import os, sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
import os
from copy import copy
import numpy as np
import fswig_hklgen as H
import hkl_model as Mod
np.seterr(divide="ignore", invalid="ignore")
DATAPATH = os.path.dirname(os.path.abspath(__file__))
backgFile = None
observedFile = os.path.join(DATAPATH, r"Mn025_4K.dat")
infoFile = os.path.join(DATAPATH, r"LFO.cfl")
(spaceGroup, crystalCell, magAtomList, symmetry) = H.readMagInfo(infoFile)
atomList = H.readInfo(infoFile)[2]
wavelength = 1.540000
ttMin = 3.0
ttMax = 167.750
ttStep = 0.05
exclusions = [[0.00, 5.00], [38.25, 39.00], [44.00, 45.50], [64.75, 65.75],
[77.5, 79.00], [81.75, 83.10], [97.00, 100.00], [111.50, 113.00],
[116.00, 118.00], [135.50, 139.50], [161.00, 169.00]]
tt, observed = H.readData(observedFile,
kind="y",
skiplines=3,
start=ttMin,
stop=ttMax,
step=ttStep,
exclusions=exclusions,
colstep=2)
def diffPattern(infoFile=None, backgroundFile=None, wavelength=1.5403,
ttMin=0, ttMax=180, ttStep=0.05, exclusions=None,
spaceGroup=None, cell=None, atomList=None,
symmetry=None, basisSymmetry=None, magAtomList=None,
uvw=[0,0,1], scale=1,
magnetic=False, info=False, plot=False, saveFile=None,
observedData=(None,None), labels=None, base=0, residuals=False, error=None, muR=None):
background = H.LinSpline(backgroundFile)
sMin, sMax = H.getS(ttMin, wavelength), H.getS(ttMax, wavelength)
if magnetic:
if (infoFile != None):
infofile = H.readMagInfo(infoFile)
if (spaceGroup == None): spaceGroup = infofile[0]
if (cell == None): cell = infofile[1]
if (magAtomList == None): magAtomList = infofile[2]
if (symmetry == None): symmetry = infofile[3]
if (basisSymmetry == None): basisSymmetry = symmetry
## magnetic peaks
# convert magnetic symmetry to space group
latt = H.getMagsymmK_latt(basisSymmetry)
if basisSymmetry.get_magsymm_k_mcentred() == 1:
latt+= " -1"
else:
latt += " 1"
spg = _SpaceGroup()
FortFuncs().set_spacegroup(latt, spg)
refList = H.hklGen(spaceGroup, cell, sMin, sMax, True, xtal=False)
refList2 = H.hklGen(spg, cell, sMin, np.sin(179.5/2)/wavelength, True, xtal=True)
magRefList = H.satelliteGen(cell, symmetry, sMax, hkls=refList2)#satelliteGen_python(cell, sMax, None)#
print "length of reflection list " + str(len(magRefList))
magIntensities = H.calcIntensity(magRefList, magAtomList, basisSymmetry,
wavelength, cell, True, muR=muR)
# add in structural peaks
if (atomList == None): atomList = H.readInfo(infoFile)[2]
#refList = hklGen(spaceGroup, cell, sMin, sMax, True, xtal=xtal)
intensities = H.calcIntensity(refList, atomList, spaceGroup, wavelength, muR=muR)
reflections = magRefList[:] + refList[:]
intensities = np.append(magIntensities, intensities)
else:
if (infoFile != None):
infofile = H.readInfo(infoFile)
if (spaceGroup == None): spaceGroup = infofile[0]
if (cell == None): cell = infofile[1]
if (atomList == None): atomList = infofile[2]
print "length of atom list is", len(atomList)
print(spaceGroup.number)
refList = H.hklGen(spaceGroup, cell, sMin, sMax, True, xtal=False)
reflections = refList[:]
intensities = H.calcIntensity(refList, atomList, spaceGroup, wavelength, muR=muR)
peaks = H.makePeaks(reflections, uvw, intensities, scale, wavelength, base=base)
numPoints = int(floor((ttMax-ttMin)/ttStep)) + 1
tt = np.linspace(ttMin, ttMax, numPoints)
intensity = H.getIntensity(peaks, background, tt, base=base)
if info:
if magnetic:
H.printInfo(cell, spaceGroup, (atomList, magAtomList), (refList, magRefList),
wavelength, basisSymmetry, muR=muR)
else:
H.printInfo(cell, spaceGroup, atomList, refList, wavelength, muR=muR)
if plot:
H.plotPattern(peaks, background, observedData[0], observedData[1],
ttMin, ttMax, ttStep, exclusions, labels=labels, base=base, residuals=residuals, error=error)
H.pylab.show()
H.pylab.savefig(os.path.join('/tmp/bland',str('plot.jpg')), dpi=2000)
if saveFile:
np.savetxt(saveFile, (tt, intensity), delimiter=" ")
tt1 = ["%.3f" % H.twoTheta(ref.s, wavelength) for ref in refList]
for atom in atomList:
print atom.label(), "element:", atom.element(), "iso:", atom.BIso(), "multip:", atom.multip(), "coords:", atom.coords(), "occupancy:", atom.occupancy()
h, k, l = tuple([str(ref.hkl[i]) for ref in refList] for i in xrange(3))
return (tt1, tt, intensities, [h,k,l], peaks, background)
import numpy as np
import fswig_hklgen as H
import hkl_model as Mod
import sxtal_model as S
#import bumps.parameter
#def dont(self, *args, **kw): raise Exception("don't")
