Exemplo n.º 1
0
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
Exemplo n.º 2
0
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
Exemplo n.º 3
0
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
Exemplo n.º 4
0
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