def rietveld_refine_structure(
crystalstructure,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
I_obs=None,
Profile=None,
ProfileFile=None):
"""This function tries to rietveld refine a structure using FullProf.
If I_obs is given neither a Profile or a ProfileFile may be specified.
'Profile' and 'ProfileFile' are also exclusive.
:param crystalstructure: the starting model for the refinement
:type crystalstructure: cctbx.xray.structure
:param wavelength: the x-ray wavelength for the given intensity data
:type wavelength: float
:param I_obs: observed Intensities
:type I_obs: cctbx.miller
:param Profile: a XRD profile given as a list/tuple of (2-theta, intensity)-tuples
:type Profile: list/tuple(tuple(2theta,I))
:param ProfileFile: path to a XRD profile as FullProf .prf file
:type ProfileFile: string
"""
# Check preconditions
if [I_obs, Profile, ProfileFile].count(None) != 2:
raise (ValueError(
"You may only pass one of I_obs, Profile and ProfileFile"))
# start work
from write_pcr import write_pcr
import tempfile
import shutil
import os
# write pcr file and execute FullProf
try:
f = tempfile.NamedTemporaryFile(suffix=".pcr", delete=False)
except IOError:
raise
pcrfile = f.name
basepath = os.path.splitext(pcrfile)[0]
write_pcr(f,
crystalstructure,
jobtype=0,
wavelength=wavelength,
I_obs=I_obs)
f.close()
try:
if ProfileFile is not None:
shutil.copyfile(ProfileFile, basepath + ".dat")
elif Profile is not None:
# write out profile file for FullProf
# XXX: todo implement
pass
except IOError:
raise
run_fullprof(pcrfile, verbose=0)
# XXX Todo: extract refined structure from resulting .pcr/.new
# XXX Todo: extract Rwp of refined structure from resulting .pcr/.new
return None, None
def rietveld_refine_structure(crystalstructure,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
I_obs=None, Profile=None, ProfileFile=None):
"""This function tries to rietveld refine a structure using FullProf.
If I_obs is given neither a Profile or a ProfileFile may be specified.
'Profile' and 'ProfileFile' are also exclusive.
:param crystalstructure: the starting model for the refinement
:type crystalstructure: cctbx.xray.structure
:param wavelength: the x-ray wavelength for the given intensity data
:type wavelength: float
:param I_obs: observed Intensities
:type I_obs: cctbx.miller
:param Profile: a XRD profile given as a list/tuple of (2-theta, intensity)-tuples
:type Profile: list/tuple(tuple(2theta,I))
:param ProfileFile: path to a XRD profile as FullProf .prf file
:type ProfileFile: string
"""
# Check preconditions
if [I_obs, Profile, ProfileFile].count(None) != 2:
raise(ValueError("You may only pass one of I_obs, Profile and ProfileFile"))
# start work
from write_pcr import write_pcr
import tempfile
import shutil
import os
# write pcr file and execute FullProf
try:
f = tempfile.NamedTemporaryFile(suffix=".pcr", delete=False)
except IOError: raise
pcrfile = f.name
basepath = os.path.splitext(pcrfile)[0]
write_pcr(f, crystalstructure, jobtype=0,
wavelength=wavelength, I_obs=I_obs)
f.close()
try:
if ProfileFile is not None:
shutil.copyfile(ProfileFile, basepath+".dat")
elif Profile is not None:
# write out profile file for FullProf
# XXX: todo implement
pass
except IOError: raise
run_fullprof(pcrfile, verbose=0)
# XXX Todo: extract refined structure from resulting .pcr/.new
# XXX Todo: extract Rwp of refined structure from resulting .pcr/.new
return None, None
def simulate_powder_pattern(crystalstructure,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
filename="",
keep_results=False,
scale_down=1.0):
"""
Get integrated intensities and a a simulated XRD profile calculated with
FullProf (has to be installed and callable via "fp2k").