#bumps.parameter.OperatorAdd.__init__ = dont
np.seterr(divide="ignore", invalid="ignore")
DATAPATH = os.path.dirname(os.path.abspath(__file__))
observedFile = os.path.join(DATAPATH,r"MnWO4_nuclear_5K.int")
infoFile = os.path.join(DATAPATH,r"AF4_5k.cfl")
magfile = os.path.join(DATAPATH, r"MnWO4_magneticAF4_5K.int")
(spaceGroup, crystalCell, magAtomList, symmetry) = H.readMagInfo(infoFile)
spaceGroup, crystalCell, atomList = H.readInfo(infoFile)
exclusions = []
# return wavelength, refList, sfs2, error, two-theta, and four-circle parameters
wavelength, refList, sfs2, error = S.readIntFile(observedFile, kind="int", cell=crystalCell)
magrefList, magsfs2, magerror = S.readMagIntFile(magfile, cell=crystalCell)
tt = [H.twoTheta(H.calcS(crystalCell, ref.hkl), wavelength) for ref in refList]
sfs2 = list(sfs2)
sfs2.extend(magsfs2)
sfs2 = np.array(sfs2)
tt.extend([H.twoTheta(H.calcS(crystalCell, ref.hkl), wavelength) for ref in magrefList])
error = list(error)
error.extend(list(magerror))
error2 = [item for item in error]
backg = None
basisSymmetry = copy(symmetry)
def diffPattern(infoFile=None,
backgroundFile=None,
wavelength=1.5403,
ttMin=0,
ttMax=180,
ttStep=0.05,
exclusions=None,
spaceGroup=None,
cell=None,
atomList=None,
symmetry=None,
basisSymmetry=None,
magAtomList=None,
uvw=[0, 0, 1],
scale=1,
magnetic=False,
info=False,
plot=False,
saveFile=None,
observedData=(None, None),
labels=None,
base=0,
residuals=False,
error=None,
muR=None):
background = H.LinSpline(backgroundFile)
sMin, sMax = H.getS(ttMin, wavelength), H.getS(ttMax, wavelength)
if magnetic:
if (infoFile != None):
infofile = H.readMagInfo(infoFile)
if (spaceGroup == None): spaceGroup = infofile[0]
if (cell == None): cell = infofile[1]
if (magAtomList == None): magAtomList = infofile[2]
if (symmetry == None): symmetry = infofile[3]
if (basisSymmetry == None): basisSymmetry = symmetry
## magnetic peaks
# convert magnetic symmetry to space group
latt = H.getMagsymmK_latt(basisSymmetry)
if basisSymmetry.get_magsymm_k_mcentred() == 1:
latt += " -1"
else:
latt += " 1"
spg = _SpaceGroup()
FortFuncs().set_spacegroup(latt, spg)
refList = H.hklGen(spaceGroup, cell, sMin, sMax, True, xtal=False)
refList2 = H.hklGen(spg,
cell,
sMin,
np.sin(179.5 / 2) / wavelength,
True,
xtal=True)
magRefList = H.satelliteGen(
cell, symmetry, sMax,
hkls=refList2) #satelliteGen_python(cell, sMax, None)#
print "length of reflection list " + str(len(magRefList))
magIntensities = H.calcIntensity(magRefList,
magAtomList,
basisSymmetry,
wavelength,
cell,
True,
muR=muR)
# add in structural peaks
if (atomList == None): atomList = H.readInfo(infoFile)[2]
#refList = hklGen(spaceGroup, cell, sMin, sMax, True, xtal=xtal)
intensities = H.calcIntensity(refList,
atomList,
spaceGroup,
wavelength,
muR=muR)
reflections = magRefList[:] + refList[:]
intensities = np.append(magIntensities, intensities)
else:
if (infoFile != None):
infofile = H.readInfo(infoFile)
if (spaceGroup == None): spaceGroup = infofile[0]
if (cell == None): cell = infofile[1]
if (atomList == None): atomList = infofile[2]
print "length of atom list is", len(atomList)
print(spaceGroup.number)
refList = H.hklGen(spaceGroup, cell, sMin, sMax, True, xtal=False)
reflections = refList[:]
intensities = H.calcIntensity(refList,
atomList,
spaceGroup,
wavelength,
muR=muR)
peaks = H.makePeaks(reflections,
uvw,
intensities,
scale,
wavelength,
base=base)
numPoints = int(floor((ttMax - ttMin) / ttStep)) + 1
tt = np.linspace(ttMin, ttMax, numPoints)
intensity = H.getIntensity(peaks, background, tt, base=base)
if info:
if magnetic:
H.printInfo(cell,
spaceGroup, (atomList, magAtomList),
(refList, magRefList),
wavelength,
basisSymmetry,
muR=muR)
else:
H.printInfo(cell,
spaceGroup,
atomList,
refList,
wavelength,
muR=muR)
if plot:
H.plotPattern(peaks,
background,
observedData[0],
observedData[1],
ttMin,
ttMax,
ttStep,
exclusions,
labels=labels,
base=base,
residuals=residuals,
error=error)
H.pylab.show()
H.pylab.savefig(os.path.join('/tmp/bland', str('plot.jpg')), dpi=2000)
if saveFile:
np.savetxt(saveFile, (tt, intensity), delimiter=" ")
tt1 = ["%.3f" % H.twoTheta(ref.s, wavelength) for ref in refList]
for atom in atomList:
print atom.label(), "element:", atom.element(), "iso:", atom.BIso(
), "multip:", atom.multip(), "coords:", atom.coords(
), "occupancy:", atom.occupancy()
h, k, l = tuple([str(ref.hkl[i]) for ref in refList] for i in xrange(3))
return (tt1, tt, intensities, [h, k, l], peaks, background)