def __init__(self):
DATAPATH = os.path.abspath("/home/pycrysfml/hklgen/examples/sxtal")
observedFile = os.path.join(DATAPATH, r"prnio.int")
infoFile = os.path.join(DATAPATH, r"prnio.cfl")
#Read data
self.spaceGroup, self.crystalCell, self.atomList = H.readInfo(infoFile)
#Return wavelength, refList, sfs2, error, two-theta, and four-circle parameters
wavelength, refList, sfs2, error = S.readIntFile(observedFile,
kind="int",
cell=self.crystalCell)
self.wavelength = wavelength
self.refList = refList
self.sfs2 = sfs2
self.error = error
self.tt = [
H.twoTheta(H.calcS(self.crystalCell, ref.hkl), wavelength)
for ref in refList
]
self.backg = None
self.exclusions = []
self.observation_space = spaces.MultiBinary(len(self.refList))
self.action_space = spaces.Discrete(len(self.refList))
self.episodeNum = 0
self.reset()
def test_pcr_reader(self):
"""Test of CrysFML PCR reader"""
DATAPATH = os.path.dirname(os.path.abspath(__file__))
pcr = os.path.join(DATAPATH, r"pbso4.pcr")
spaceGroup, cell, atomList = readInfo(pcr)
self.assertEqual(np.allclose(np.array([8.478, 5.3967, 6.958]),
np.array(cell.length()),
rtol=0.0001),
True,
msg="Crystal Cell populated incorrectly (a, b, c)")
self.assertEqual(
np.allclose(np.array([90.0, 90.0, 90.0]), np.array(cell.angle())),
True,
msg="Crystal Cell populated incorrectly (alpha, beta, gamma)")
self.assertEqual(spaceGroup.xtalSystem.lower(),
"orthorhombic",
msg="SpaceGroup error: xtalSystem")
self.assertEqual(spaceGroup.number, 62, msg="SpaceGroup error: number")
self.assertEqual(len(atomList),
5,
msg="AtomList length = " + str(len(atomList)) +
" Should be 5")
atom = atomList[0]
self.assertEqual(atom.label().lower(),
"pb",
msg="Wrong atom in atomList")
self.assertEqual(np.allclose(np.array([0.188, 0.25, 0.167]),
np.array(atom.coords()),
rtol=0.01),
True,
msg="Atom coordinates wrong")
self.assertEqual(atom.occupancy(), 0.5, msg="Atom Occupancy wrong")
def upload(request):
fp = request.FILES['file']
handle_uploaded_file(fp)
spaceGroup, cell, atomList = H.readInfo(os.path.join('/tmp/bland',str(fp.name)))
request.session['sg'] = pyc.getSpaceGroup_spg_symb(spaceGroup)
ret = [spaceGroup.number, list(cell.length()), list(cell.angle())]
for atom in atomList:
for el in periodictable.elements:
if(el.symbol == pyc.getAtom_chemsymb(atom)):
ell = el.number
ret.append([pyc.getAtom_lab(atom), pyc.getAtom_chemsymb(atom), atom.coords(), atom.occupancy(), atom.BIso(), ell])
ret = json.dumps(ret)
return HttpResponse(ret)
def test_cif_reader(self):
""" Test of CrysFML cif reader"""
DATAPATH = os.path.dirname(os.path.abspath(__file__))
cif = os.path.join(DATAPATH,r"al2o3.cif")
spaceGroup, cell, atomList = readInfo(cif)
self.assertEqual(np.allclose(np.array([4.7698, 4.769, 13.024]), np.array(cell.length()), rtol=0.001), True,
msg="Crystal Cell populated incorrectly (a, b, c)")
self.assertEqual(np.allclose(np.array([90.0, 90.0, 120.0]), np.array(cell.angle())), True,
msg="Crystal Cell populated incorrectly (alpha, beta, gamma)")
self.assertEqual(spaceGroup.xtalSystem.lower(), "trigonal", msg="SpaceGroup error: xtalSystem")
self.assertEqual(spaceGroup.number, 167, msg="SpaceGroup error: number")
self.assertEqual(len(atomList), 2, msg="AtomList length = "+str(len(atomList))+" Should be 2")
atom = atomList[0]
self.assertEqual(atom.label().lower(), "al1", msg="Wrong atom in atomList")
self.assertEqual(np.allclose(np.array([0.0, 0.00, 0.352]), np.array(atom.coords()), rtol=0.01), True,
msg="Atom coordinates wrong")
self.assertAlmostEqual(atom.occupancy(), 0.3333333, msg="Atom Occupancy wrong")
def test_pcr_reader(self):
"""Test of CrysFML PCR reader"""
DATAPATH = os.path.dirname(os.path.abspath(__file__))
pcr = os.path.join(DATAPATH,r"pbso4.pcr")
spaceGroup, cell, atomList = readInfo(pcr)
self.assertEqual(np.allclose(np.array([8.478, 5.3967, 6.958]), np.array(cell.length()), rtol=0.0001), True,
