def setIon(self, symnum):
"""
set ion's information
synumber -- string, the symbol+number, such as O+2
return -- None
"""
verifyType(symnum, str)
# split by + or -
if symnum.count("+") == 1:
terms = symnum.split("+")
number = int(terms[1])
elif symnum.count("-") == 1:
terms = symnum.split("-")
number = -1 * int(terms[1])
else:
errmsg = "%-30s: Input parameter 'symnum' is invalid! symnum = %-15s"%\
(self.__class__.__name___+".setIon( )", symnum)
raise RietError, errmsg
self.set("Symbol", terms[0])
self.set("number", number)
return
def setIon(self, symnum):
"""
set ion's information
synumber -- string, the symbol+number, such as O+2
return -- None
"""
verifyType(symnum, str)
# split by + or -
if symnum.count("+") == 1:
terms = symnum.split("+")
number = int(terms[1])
elif symnum.count("-") == 1:
terms = symnum.split("-")
number = -1*int(terms[1])
else:
errmsg = "%-30s: Input parameter 'symnum' is invalid! symnum = %-15s"%\
(self.__class__.__name___+".setIon( )", symnum)
raise RietError, errmsg
self.set("Symbol", terms[0])
self.set("number", number)
return
def addContribution(self, contribution):
"""
add a Contribution pertinent to this phase
return -- None
contribution -- Contribution instance
"""
from diffpy.pyfullprof.contribution import Contribution2Theta
verifyType(contribution, Contribution2Theta)
self._contributionlist.append(contribution)
return
def delContribution(self, contribution):
"""
remove the Contribution instance from the Contribution-list
return -- None
contribution -- instance of Contribution
Exception
1. if contribution is not in self._contributionlist
"""
verifyType(contribution, Contribution)
self._contributionlist.remove(contribution)
return
def delContribution(self, contribution):
"""
remove the Contribution instance from the Contribution-list
return -- None
contribution -- instance of Contribution
Exception
1. if contribution is not in self._contributionlist
"""
verifyType(contribution, Contribution)
self._contributionlist.remove(contribution)
return
def shiftOrigin(self, dx, dy, dz):
"""
for the Space group with multiple origin, the implementation in FullProf
is to shift the position of each atom by a specified amount
return -- None
dx -- float, -1 < dx < 1
dy -- float, -1 < dy < 1
dz -- float, -1 < dz < 1
"""
verifyType(dx, float)
verifyType(dy, float)
verifyType(dz, float)
# check range
if abs(dx)>1 or abs(dy)>1 or abs(dz)>1:
errmsg = "Phase.shiftOrigin(%-5s, %-5s, %-5s), Shift amount our of range"\
(str(dx), str(dy), str(dz))
raise RietError(errmsg)
# set shift
for atom in self.get("Atom"):
atom.shiftPosition(dx, dy, dz)
return
def shiftOrigin(self, dx, dy, dz):
"""
for the Space group with multiple origin, the implementation in FullProf
is to shift the position of each atom by a specified amount
return -- None
dx -- float, -1 < dx < 1
dy -- float, -1 < dy < 1
dz -- float, -1 < dz < 1
"""
verifyType(dx, float)
verifyType(dy, float)
verifyType(dz, float)
# check range
if abs(dx) > 1 or abs(dy) > 1 or abs(dz) > 1:
errmsg = "Phase.shiftOrigin(%-5s, %-5s, %-5s), Shift amount our of range"\
(str(dx), str(dy), str(dz))
raise RietError(errmsg)
# set shift
for atom in self.get("Atom"):
atom.shiftPosition(dx, dy, dz)
return
def runFullProf(fit, pcrfilename, mode="refine", srtype="r", processdir=dir, userinfo=None, exportsub=False):
"""
convert fit to FullProf pcr file
execute Rietveld refinement by FullProf,
Arguments:
- fit : a fit object to convert to a pcr file and run by FullProf
- pcrfilename : the name of the pcr file that is to write on the disk
- mode : string, for mode.. options =
1. "Refine" least square refine
2. "Calculate" just calculate the pattern as the forward calculator
3. "pcr" just print out pcr file
- srtype : string, structure solution type, "r" for "Rietveld", "l" for Lebail
- userinfo: : string, user information to add to pcr file
- exportsub : Boolean (export result in .sub in calculation mode)
Return : 1. Refine Mode FitSummary object
2. Calculate Mode list of list of 2-tuple (or list) for a phase or None
"""
from diffpy.pyfullprof.fit import Fit
from diffpy.pyfullprof.pcrfilewriter import pcrFileWriter
from diffpy.pyfullprof.pcrfilereader import ImportFitFromFullProf
from diffpy.pyfullprof.fpoutputfileparsers import FPOutFileParser
from diffpy.pyfullprof.fpuncertaintyreader import FPUncertainty
# FIXME in 'Calculate' mode, only 1 pattern is allowed NOW!
def ProcessOutput(infile):
"""
processing an file thread
(1) each line in intfile will be stored into a list as string without EOF
(2) all lines are ordered according to the original order in infile
infile: an file object
"""
OutLines = []
InLines = infile.readlines()
for line in InLines:
newline = line.split("\n")[0]
OutLines.append(newline)
return OutLines
# END FUNCTION: def ProcessOutput(infile)
def readFPOutput(lines):
""" read the output of FullProf output file
1. Last line contains "=> END"
- check Chi2: is last Chi2 = "NaN"? "Chi2:-NaN,
- refined output
2. otherwise to 1
a) "Error During Opening File" + file_name : terminate the program
b) "NO REFLECTIONS FOUND": as Chi2 = NaN
algorithm:
(1) split Chi2 line with ":"
return 1: good refinement
0 not refined
-1: setup error
-2: excessive peak overlap
-3: singular matrix
"""
