from __future__ import absolute_import, division, print_function import six from six.moves import range from six.moves import zip class pcr_parser(object): def __init__(self, inputstring=None, pcrfile=None, enforce_valid_comments=True): """Function to parse a FullProf command file into a ConfigObj It was modeled according to the FullProf manual and actual output files from FullProf and still far from being complete. :param inputstring: a string containing a whole commented pcr file like fp2k \ would format it. :type inputstring: string """ from configobj import ConfigObj self.LO = 0 self.cfg = ConfigObj() self.lines = inputstring.splitlines() self.enforce_valid_comments = enforce_valid_comments for line in self.lines: print(line) # for debugging if not self.lines[1].startswith("!"): if self.enforce_valid_comments: raise ValueError("""\ This function only works with correctly commented FullProf files! Please run fp2k on your input file first.""") else: for line in self.lines.copy(): if line.startswith("!"): self.lines.remove(line) self._parse() def __get_next_line(self, raw=False): self.LO += 1 # (increment line counter) if raw: return self.lines[self.LO] else: return self.lines[self.LO].split() def __parse_line(self, dict_to_append_to, KEYS, typeselect=" "): linevals = self.__get_next_line() i = 0 for val in KEYS.split(", "): if len(linevals) < 1: break if len(typeselect) > i: typesel = typeselect[i].lower() else: typsel = typeselect[-1].lower() if typesel == "i": # integer dict_to_append_to[val.strip()] = int(linevals.pop(0)) elif typesel == "f": # float dict_to_append_to[val.strip()] = float(linevals.pop(0)) else: dict_to_append_to[val.strip()] = linevals.pop(0) i += 1 def __check_comment(self, expected_comment="!"): if self.enforce_valid_comments: self.LO += 1 line = self.lines[self.LO] if not line.startswith(expected_comment): raise ValueError("Expected to find comment '{comm}',\ but found '{line}'".format(expected_comment, line)) def extract_structures(self): structures = {} for i in range(len(self.cfg['phases'])): structures[i+1]= self.extract_structure(phase_nr=i+1) return structures def extract_structure(self, phase_nr=1): """This method tries to extract the crystal structure from the parsed pcrfile. :returns: the extracted structure :rtype: cctbx.xray.structure """ from cctbx import xray from cctbx import crystal from cctbx.array_family import flex p = self.cfg['phases'][str(phase_nr)] atoms = p['atoms'] unit_cell = [ p['a'], p['b'], p['c'], p['alpha'], p['beta'], p['gamma'] ] special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=unit_cell, space_group_symbol=p['SYMB'])) scatterers = [] for k, a in six.iteritems(atoms): scatterers.append(xray.scatterer(label=a['LABEL'], scattering_type=a['NTYP'], site=(a['X'], a['Y'], a['Z']), b=a['B'])) scatterers_flex=flex.xray_scatterer(scatterers) structure = xray.structure(special_position_settings=special_position_settings, scatterers=scatterers_flex) return structure.as_py_code() def _parse(self): """Function to parse a FullProf command file into a ConfigObj """ # XXX Todo: Implement a lot more (TOF, special cases) self.cfg['TITLE'] = self.lines[0][5:].strip() if self.enforce_valid_comments: for line in self.lines: if line.startswith("!Job "): break self.LO += 1 # alias private class functions for conveniance get_next_line = self.__get_next_line parse_line = self.__parse_line check_comment = self.__check_comment parse_line(self.cfg, 'JOBTYP, NPROF, NPHASE, NBCKGD, NEXCRG, NSCAT, NORI, IDUM, IWGT,\ ILOR, IASG, IRESO, ISTEP, NRELL, ICRYG, IXUNIT, ICORR', "i") if self.cfg['IRESO'] != 0: raise ValueError("IRESO<>0 not supported (yet)! IRESO={}".format(self.cfg['IRESO'])) check_comment("!") check_comment("!Ipr ") parse_line(self.cfg, 'IOT, IPL, IPC, MAT, NXT, LST1, LST2, LST3, IPL1, IPL2, INSTRM,\ JCIL, JSY, JLKH, JFOU, ISHOR, IANALY', "i") check_comment("!") check_comment("! Lambda1 ") parse_line(self.cfg, 'LAMDA1, LAMDA2, RATIO, BKPOS, WDT, CTHM, TMR, RLIM, K', "f") check_comment("!") check_comment("!NCY ") parse_line(self.cfg, 'MCYCLE, EPS, RELAX1, RELAX2, RELAX3, RELAX4, THMIN, STEP, THMAX,\ ALPSD, SENT0', "if") if self.cfg['ICRYG'] == 0: NBCKGD = self.cfg['NBCKGD'] if NBCKGD > 2 or NBCKGD < -3: check_comment("!") check_comment("! 