Esempio n. 1
0
 def feffterms(self, nnnn=1):
     """
     Fetch the various numbers in the feffNNNN.dat header for both the
     baseline and testrun.  A table of these values is printed.
     Return True is all are equal.
     """
     nnnndat = "feff%4.4d.dat" % nnnn
     bl      = feffpath(join(self.baseline, nnnndat))
     tr      = feffpath(join(self.testrun,  nnnndat))
     
     termdict = {'edge':   'energy threshold relative to atomic value',
                 'gam_ch': 'core level energy width',
                 'kf':     'k value at Fermi level',
                 'mu':     'Fermi level in eV',
                 'rs_int': 'interstitial radius',
                 'vint':   'interstitial potential'}
     if self.verbose:
         print "%-8s %-42s   %10s  %10s  %s" % ('key', 'component', 'baseline', 'testrun', 'same?')
         print "-----------------------------------------------------------------------------------"
     ok = True
     for key in termdict:
         same = getattr(bl._feffdat, key) == getattr(tr._feffdat, key)
         if self.verbose: print "%-6s   %-42s : %10s  %10s  %s" % (key, termdict[key], getattr(bl._feffdat, key),
                                                                   getattr(tr._feffdat, key), same)
         ok = ok and same
     return ok
Esempio n. 2
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def check_feffterms(folder, term):
    if not tests[folder].feffran:
        assert False, "failed to find results of feff calculation for %s" % folder
    bl = feffpath(join(tests[folder].baseline, 'feff0001.dat'))
    tr = feffpath(join(tests[folder].testrun, 'feff0001.dat'))
    assert abs(
        getattr(bl._feffdat, term) - getattr(tr._feffdat, term)
    ) < tests[folder].eps4, "feff term %s calculated incorrectly for %s" % (
        term, folder)
Esempio n. 3
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def do_fit(self, which):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, 'baseline', which))
    #endif

    print '>>>>>> %s' % folder

    data = read_xdi(join(self.path, 'Copper.chik'), _larch=self._larch)

    gds = Group(amp    = Parameter(1,     vary=True),
                enot   = Parameter(1e-7,  vary=True),
                thetad = Parameter(500,   vary=True),
                temp   = Parameter(10,    vary=False),
                alpha  = Parameter(1e-7,  vary=True),
                ss1    = Parameter(0.003, vary=True),
                _larch=self._larch  )

    paths = list()
    for index in range(1,14):
        nnnn = realpath(join(folder, "feff%4.4d.dat" % index))
        if not exists(nnnn):
            continue
        #end if
        if index > 1:
            sigsqr = 'sigma2_debye(temp, thetad)' 
        else:
            sigsqr = 'ss1'
        #end if
        paths.append(feffpath(nnnn,
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = sigsqr,
                              deltar = 'alpha*reff', _larch=self._larch))
    #end for

    trans = feffit_transform(kmin=3, kmax=16, kw=(2,1,3), dk=1, window='hanning', rmin=1.7, rmax=5.1, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8, win=2,
              xlabel=r'$R \rm\,(\AA)$', label='data',
              ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
              title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', win=2, _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', win=2, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', win=2, _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    return fit
Esempio n. 4
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    def feffterms(self, nnnn=1):
        """
        Fetch the various numbers in the feffNNNN.dat header for both
        the baseline and testrun.  A table of these values is printed
        if the verbose flag is True.  Return True if all are equal.

        """
        if (not self.feffran):
            #if self.verbose: print colored("You have not yet made the test run of Feff", 'magenta', attrs=['bold'])
            raise Exception("You have not yet made the test run of Feff")
        nnnndat = "feff%4.4d.dat" % nnnn
        bl = feffpath(join(self.baseline, nnnndat))
        tr = feffpath(join(self.testrun, nnnndat))

        termdict = {
            'edge': 'energy threshold relative to atomic value',
            'gam_ch': 'core level energy width',
            'kf': 'k value at Fermi level',
            'mu': 'Fermi level in eV',
            'rs_int': 'interstitial radius',
            'vint': 'interstitial potential'
        }
        if self.verbose:
            print "%-8s %-42s   %10s  %10s  %s" % (
                'key', 'description', 'baseline', 'testrun', 'same?')
            print "-----------------------------------------------------------------------------------"
        ok = True
        for key in termdict:
            same = abs(getattr(bl._feffdat, key) - getattr(tr._feffdat, key)
                       ) / getattr(bl._feffdat, key) < self.epsilon
            if self.verbose:
                print "%-6s   %-42s : %10s  %10s  %s" % (
                    key, termdict[key], getattr(
                        bl._feffdat, key), getattr(tr._feffdat, key), same)
            ok = ok and same
        return ok
Esempio n. 5
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def do_fit(self, which):

