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 main():
tt = [H.twoTheta(H.calcS(cell, ref.hkl),wavelength) for ref in magRefList]
print getMagStrFacts()
S.diffPatternXtal(infoFile=infoFile, cell=cell, scale=1, tt=tt,
obsIntensity=np.zeros(len(magRefList)), wavelength=wavelength, basisSymmetry=symmetry,
magAtomList=magAtomList, plot=True, residuals=True, nuclear=False, error=None, magnetic=True,
info=True, base=0, refList=refList, extinctions=None)
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()
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)
for atomModel in m.atomListModel.atomModels:
#atomModel.x.range(0,1)
#atomModel.y.range(0,1)
#atomModel.z.range(0,1)
#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 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,
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)
#Define a model
m = S.Model([], [], backg, wavelength, spaceGroup, cell,
[atomList], exclusions,