2Theta") # extract background from file background = [] for i in range(abs(NBCKGD)): linevals = get_next_line() background += ( float(linevals[0]), float(linevals[1]) ) self.cfg['background'] = background #check_comment("!") #check_comment("! Excluded ") # XXX Todo: implement check_comment("!") check_comment("!") self.cfg['MAXS'] = int(get_next_line()[0]) if self.cfg['ICRYG'] == 0: check_comment("!") check_comment("! Zero ") parse_line(self.cfg, 'ZER, FLGZER, SYCOS, FLCOS, SYSIN, FLSYN, LAMBDA, FLAMBDA, IGLMORE', "f"*8+"i") if self.cfg['IGLMORE'] == 1: check_comment("!") check_comment("! Microabsorption") check_comment("! P0 ") parse_line(self.cfg, 'CPO, Cp, CCp, Tau, CTau', "f") check_comment("! Background") linevals = get_next_line() lineflags = get_next_line() backgroundpoly = {} i = 0 for (v, f) in zip(linevals, lineflags): backgroundpoly[str(i)] = [ v, f ] i += 1 self.cfg['backgroundpoly'] = backgroundpoly phases = {} for p in range(self.cfg['NPHASE']): check_comment("!-------") check_comment("! Data for PHASE") check_comment("!-------") phase = {} phase['PHSNM'] = get_next_line() check_comment("!") check_comment("!Nat ") parse_line(phase, 'NAT, NDIST, NMAGC, PREF1, PREF2, PREF3,\ JBT, IRF, ISYM, ISTR, IFURT, ATZ, NVK, NPRO, IMORE', "iiifffiiiiifiii") if phase['IMORE'] != 0: # XXX Todo: read more phase data pass check_comment("!") phase['SYMB'] = get_next_line(raw=True)[:20].strip() if phase['ISYM'] != 0: # XXX Todo: read more phase data pass check_comment("!Atom ") atoms = {} for a in range(phase['NAT']): atom = {} parse_line(atom, 'LABEL, NTYP, X, Y, Z, B, N, IOPIN, IOPFIN, N_Type', "ssfffffiii") parse_line(atom, 'CX, CY, CZ, CB, CN, CMx, CMy, CMz', "f") atoms[str(a)] = atom phase['atoms'] = atoms check_comment("!-------> Profile ") check_comment("! Scale ") parse_line(phase, 'S, GAM1, Bov, STR1, STR2, STR3, IstrainModel', "ffffffi") parse_line(phase, 'CS, FLGAM1, CBov, CSTR1, CSTR2, CSTR3', "f") if phase['IRF'] == 4: # XXX Todo: read more phase data pass else: check_comment("! U") parse_line(phase, 'U, V, W, X, Y, IG, SZ, IsizeModel', "fffffffi") parse_line(phase, 'CU, CV, CW, CX, CY CIG CSZ', "f") check_comment("! a ") parse_line(phase, 'a, b, c, alpha, beta, gamma', "f") parse_line(phase, 'CA, CB, CC, CD, CE, CF', "f") check_comment("! Pref1 ") parse_line(phase, 'G1, G2, Pas1, Pas2, Pas3, Pas4', "f") parse_line(phase, 'CG1, CG2, CPas1, CPas2, CPas3, CPas4', "f") if self.cfg['RATIO'] < 0: check_comment("!Additional U,V,W") parse_line(phase, 'U2, V2, W2', "f") parse_line(phase, 'CU2, CV2, CW2', "f") phases[str(p+1)] = phase self.cfg['phases'] = phases if __name__ == '__main__': # just a little test for debugging testfile1="""\ COMM CeO2 CSIRO Test 25-143 ! Current global Chi2 (Bragg contrib.) = 11.67 ! Files => DAT-file: ce1.dat, PCR-file: ce1 !Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut 0 5 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 1 ! !Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana 0 0 1 0 1 0 4 0 0 1 0 1 1 1 2 0 0 ! ! Lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz 2nd-muR -> Patt# 1 1.540560 1.544330 -0.50000 25.000 15.0000 0.9100 0.0000 30.00 0.0000 0.0000 ! !NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 6 0.10 1.00 1.00 1.00 1.00 25.0000 0.025000 143.0000 0.000 0.000 ! ! 20 !Number of refined parameters ! ! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1 0.02573 11.0 0.00000 0.0 0.00000 0.0 0.000000 0.00 1 ! ! Microabsorption coefficients for Pattern# 1 ! P0 Cod_P0 Cp Cod_Cp Tau Cod_Tau 0.0000 0.00 1.2313 141.00 0.1340 151.00 ! Background coefficients/codes for Pattern# 1 (Polynomial of 6th degree) 24.538 -17.709 6.313 -0.604 0.000 0.000 21.00 31.00 41.00 51.00 0.00 0.00 !------------------------------------------------------------------------------- ! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.00 !------------------------------------------------------------------------------- CeO2 ! !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 2 0 0 1.0 1.0 1.0 0 0 0 0 0 688.480 0 5 0 ! F m 3 m <--Space group symbol !Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes Ce CE 0.00000 0.00000 0.00000 0.46033 0.02000 0 0 0 0 # color green conn O O 0.0 3.2 0.00 0.00 0.00 161.00 0.00 O O 0.25000 0.25000 0.25000 0.92218 0.04000 0 0 0 0 # color blue 0.00 0.00 0.00 171.00 0.00 !-------> Profile Parameters for Pattern # 1 ! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model 0.10216E-02 0.36723 0.00000 0.00000 0.00000 0.00000 0 61.00000 81.000 0.000 0.000 0.000 0.000 ! U V W X Y GauSiz LorSiz Size-Model 0.007618 -0.008887 0.010210 0.003351 0.000000 0.000000 0.000000 0 101.000 91.000 111.000 121.000 0.000 0.000 0.000 ! a b c alpha beta gamma #Cell Info 5.412223 5.412223 5.412223 90.000000 90.000000 90.000000 #multiple box -1 1 -1 1 0 1 71.00000 71.00000 71.00000 0.00000 0.00000 0.00000 ! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4 0.00000 0.00000 0.06233 0.00000 0.00000 0.00000 0.00 0.00 131.00 0.00 0.00 0.00 !Additional U,V,W parameters for Lambda2 0.007461 -0.005255 0.008197 <-- U2,V2,W2 for lambda(2) 191.000000 201.000000 181.000000 ! Limits for selected parameters : 14 0.0010 2.0000 0.0000 0 Cp_mabs_pat1 15 0.0010 2.0000 0.0000 0 Tau_mabs_pat1 ! 2Th1/TOF1 2Th2/TOF2 Pattern # 1 25.000 143.000 1 """ testfile2="""\ COMM unnamed ! Files => DAT-file: rnd_27A_15L_10M_02H_P_1_25_, PCR-file: rnd_27A_15L_10M_02H_P_1_25_ !Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut 2 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 ! !Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana 2 0 1 1 1 0 4 0 0 1 10 0 1 4 2 0 0 ! ! Lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz 2nd-muR -> Patt# 1 1.541800 1.541800 1.00000 60.000 5.0000 0.0000 0.0000 50.00 0.0000 0.0000 ! !NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 1 0.01 1.00 1.00 1.00 1.00 10.0000 0.100000 100.0000 0.000 0.000 ! ! 0 !Number of refined parameters ! ! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1 0.00000 0.0 0.00000 0.0 0.00000 0.0 0.000000 0.00 0 ! Background coefficients/codes for Pattern# 1 (Polynomial of 6th degree) 0.000 0.000 0.000 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 !------------------------------------------------------------------------------- ! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.00 !------------------------------------------------------------------------------- Phase_1 ! !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 27 0 0 0.0 0.0 1.0 0 0 0 0 0 924.976 0 0 0 ! P 1 <--Space group symbol !Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes Cs1 Cs 0.25575 0.74218 0.01280 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Cs2 Cs 0.76337 0.84611 0.64963 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C1 C 0.80799 0.01687 0.87219 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C2 C 0.95999 0.89218 0.97716 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C3 C 0.61730 0.40423 0.22206 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C4 C 0.96991 0.50496 0.26698 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C5 C 0.27434 0.34505 0.32297 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C6 C 0.51741 0.89889 0.90591 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C7 C 0.28570 0.06143 0.11813 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C8 C 0.85987 0.32773 0.87587 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C9 C 0.57367 0.37951 0.94405 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C10 C 0.74819 0.35206 0.92477 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C11 C 0.11661 0.17692 0.48152 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C12 C 0.68782 0.53267 0.57410 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C13 C 0.35920 0.22199 0.20957 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C14 C 0.54158 0.59845 0.57855 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C15 C 0.10057 0.16401 0.79612 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti1 Ti 0.42526 0.93883 0.93721 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti2 Ti 0.81513 0.52398 0.20025 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti3 Ti 0.51151 0.35888 0.34305 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti4 Ti 0.43735 0.05657 0.82934 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti5 Ti 0.96559 0.21095 0.23956 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti6 Ti 0.59096 0.29067 0.09393 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti7 Ti 0.24350 0.09520 0.50214 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti8 Ti 0.60861 0.39336 0.54098 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti9 Ti 0.80180 0.14419 0.13294 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti10 Ti 0.49678 0.67274 0.97981 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 !-------> Profile Parameters for Pattern # 1 ! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model 0.10000E-01 0.00000 0.03837 0.00000 0.00000 0.00000 0 0.00000 0.000 0.000 0.000 0.000 0.000 ! U V W X Y GauSiz LorSiz Size-Model 1.706310 -1.179299 0.405540 0.000000 0.000000 0.000000 0.000000 0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 ! a b c alpha beta gamma #Cell Info 9.422933 12.249814 16.018988 83.000000 109.000000 129.000000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00 0.00 0.00 0.00 0.00 0.00 ! 2Th1/TOF1 2Th2/TOF2 Pattern # 1 10.000 100.000 1 """ x = pcr_parser(testfile1) print(x.cfg) x = pcr_parser(testfile2) print(x.cfg) print(x.extract_structure())