    if which == 'testrun':
        folder = self.testrun
    else:
        folder = self.baseline
    #end if

    data = read_xdi(join(self.path, 'bromoadamantane.chik'),
                    _larch=self._larch)

    gds = Group(amp=Parameter(1.021, vary=True, _larch=self._larch),
                enot=Parameter(4.01, vary=True, _larch=self._larch),
                delr=Parameter(-0.007, vary=True, _larch=self._larch),
                brc=Parameter(expr='1.9521+delr', _larch=self._larch),
                ss=Parameter(0.003, vary=True, _larch=self._larch),
                phir=Parameter(109.29960 * 3.141592653589793 / 180,
                               vary=False,
                               _larch=self._larch),
                cc=Parameter(1.53780, vary=False, _larch=self._larch),
                tanbeta=Parameter(expr='(brc+cc)*tan(phir/2) / (brc-cc)',
                                  _larch=self._larch),
                beta=Parameter(expr='atan(tanbeta)', _larch=self._larch),
                brc2=Parameter(expr='(brc-cc)*cos(phir/2)/cos(beta)',
                               _larch=self._larch),
                drh=Parameter(0.04, vary=True, _larch=self._larch),
                ssh=Parameter(0.005, vary=True, _larch=self._larch),
                ss2=Parameter(expr='ss*(brc2/brc)**2', _larch=self._larch),
                c3=Parameter(-0.0007, vary=True, _larch=self._larch),
                _larch=self._larch)

    paths = list()
    paths.append(
        feffpath(realpath(join(folder, "feff0001.dat")),
                 s02='amp',
                 e0='enot',
                 sigma2='ss',
                 deltar='delr',
                 third='c3',
                 _larch=self._larch))
    paths.append(
        feffpath(realpath(join(folder, "feff0002.dat")),
                 s02='amp',
                 e0='enot',
                 sigma2='ss2',
                 deltar='brc2-2.8565',
                 _larch=self._larch))
    paths.append(
        feffpath(realpath(join(folder, "feff0003.dat")),
                 s02='amp',
                 e0='enot',
                 sigma2='ssh',
                 deltar='drh',
                 _larch=self._larch))
    paths.append(
        feffpath(realpath(join(folder, "feff0004.dat")),
                 s02='amp',
                 e0='enot',
                 sigma2='(ss+ss2)/2',
                 deltar='(brc+brc2+cc)/2 - 3.173',
                 _larch=self._larch))
    paths.append(
        feffpath(realpath(join(folder, "feff0005.dat")),
                 s02='amp',
                 e0='enot',
                 sigma2='(ss+ss2)/2',
                 deltar='(brc+brc2+cc)/2 - 3.173',
                 _larch=self._larch))

    trans = feffit_transform(kmin=2.5,
                             kmax=13,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1.25,
                             rmax=3,
                             _larch=self._larch)
    dset = feffit_dataset(data=data,
                          pathlist=paths,
                          transform=trans,
                          _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,
                 dset.data.chir_mag + offset,
                 xmax=8,
                 win=2,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_mag + offset,
              label='fit',
              win=2,
              _larch=self._larch)
        _plot(dset.data.r,
              dset.data.chir_re,
              label='data',
              win=2,
              _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_re,
              label='fit',
              win=2,
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    return fit
Esempio n. 6
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def do_fit(self, which):

    if which == 'testrun':
        folder = self.testrun
    else:
        folder = self.baseline

    data = read_xdi(join(self.path, 'NiO.chik'), _larch=self._larch)
    if hasattr(data, 'wavenumber'):
        data.k = data.wavenumber

