion
def Qtox(hkl):
if LooseVersion(np.__version__) >= LooseVersion("1.8"):
x = np.linalg.norm(hkl - start, axis=-1)
else:
x = np.array(map(np.linalg.norm, hkl - start))
mask = x == x
return x, mask
# histogramming
h = makeSlice(events, xaxis, Eaxis, Qtox)
# output
import histogram.hdf as hh
hh.dump(h, outhist)
return
import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import leastsq
from diffpy.mpdf import *
from diffpy.Structure.Parsers import getParser
from diffpy.srfit.pdf import PDFGenerator, PDFParser
from diffpy.srfit.fitbase import FitRecipe, FitResults
from diffpy.srfit.fitbase import Profile, FitContribution
# Files containing our experimental data and structure file
dataFile = "npdf_07334.gr"
structureFile = "MnO_R-3m.cif"
# load structure and space group from the CIF file
pcif = getParser('cif')
mno = pcif.parseFile(structureFile)
# prepare profile object with experimental data
profile = Profile()
parser = PDFParser()
parser.parseFile(dataFile)
profile.loadParsedData(parser)
# define range for pdf calculation
rmin = 0.01
rmax = 20
rstep = 0.01
# setup calculation range for the PDF simulation
profile.setCalculationRange(xmin=rmin, xmax=rmax, dx=rstep)
def ciffile2unitcell(filename):
from diffpy.Structure.Parsers import getParser
p = getParser('cif')
return p.parseFile(filename)
import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize.minpack import leastsq
from diffpy.magpdf import *
from diffpy.Structure.Parsers import getParser
from diffpy.srfit.pdf import PDFGenerator, PDFParser
from diffpy.srfit.fitbase import FitRecipe, FitResults
from diffpy.srfit.fitbase import Profile, FitContribution
# Files containing our experimental data and structure file
dataFile = "npdf_07334.gr"
structureFile = "MnO_R-3m.cif"
# load structure and space group from the CIF file
pcif = getParser('cif')
mno = pcif.parseFile(structureFile)
# prepare profile object with experimental data
profile = Profile()
parser = PDFParser()
parser.parseFile(dataFile)
profile.loadParsedData(parser)
# define range for pdf calculation
rmin = 0.01
rmax = 20
rstep = 0.01
# setup calculation range for the PDF simulation
profile.setCalculationRange(xmin=rmin, xmax=rmax, dx=rstep)
def ciffile2unitcell(filename):
from diffpy.Structure.Parsers import getParser
p = getParser('cif')
return p.parseFile(filename)