result = 0
# 1. Exception!
if len(lines) == 1:
raise RietError("Fullprof fp2k Does Not Work")
lastline = lines[-1]
if lastline.count("=> END") >= 1:
# 1. collect Chi2
chi2lines = []
for line in lines:
if line.count("Chi2") == 1 and line.count("Rp")==1:
chi2lines.append(line)
# 2. process last chi2 line
# lastchi2line = chi2lines[len(chi2lines)-1]
if len(chi2lines) > 1:
# refinement mode
lastchi2line = chi2lines[-1]
if lastchi2line.count("NaN") > 0:
# NaN appears in statistic: refine not done
result = 0
else:
# good refinement
result = 1
else:
# calcuation mode
result = -1
else: # not a normal end
if lastline.count("Error") > 0:
# Error
result = -1
print "Exception! FullProf set up error! " + lastline + "\n"
elif lastline.count("Excessive peak overlap") == 1:
# Excessive peak overlap error
result = -2
elif lastline.count("Singular Matrix") == 1:
# Singular Matrix Error
result = -3
elif lastline.count("NO REFLECTIONS FOUND") == 1:
# Singular Matrix Error
result = -4
else:
# intial value error
result = 0
return result
# END FUNCTION: def readFPOutput(lines)
# -1: process input argument
if userinfo is None:
userinfo = []
verifyType(userinfo, list)
# 0. mandatory setup
fit.set("Pcr", 1)
fit.set("Aut", True)
# 1. check fit object:
isvalid = fit.validate(mode)
if not isvalid:
dbtag = "1721"
refine = fit.get("Refine")
print "Debug Tag: %-20s" % (dbtag)
print str(refine)
errmsg = "runFullProf() Fit object is not valid. Abort!"
raise RietError(errmsg)
if mode == "calculate":
# in this mode, data file is not used, but FullProf needs it!
from diffpy.pyfullprof.utilfunction import checkFileExistence
pattern = fit.get("Pattern")[0]
datafname = pattern.get("Datafile")
isexist = checkFileExistence(datafname)
if isexist is not True:
fakedatafile = True
fakefilename = datafname
cmd = "touch %-10s"% (fakefilename)
os.system(cmd)
else:
fakedatafile = False
# 2. write out the pcr file and run FullProf
pcrFileWriter(fit, pcrfilename, userinfo, srtype=srtype)
# get the root name and ext name of the pcr file
rootName, extname= os.path.splitext(os.path.basename(pcrfilename))
baseName = os.path.basename(pcrfilename)
if mode=="pcr":
return
shutil.copyfile(pcrfilename, rootName + '.prefit')
cmd = 'fp2k ' + baseName
import subprocess
from diffpy.pyfullprof.environment import FullProfSubprocessArgs
fp2kArgs = FullProfSubprocessArgs(cwd=processdir, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, stdin=open(os.devnull))
output = subprocess.Popen(('fp2k', baseName ), **fp2kArgs)
# 3. process output
CodeOutput = ProcessOutput(output.stdout)
#print '\n'.join(CodeOutput)
CodeError = ProcessOutput(output.stderr)
output.stdout.close()
output.stderr.close()
output.wait()
if mode == "refine":
# 4. process fit result
newfit = Fit(None)
try:
importfile = ImportFitFromFullProf(pcrfilename)
importresult = importfile.ImportFile(newfit)
except RietPCRError, err:
print "Error Message: %-30s"% (err)
importresult = False
# 5. pass the parameter and constraint information
summary = FitSummary()
if importresult is True:
# 6. build output
result = readFPOutput(CodeOutput)
outfname = rootName +".out"
# 6.2 Judge refine result
# Note: result > 0 is a more robust flag than refinesuccess
if result == 0:
refinesuccess = False
errmsg = "NAN"
elif result == -1:
outparser = FPOutFileParser(newfit, outfname)
refinesuccess = outparser.getStatus()
errmsg = outparser.getErrorReason()
elif result == -2:
refinesuccess = False
errmsg = "Excessive Peak Overlap"
elif result == -3:
refinesuccess = False
errmsg = "Singular Matrix"
elif result == -4:
refinesuccess = False
errmsg = "NO REFLECTIONS FOUND"
else:
refinesuccess = True
errmsg = None
if result < 0:
quitmessage = "result = %-5s < 0 means a failure error" % result
raise ValueError, quitmessage
# END-IF-ELSE
# 6.3 read uncertainty and phase fraction if refine is good
if refinesuccess is True:
# a) Uncertainty
fpsigma = FPUncertainty(outfname)
fpsigma.importUncertainty()
fpsigma.exportToFit(newfit)
# b) Phase Fraction
sumfilename = rootName + ".sum"
sumparse = FPSumFileParser(sumfilename)
sumparse.parsePhaseFraction(newfit)
# END-IF
# 6.4 Construct Summary
if result > 0:
outparser = FPOutFileParser(newfit, outfname)
summary.set(newfit, outparser, refinesuccess, srtype, errmsg, CodeOutput, CodeError)
else:
summary.setRefineStatus(False)
else:
# Bad refinement
summary.setRefineStatus(False)
# END-IF-ELSE
# 7. Process fp2k remainder
os.rename(pcrfilename, rootName+".posfit")
# 8. return
return summary