    gds = Group(
        amp=Parameter(1, vary=True, _larch=self._larch),
        enot=Parameter(0.01, vary=True, _larch=self._larch),
        alpha=Parameter(0.0001, vary=True, _larch=self._larch),
        sso=Parameter(0.003, vary=True, _larch=self._larch),
        ssni=Parameter(0.003, vary=True, _larch=self._larch),
        sso2=Parameter(0.003, vary=True, _larch=self._larch),
        #sso3   = Parameter(0.003,  vary=True, _larch=self._larch),
        ssni2=Parameter(0.003, vary=True, _larch=self._larch),
        #ssni3  = Parameter(0.003,  vary=True, _larch=self._larch),
        #ssni4  = Parameter(0.003,  vary=True, _larch=self._larch),
        _larch=self._larch)

    paths = list()
    paths.append(
        feffpath(
            realpath(join(folder, "feff0001.dat")),  # 1st shell O SS
            s02='amp',
            e0='enot',
            sigma2='sso',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0002.dat")),  # 2nd shell Ni SS
            s02='amp',
            e0='enot',
            sigma2='ssni',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0003.dat")),  # O-O triangle
            s02='amp',
            e0='enot',
            sigma2='1.5*sso',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0004.dat")),  # O-Ni triangle
            s02='amp',
            e0='enot',
            sigma2='sso+ssni',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0005.dat")),  # 3rd shell O SS
            s02='amp',
            e0='enot',
            sigma2='sso2',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0006.dat")),  # 4th shell Ni SS
            s02='amp',
            e0='enot',
            sigma2='ssni2',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0007.dat")),  # O-O non-forward linear
            s02='amp',
            e0='enot',
            sigma2='sso*2',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0008.dat")),  # O-Ni forward scattering
            s02='amp',
            e0='enot',
            sigma2='ssni2',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder,
                          "feff0009.dat")),  # O-O forward through absorber
            s02='amp',
            e0='enot',
            sigma2='sso*2',
            deltar='alpha*reff',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0010.dat")),  # O-Ni-O double forward
            s02='amp',
            e0='enot',
            sigma2='ssni2',
            deltar='alpha*reff',
            _larch=self._larch))

    trans = feffit_transform(kmin=3,
                             kmax=15.938,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1.5,
                             rmax=4.2,
                             _larch=self._larch)
    dset = feffit_dataset(data=data,
                          pathlist=paths,
                          transform=trans,
                          _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = 0.6 * max(dset.data.chir_mag)
        _newplot(dset.data.r,
                 dset.data.chir_mag + offset,
                 xmax=8,
                 win=2,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_mag + offset,
              label='fit',
              win=2,
              _larch=self._larch)
        _plot(dset.data.r,
              dset.data.chir_re,
              label='data',
              win=2,
              _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_re,
              label='fit',
              win=2,
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    return fit
Esempio n. 7
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def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'NiO.chik'), _larch=self._larch)
    if hasattr(data, 'wavenumber'):
        data.k = data.wavenumber

    gds = Group(amp    = Parameter(1,      vary=True, _larch=self._larch),
                enot   = Parameter(1e-7,   vary=True, _larch=self._larch),
                sso    = Parameter(0.003,  vary=True, _larch=self._larch), _larch=self._larch  )

    if firstshell:
        gds.delr   = Parameter(1e-7,   vary=True, _larch=self._larch)
        dr1param   = 'delr'
    else:
        gds.alpha  = Parameter(1e-7,   vary=True, _larch=self._larch)
        gds.ssni   = Parameter(0.003,  vary=True, _larch=self._larch)
        gds.sso2   = Parameter(0.003,  vary=True, _larch=self._larch)
        #gds.sso3   = Parameter(0.003,  vary=True, _larch=self._larch)
        gds.ssni2  = Parameter(0.003,  vary=True, _larch=self._larch)
        #gds.ssni3  = Parameter(0.003,  vary=True, _larch=self._larch)
        #gds.ssni4  = Parameter(0.003,  vary=True, _larch=self._larch)
        dr1param   = 'alpha*reff'

