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, 1, wavelength, spaceGroup, cell, atoms, exclusions, base=min(observed), zero=-0.09459) m.u.range(0,2) m.zero.pm(0.1) m.v.range(-2,0) m.w.range(0,2) m.eta.range(0,1) m.scale.range(0,10) m.base.pm(250) for atomModel in m.atomListModel.atomModels: atomModel.x.range(0,1.0) if H.getAtom_chemsymb(atomModel.atom).lower() != "ca": atomModel.y.range(0,1.0) atomModel.z.range(0,1.0) if (atomModel.atom.multip == atomModel.sgmultip): # atom lies on a general position atomModel.x.pm(0.1) atomModel.y.pm(0.1) atomModel.z.pm(0.1) #m.atomListModel["Al1"].z.pm(0.1) #m.atomListModel["O1"].x.pm(0.1) #m.atomListModel["O3"].y.pm(0.1) #m.atomListModel["Pb"].B.range(0,10) M = bumps.FitProblem(m) M.model_update() return M
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.b.pm(0.5) cell.c.pm(0.5) m = Mod.Model(tt, observed, backg, 0, 0, 1, wavelength, spaceGroup, cell, atoms, exclusions, base=min(observed), zero=0.00029, error=error) m.u.range(0,2) m.zero.pm(0.1) m.v.range(-2,0) m.w.range(0,2) m.eta.range(0,1) m.scale.range(0,10) m.base.pm(250) for atomModel in m.atomListModel.atomModels: atomModel.B.range(0,10) if H.getAtom_chemsymb(atomModel.atom).lower() != "mn": atomModel.x.pm(1.0) atomModel.y.pm(1.0) if (atomModel.atom.multip == atomModel.sgmultip): # atom lies on a general position atomModel.x.pm(0.1) atomModel.y.pm(0.1) atomModel.z.pm(0.1) m.atomListModel["O2"].z.pm(1.0) #m.atomListModel["O1"].x.pm(0.1) #m.atomListModel["O3"].y.pm(0.1) #m.atomListModel["Pb"].B.range(0,10) M = bumps.FitProblem(m) M.model_update() return M
def fit(): # PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500 cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem()) cell.a.pm(0.000001) cell.b.pm(0.000001) cell.c.pm(0.000001) cell.a.set([5.536482,5.747128,7.692561][0]) cell.b.set([5.536482,5.747128,7.692561][1]) cell.c.set([5.536482,5.747128,7.692561][2]) m = Mod.Model(tt, observed, backg, 0.176001,-0.197806,0.091452, wavelength, spaceGroup, cell, atoms, exclusions, base=min(observed), zero=0.00029) m.u.pm(0.00001) m.v.pm(0.00001) m.w.pm(0.00001) m.u.set([0.176001,-0.197806,0.091452][0]) m.v.set([0.176001,-0.197806,0.091452][1]) m.w.set([0.176001,-0.197806,0.091452][2]) #m.u.range(0,2) m.zero.pm(0.1) #m.v.range(-2,0) #m.w.range(0,2) m.eta.range(0,1) m.scale.range(0,10) m.base.pm(250) for atomModel in m.atomListModel.atomModels: atomModel.B.range(0,10) if H.getAtom_chemsymb(atomModel.atom).lower() != "mn": atomModel.x.range(0,1) atomModel.y.range(0,1) if (atomModel.atom.multip == atomModel.sgmultip): # atom lies on a general position atomModel.x.pm(0.1) atomModel.y.pm(0.1) atomModel.z.pm(0.1) m.atomListModel["O2"].z.range(0,1) #m.atomListModel["O1"].x.pm(0.1) #m.atomListModel["O3"].y.pm(0.1) #m.atomListModel["Pb"].B.range(0,10) M = bumps.FitProblem(m) M.model_update() return M
def fit(): # PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500 cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem()) cell.a.pm(0.000001) cell.b.pm(0.000001) cell.c.pm(0.000001) cell.a.set([5.536482,5.747128,7.692561][0]) cell.b.set([5.536482,5.747128,7.692561][1]) cell.c.set([5.536482,5.747128,7.692561][2]) m = Mod.Model(tt, observed, backg, 0.176001,-0.197806,0.091452, wavelength, spaceGroup, cell, atoms, exclusions, base=min(observed), zero=0.00029) m.u.pm(0.00001) m.v.pm(0.00001) m.w.pm(0.00001) m.u.set([0.176001,-0.197806,0.091452][0]) m.v.set([0.176001,-0.197806,0.091452][1]) m.w.set([0.176001,-0.197806,0.091452][2]) #m.u.range(0,2) m.zero.pm(0.1) #m.v.range(-2,0) #m.w.range(0,2) m.eta.range(0,1) m.scale.range(0,10) m.base.pm(250) for atomModel in m.atomListModel.atomModels: #atomModel.B.range(0,10) if H.getAtom_chemsymb(atomModel.atom).lower() != "mn": atomModel.x.range(0,1) atomModel.y.range(0,1) if (atomModel.atom.multip == atomModel.sgmultip): # atom lies on a general position atomModel.x.pm(0.1) atomModel.y.pm(0.1) atomModel.z.pm(0.1) m.atomListModel["O2"].z.range(0,1) #m.atomListModel["O1"].x.pm(0.1) #m.atomListModel["O3"].y.pm(0.1) #m.atomListModel["Pb"].B.range(0,10) M = bumps.FitProblem(m) M.model_update() return M