msg="Crystal Cell populated incorrectly (a, b, c)")
self.assertEqual(np.allclose(np.array([90.0, 90.0, 90.0]), np.array(cell.angle())), True,
msg="Crystal Cell populated incorrectly (alpha, beta, gamma)")
self.assertEqual(spaceGroup.xtalSystem.lower(), "orthorhombic", msg="SpaceGroup error: xtalSystem")
self.assertEqual(spaceGroup.number, 62, msg="SpaceGroup error: number")
self.assertEqual(len(atomList), 5, msg="AtomList length = "+str(len(atomList))+" Should be 5")
atom = atomList[0]
self.assertEqual(atom.label().lower(), "pb", msg="Wrong atom in atomList")
self.assertEqual(np.allclose(np.array([0.188, 0.25, 0.167]), np.array(atom.coords()), rtol=0.01), True,
msg="Atom coordinates wrong")
self.assertEqual(atom.occupancy(), 0.5, msg="Atom Occupancy wrong")
def main():
wavelength = 1.5403
cell = H.CrystalCell([11.372,10.272,7.359],[108.92,71.07,96.16]) # AABHTZ cell parameters
uvw = [0.151066141044763,-0.0914698313404034,0.0693509296318546] ## this is for a uvw transformation
#H.diffPattern(infoFile=infoFile, wavelength=wavelength,
# cell=cell, uvw=uvw, scale=1.40313478468024,
# info=True,plot=True)
# this created the diffraction pattern but relies of the type of atoms
sMin, sMax = getS(0.0, wavelength), getS(180.0, wavelength)
spaceGroup = None
infofile = H.readInfo(infoFile)
if (spaceGroup == None): spaceGroup = infofile[0]
if (cell == None): cell = infofile[1]
refList = H.hklGen(spaceGroup, cell, sMin, sMax, True, xtal=False) # generates list of hkl [1,1,1]
for value in refList:
print value.hkl
def upload(request):
fp = request.FILES['file']
handle_uploaded_file(fp)
spaceGroup, cell, atomList = H.readInfo(
os.path.join('/tmp/bland', str(fp.name)))
request.session['sg'] = pyc.getSpaceGroup_spg_symb(spaceGroup)
ret = [spaceGroup.number, list(cell.length()), list(cell.angle())]
for atom in atomList:
for el in periodictable.elements:
if (el.symbol == pyc.getAtom_chemsymb(atom)):
ell = el.number
ret.append([
pyc.getAtom_lab(atom),
pyc.getAtom_chemsymb(atom),
atom.coords(),
atom.occupancy(),
atom.BIso(), ell
])
ret = json.dumps(ret)
return HttpResponse(ret)
def __init__(self, observedFile, infoFile, backgFile=None, sxtal=True):
#Read data
self.spaceGroup, self.crystalCell, self.atomList = H.readInfo(infoFile)
# return wavelength, refList, sfs2, error, two-theta, and four-circle parameters
wavelength, refList, sfs2, error = S.readIntFile(observedFile,
kind="int",
cell=self.crystalCell)
self.wavelength = wavelength
self.refList = refList
self.sfs2 = sfs2
self.error = error
self.tt = [
H.twoTheta(H.calcS(self.crystalCell, ref.hkl), wavelength)
for ref in refList
]
self.backg = None
self.exclusions = []
self.reset()
def test_cif_reader(self):
""" Test of CrysFML cif reader"""
DATAPATH = os.path.dirname(os.path.abspath(__file__))
cif = os.path.join(DATAPATH, r"al2o3.cif")
spaceGroup, cell, atomList = readInfo(cif)
self.assertEqual(np.allclose(np.array([4.7698, 4.769, 13.024]),
np.array(cell.length()),
rtol=0.001),
True,
msg="Crystal Cell populated incorrectly (a, b, c)")
self.assertEqual(
np.allclose(np.array([90.0, 90.0, 120.0]), np.array(cell.angle())),
True,
msg="Crystal Cell populated incorrectly (alpha, beta, gamma)")
self.assertEqual(spaceGroup.xtalSystem.lower(),
"trigonal",
msg="SpaceGroup error: xtalSystem")
self.assertEqual(spaceGroup.number,
167,
msg="SpaceGroup error: number")
self.assertEqual(len(atomList),
2,
msg="AtomList length = " + str(len(atomList)) +
" Should be 2")
atom = atomList[0]
self.assertEqual(atom.label().lower(),
"al1",
msg="Wrong atom in atomList")
self.assertEqual(np.allclose(np.array([0.0, 0.00, 0.352]),
np.array(atom.coords()),
rtol=0.01),
True,
msg="Atom coordinates wrong")
self.assertAlmostEqual(atom.occupancy(),
0.3333333,
msg="Atom Occupancy wrong")
import os, sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