    paths = list() 
    paths.append(feffpath(realpath(join(folder, "feff0001.dat")), # 1st shell O SS
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'sso',
                          deltar = dr1param, _larch=self._larch))
    if not firstshell:
        paths.append(feffpath(realpath(join(folder, "feff0002.dat")), # 2nd shell Ni SS
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ssni',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0003.dat")), # O-O triangle
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = '1.5*sso',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0004.dat")), # O-Ni triangle
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'sso+ssni/2',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0005.dat")), # 3rd shell O SS
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'sso2',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0006.dat")), # 4th shell Ni SS
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ssni2',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0007.dat")), # O-O non-forward linear
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'sso*2',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0008.dat")), # O-Ni forward scattering
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ssni2',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0009.dat")), # O-O forward through absorber
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'sso*2',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0011.dat")), # O-Ni-O double forward
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ssni2',
                              deltar = 'alpha*reff', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0010.dat")), # O-O rattle (the order of 10 and 11 is different in Demeter's pathfinder!)
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'sso*4',
                              deltar = 'alpha*reff', _larch=self._larch))

    rx  = 4.2
    if firstshell: rx  = 1.95

    trans = feffit_transform(kmin=3, kmax=15.938, kw=(2,1,3), dk=1, window='hanning', rmin=1.0, rmax=rx, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = 0.6*max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8,
              xlabel=r'$R \rm\,(\AA)$', label='data',
              ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
              title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells='_1st'

    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".k"), dset.data.k, dset.data.chi, dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
                dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest,'fit_'+which+shells+'.gp'), 'w') as inp:
        inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
                                        {'material': 'NiO',
                                         'model': which,
                                         'fittest': fittest,
                                         'shells': shells,
                                         'kmin': 3,
                                         'kmax': 15.938,
                                         'rmin': 1.0,
                                         'rmax': rx,
                                         'offset': 1,
                                     } ))

    return fit
Esempio n. 8
0
def do_fit(self, which):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, 'baseline', which))
    #endif

    print '>>>>>> %s' % folder

    data = read_xdi(join(self.path, 'Copper.chik'), _larch=self._larch)

    gds = Group(amp=Parameter(1, vary=True),
                enot=Parameter(1e-7, vary=True),
                thetad=Parameter(500, vary=True),
                temp=Parameter(10, vary=False),
                alpha=Parameter(1e-7, vary=True),
                ss1=Parameter(0.003, vary=True),
                _larch=self._larch)

    paths = list()
    for index in range(1, 14):
        nnnn = realpath(join(folder, "feff%4.4d.dat" % index))
        if not exists(nnnn):
            continue
        #end if
        if index > 1:
            sigsqr = 'sigma2_debye(temp, thetad)'
        else:
            sigsqr = 'ss1'
        #end if
        paths.append(
            feffpath(nnnn,
                     s02='amp',
                     e0='enot',
                     sigma2=sigsqr,
                     deltar='alpha*reff',
                     _larch=self._larch))
    #end for

    trans = feffit_transform(kmin=3,
                             kmax=16,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1.7,
                             rmax=5.1,
                             _larch=self._larch)
    dset = feffit_dataset(data=data,
                          pathlist=paths,
                          transform=trans,
                          _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,
                 dset.data.chir_mag + offset,
                 xmax=8,
                 win=2,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_mag + offset,
              label='fit',
              win=2,
              _larch=self._larch)
        _plot(dset.data.r,
              dset.data.chir_re,
              label='data',
              win=2,
              _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_re,
              label='fit',
              win=2,
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    return fit
Esempio n. 9
0
def do_fit(self, which):

    if which == 'testrun':
        folder = self.testrun
    else:
        folder = self.baseline
    #end if

    data = read_xdi(join(self.path, 'bromoadamantane.chik'), _larch=self._larch)

    gds = Group(amp     = Parameter(1.021,     vary=False, _larch=self._larch),
                enot    = Parameter(4.01,      vary=True,  _larch=self._larch),
                delr    = Parameter(-0.007,    vary=True,  _larch=self._larch),
                brc     = Parameter(expr = '1.9521+delr',  _larch=self._larch),
                ss      = Parameter(0.003,     vary=True,  _larch=self._larch),
                phir    = Parameter(109.29960 * 3.141592653589793 / 180,   vary=False, _larch=self._larch),
                cc      = Parameter(1.53780,   vary=False, _larch=self._larch),
                tanbeta = Parameter(expr = '(brc+cc)*tan(phir/2) / (brc-cc)', _larch=self._larch),
                beta    = Parameter(expr = 'atan(tanbeta)', _larch=self._larch),
                brc2    = Parameter(expr = '(brc-cc)*cos(phir/2)/cos(beta)', _larch=self._larch),
                drh     = Parameter(0.04,      vary=True,  _larch=self._larch),
                ssh     = Parameter(0.005,     vary=True,  _larch=self._larch),
                ss2     = Parameter(expr = 'ss*(brc2/brc)**2', _larch=self._larch),
                c3      = Parameter(-0.0007,   vary=True,  _larch=self._larch),
                _larch=self._larch  )

