from __future__ import absolute_import, division, print_function from cctbx.eltbx import wavelengths """ The purpose of this module is to interface cctbx with the FullProf progamm suite. FullProf can be obtained from http://www.ill.eu/sites/fullprof/ """ 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 iotbx.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 iotbx.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 run_fullprof(pcrfile, verbose=0): from libtbx import easy_run import sys, os """Run fullprof on a prepared .pcr file :param verbose: be verbose :type verbose: integer """ sys.stdout.flush() sys.stderr.flush() if pcrfile.lower().endswith(".pcr"): pcrfile = os.path.splitext(pcrfile)[0] if not os.path.exists(pcrfile + ".pcr"): raise IOError(pcrfile + ".pcr not found!") pcrfile = os.path.abspath(pcrfile) old_cwd = os.getcwd() workdir = os.path.split(pcrfile)[0] try: os.chdir(workdir) os.unlink(pcrfile + ".out") except KeyboardInterrupt: raise except Exception: pass fullprof_out = easy_run.fully_buffered(command="fp2k "+os.path.split(pcrfile)[1]) \ .raise_if_errors() \ .stdout_lines if (0 or verbose): for l in fullprof_out: print(l) f = open(pcrfile + ".out", "r") fullprof_out = f.readlines() f.close() sys.stderr.flush() if (0 or verbose): for l in fullprof_out: print(l[:-1]) sys.stdout.flush() os.chdir(old_cwd) if __name__ == '__main__': # just a little test for debugging from cctbx import sgtbx from cctbx.development import random_structure xrs = random_structure.xray_structure( space_group_info=sgtbx.space_group_info(number=1), elements=["C"]*10,u_iso=0.005) print(list(simulate_powder_pattern(xrs)[0]))#, filename="/tmp/test.pcr", keep_results=True))