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 = os.path.join(DATAPATH, "ce1.bac")
observedFile = os.path.join(DATAPATH, "ceo2.dat")
infoFile = os.path.join(DATAPATH, "ce1.pcr")
(spaceGroup, crystalCell, atoms) = H.readInfo(infoFile)
wavelength = 1.540560 #+1.544330
backg = H.LinSpline(None)
ttMin = 25.0
ttMax = 143.0
ttStep = 0.0249947045118
exclusions = None
tt, observed, error = H.readIllData(observedFile, "", backgFile)
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem())
cell.a.pm(0.5)
m = Mod.Model(tt,
observed,
backg,
0,
0,
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)
import os,sys;sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
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 = os.path.join(DATAPATH,"Al2O3 Background.BGR")
observedFile = os.path.join(DATAPATH,"Al2O3.dat")
infoFile = os.path.join(DATAPATH,"Al2O3.cif")
(spaceGroup, crystalCell, atoms) = H.readInfo(infoFile)
wavelength = 1.5403
backg = H.LinSpline(backgFile)
ttMin = 3
ttMax = 167.75
ttStep = 0.05
exclusions = None
tt, observed = H.readData(observedFile, kind="y", skiplines=1, start=ttMin,
stop=ttMax, step=ttStep)
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem())
cell.a.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 0, 0, 1, wavelength, spaceGroup, cell,
atoms, exclusions)
m.u.range(0,2)
m.v.range(-2,0)
m.w.range(0,2)
m.eta.range(0,1)
from copy import copy
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__))
backgFile = None#os.path.join(DATAPATH,r"hobk_bas.bac")
observedFile = os.path.join(DATAPATH,r"prnio.int")
infoFile = os.path.join(DATAPATH,r"prnio.cfl")
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)
tt = [H.twoTheta(H.calcS(crystalCell, ref.hkl), wavelength) for ref in refList]
backg = None
def fit():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#cell.a.pm(5.0)
#cell.c.pm(5.0)
m = S.Model(tt, sfs2, backg, wavelength, spaceGroup, cell,
[atomList], exclusions,
scale=0.06298, error=error, hkls=refList, extinction=[0.0001054])
m.scale.range(0,100)
#m.base.pm(1000)
DATAPATH = os.path.dirname(os.path.abspath(__file__))
backgFile = None
observedFile = os.path.join(DATAPATH,r"../simulation.int")
infoFile = os.path.join(DATAPATH,r"../mote2.cfl")
inFile = open(observedFile, "r")
inFile.readline()
inFile.readline()
inFile.readline()
line = inFile.readline().split()
A = float(line[1])
B = float(line[2])
C = float(line[3])
#Read data
spaceGroup, crystalCell, atomList = H.readInfo(infoFile)
# return wavelength, refList, sfs2, error, two-theta, and four-circle parameters
wavelength, refList, sfs2, error = S.readIntFile(observedFile, kind="int", cell=crystalCell)
tt = [H.twoTheta(H.calcS(crystalCell, ref.hkl), wavelength) for ref in refList]
backg = None
exclusions = []
#Make a dictionary of the indices of each HKL value for the given crystal
d = {}
for i in range(len(refList)):
d[str(refList[i].hkl).replace("[","").replace("]","").replace(",","")] = i
def setInitParams():
#Make a cell
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
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__))
print DATAPATH
backgFile = os.path.join(DATAPATH,r"background_ge.BGR")
observedFile = os.path.join(DATAPATH,r"lufmo001.gsas")
infoFile = os.path.join(DATAPATH,r"LuFeMnO3_BT1fit.cfl")
(spaceGroup, crystalCell, magAtomList, symmetry) = H.readMagInfo(infoFile)
atomList = H.readInfo(infoFile)[2]
wavelength = 2.07750
ttMin = 3.0
ttMax = 166.3
ttStep = 0.05
exclusions = [[52,54],[60.5,62.5],[92.5,95],[115.0,117],[125.0,126]]
tt, observed = H.readData(observedFile, kind="y", skiplines=3,
start=ttMin, stop=ttMax, step=ttStep,
exclusions=exclusions, colstep=2)
backg = H.LinSpline(backgFile)
basisSymmetry = copy(symmetry)
#basisSymmetry = symmetry
if (basisSymmetry.centerType() == 2):
# change to acentric
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)
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)