    paths = list()
    paths.append(feffpath(realpath(join(folder, "feff0001.dat")),
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'ss',
                          deltar = 'delr',
                          third  = 'c3', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0002.dat")),
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'ss2',
                          deltar = 'brc2-2.8565', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0003.dat")),
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'ssh',
                          deltar = 'drh', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0004.dat")),
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = '(ss+ss2)/2',
                          deltar = '(brc+brc2+cc)/2 - 3.173', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0005.dat")),
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = '(ss+ss2)/2',
                          deltar = '(brc+brc2+cc)/2 - 3.173', _larch=self._larch))


    trans = feffit_transform(kmin=3, kmax=13, kw=(2,1,3), dk=1, window='hanning', rmin=1.25, rmax=3, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8, win=2,
                 xlabel=r'$R \rm\,(\AA)$', label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', win=2, _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', win=2, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', win=2, _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    return fit
Esempio n. 10
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    firstshell = False          # no 1st shell fit for this material

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'uranyl.chik'), _larch=self._larch)

    gds = Group(amp    = Parameter(1,      vary=True,  _larch=self._larch),
                enot   = Parameter(1e-7,   vary=True,  _larch=self._larch),
                #enot   = Parameter(1e-7,   vary=True,  _larch=self._larch, min=0, max=13),
                enoteq = Parameter(expr= 'enot',     _larch=self._larch),
                deloax = Parameter(1e-7,   vary=True,  _larch=self._larch),
                deloeq = Parameter(1e-7,   vary=True,  _larch=self._larch),
                sigoax = Parameter(0.003,  vary=True,  _larch=self._larch),
                sigoeq = Parameter(0.003,  vary=True,  _larch=self._larch),
                nax    = Parameter(2.0,    vary=False, _larch=self._larch),
                neq    = Parameter(6,      vary=False, _larch=self._larch), #, min=0, max=12),
                _larch=self._larch  )

    paths = list() 
    paths.append(feffpath(realpath(join(folder, "feff0001.dat")), # axial oxygen
                          degen  = 1,
                          s02    = 'amp*nax',
                          e0     = 'enot',
                          sigma2 = 'sigoax',
                          deltar = 'deloax', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0003.dat")), # equatorial oxygen
                          degen  = 1,
                          s02    = 'amp*neq',
                          e0     = 'enoteq',
                          sigma2 = 'sigoeq',
                          deltar = 'deloeq', _larch=self._larch))

    paths.append(feffpath(realpath(join(folder, "feff0008.dat")), # axial oxygen, rattle
                          degen  = 1,
                          s02    = 'amp*nax',
                          e0     = 'enot',
                          sigma2 = 'sigoax*4',
                          deltar = 'deloax*2', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0009.dat")), # axial oxygen, non-forward
                          degen  = 1,
                          s02    = 'amp*nax',
                          e0     = 'enot',
                          sigma2 = 'sigoax',
                          deltar = 'deloax*2', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0010.dat")), # axial oxygen, forward
                          degen  = 1,
                          s02    = 'amp*nax',
                          e0     = 'enot',
                          sigma2 = 'sigoax',
                          deltar = 'deloax*2', _larch=self._larch))




    trans = feffit_transform(kmin=3, kmax=11, kw=(2,1,3), dk=1, window='hanning', rmin=1.0, rmax=3.2, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8, win=2,
              xlabel=r'$R \rm\,(\AA)$', label='data',
              ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
              title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', win=2, _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', win=2, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', win=2, _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells='_1st'

    write_ascii(join(self.folder, fittest, "fit_"+which+".k"), dset.data.k, dset.data.chi, dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_"+which+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
                dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_'+which+'.gp'), 'w') as inp:
        inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
                                        {'material': 'uranyl',
                                         'model': which,
                                         'fittest': fittest,
                                         'shells': shells,
                                         'kmin': 3,
                                         'kmax': 11,
                                         'rmin': 1.0,
                                         'rmax': 3.2,
                                         'offset': 1,
                                     } ))