:param crystalstructure: a crystal structure to calculate the intensities for
:type crystalstructure: cctbx.xray.structure
:param wavelength: x-ray wavelength in angstroms
:type wavelength: float
:param filename: a filepath to save the in- and output of FullProf to
:type filename: string
:param keep_results: keep the (temporary) files from FullProf for a later \
manual inspection
:type keep_results: boolean
:param scale_down: factor to divide intensities by (to avoid overflows)
:type scale_down: float
:returns: calculated integral intensities, calculated profile
:rtype: cctbx.miller, list(tuple(float,int))
XXX Todo: implement extraction of calculated profile
"""
from write_pcr import write_pcr
from iotbx.reflection_file_reader import any_reflection_file
import tempfile
import os
# write pcr file and execute FullProf
try:
if filename == "":
f = tempfile.NamedTemporaryFile(suffix=".pcr", delete=False)
else:
f = open(filename, "w")
except IOError: raise
pcrfile = f.name
basepath = os.path.splitext(pcrfile)[0]
write_pcr(f, crystalstructure, jobtype=2,
wavelength=wavelength, scale_down=scale_down)
f.close()
if scale_down > 10000: raise
run_fullprof(pcrfile, verbose=0)
# fix hkl file for hkl reader
hklfile = basepath + ".fou"
f = open(hklfile, "r")
lines = f.readlines()[1:]
f.close()
hklfile = basepath + ".hkl"
if keep_results == True:
os.rename(hklfile, basepath + ".hkldata") # backup old hkl file
f = open(hklfile, "w")
f.writelines(lines)
f.close()
# extract intensities
f_calc = None
try:
rf = any_reflection_file(file_name=hklfile)
f_calc = rf.as_miller_arrays(
crystal_symmetry=crystalstructure.crystal_symmetry(),
assume_shelx_observation_type_is="intensities")[0]
except KeyboardInterrupt: raise
except Exception:
# an overflow occured
return simulate_powder_pattern(crystalstructure, wavelength=wavelength,
filename=filename, keep_results=keep_results,
scale_down=scale_down*10.0)
profile = None
# clean up
if keep_results == False:
for ext in [".pcr", ".sym", ".fou", ".ins", ".prf", ".sim", ".sum", ".out",
".hkl", ".hkldata", "1.fst", "1.sub"]:
try:
os.unlink(basepath + ext)
except KeyboardInterrupt: raise
except Exception: pass
return f_calc, profile
def simulate_powder_pattern(
crystalstructure,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
filename="",
keep_results=False,
scale_down=1.0):
"""
Get integrated intensities and a a simulated XRD profile calculated with
FullProf (has to be installed and callable via "fp2k").
:param crystalstructure: a crystal structure to calculate the intensities for
:type crystalstructure: cctbx.xray.structure
:param wavelength: x-ray wavelength in angstroms
:type wavelength: float
:param filename: a filepath to save the in- and output of FullProf to
:type filename: string
:param keep_results: keep the (temporary) files from FullProf for a later \
manual inspection
:type keep_results: boolean
:param scale_down: factor to divide intensities by (to avoid overflows)
:type scale_down: float
:returns: calculated integral intensities, calculated profile
:rtype: cctbx.miller, list(tuple(float,int))
XXX Todo: implement extraction of calculated profile
"""
from write_pcr import write_pcr
from iotbx.reflection_file_reader import any_reflection_file
import tempfile
import os
# write pcr file and execute FullProf
try:
if filename == "":
f = tempfile.NamedTemporaryFile(suffix=".pcr", delete=False)
else:
f = open(filename, "w")
except IOError:
raise
pcrfile = f.name
basepath = os.path.splitext(pcrfile)[0]
write_pcr(f,
crystalstructure,
jobtype=2,
wavelength=wavelength,
scale_down=scale_down)
f.close()
if scale_down > 10000: raise
run_fullprof(pcrfile, verbose=0)
# fix hkl file for hkl reader
hklfile = basepath + ".fou"
f = open(hklfile, "r")
lines = f.readlines()[1:]
f.close()
hklfile = basepath + ".hkl"
if keep_results == True:
os.rename(hklfile, basepath + ".hkldata") # backup old hkl file
f = open(hklfile, "w")
f.writelines(lines)
f.close()
# extract intensities
f_calc = None
try:
rf = any_reflection_file(file_name=hklfile)
f_calc = rf.as_miller_arrays(
crystal_symmetry=crystalstructure.crystal_symmetry(),
assume_shelx_observation_type_is="intensities")[0]
except KeyboardInterrupt:
raise
except Exception:
# an overflow occured
return simulate_powder_pattern(crystalstructure,
wavelength=wavelength,
filename=filename,
keep_results=keep_results,
scale_down=scale_down * 10.0)
profile = None
# clean up
if keep_results == False:
for ext in [
".pcr", ".sym", ".fou", ".ins", ".prf", ".sim", ".sum", ".out",
".hkl", ".hkldata", "1.fst", "1.sub"
]:
try:
os.unlink(basepath + ext)
except KeyboardInterrupt:
raise
except Exception:
pass
return f_calc, profile