    return fit
Esempio n. 11
0
def do_fit(self, which):

    if which == 'testrun':
        folder = self.testrun
    else:
        folder = self.baseline

    data = read_xdi(join(self.path, 'NiO.chik'), _larch=self._larch)
    if hasattr(data, 'wavenumber'):
        data.k = data.wavenumber

    gds = Group(amp    = Parameter(1,      vary=True, _larch=self._larch),
                enot   = Parameter(0.01,   vary=True, _larch=self._larch),
                alpha  = Parameter(0.0001, vary=True, _larch=self._larch),
                sso    = Parameter(0.003,  vary=True, _larch=self._larch),
                ssni   = Parameter(0.003,  vary=True, _larch=self._larch),
                sso2   = Parameter(0.003,  vary=True, _larch=self._larch),
                #sso3   = Parameter(0.003,  vary=True, _larch=self._larch),
                ssni2  = Parameter(0.003,  vary=True, _larch=self._larch),
                #ssni3  = Parameter(0.003,  vary=True, _larch=self._larch),
                #ssni4  = Parameter(0.003,  vary=True, _larch=self._larch),
                _larch=self._larch  )

    paths = list() 
    paths.append(feffpath(realpath(join(folder, "feff0001.dat")), # 1st shell O SS
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'sso',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0002.dat")), # 2nd shell Ni SS
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'ssni',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0003.dat")), # O-O triangle
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = '1.5*sso',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0004.dat")), # O-Ni triangle
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'sso+ssni',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0005.dat")), # 3rd shell O SS
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'sso2',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0006.dat")), # 4th shell Ni SS
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'ssni2',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0007.dat")), # O-O non-forward linear
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'sso*2',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0008.dat")), # O-Ni forward scattering
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'ssni2',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0009.dat")), # O-O forward through absorber
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'sso*2',
                          deltar = 'alpha*reff', _larch=self._larch))
    paths.append(feffpath(realpath(join(folder, "feff0010.dat")), # O-Ni-O double forward
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'ssni2',
                          deltar = 'alpha*reff', _larch=self._larch))


    trans = feffit_transform(kmin=3, kmax=15.938, kw=(2,1,3), dk=1, window='hanning', rmin=1.5, rmax=4.2, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = 0.6*max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8, win=2,
              xlabel=r'$R \rm\,(\AA)$', label='data',
              ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
              title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', win=2, _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', win=2, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', win=2, _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    return fit
Esempio n. 12
0
def do_fit(self, which):

    if which == 'testrun':
        folder = self.testrun
    else:
        folder = self.baseline

    data = read_xdi(join(self.path, 'UO2.chik'), _larch=self._larch)

    gds = Group(amp=Parameter(1, vary=True, _larch=self._larch),
                enot=Parameter(0.01, vary=True, _larch=self._larch),
                sso=Parameter(0.003, vary=True, _larch=self._larch),
                ssu=Parameter(0.003, vary=True, _larch=self._larch),
                sso2=Parameter(0.003, vary=True, _larch=self._larch),
                dro=Parameter(0.0001, vary=True, _larch=self._larch),
                dru=Parameter(0.0001, vary=True, _larch=self._larch),
                dro2=Parameter(0.0001, vary=True, _larch=self._larch),
                nu=Parameter(12, vary=True, _larch=self._larch),
                no2=Parameter(expr='2*nu', _larch=self._larch),
                _larch=self._larch)

    paths = list()
    paths.append(
        feffpath(
            realpath(join(folder, "feff0001.dat")),  # 1st shell O SS
            s02='amp',
            e0='enot',
            sigma2='sso',
            deltar='dro',
            _larch=self._larch))
    # paths.append(feffpath(realpath(join(folder, "feff0002.dat")), # triangle in first shell
    #                       s02    = 'amp',
    #                       e0     = 'enot',
    #                       sigma2 = 'sso*1.5',
    #                       deltar = 'dro*(1+sqrt(2))/2', _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0003.dat")),  # 2nd shell U SS
            degen=1,
            s02='amp*nu',
            e0='enot',
            sigma2='ssu',
            deltar='dru',
            _larch=self._larch))
    # paths.append(feffpath(realpath(join(folder, "feff0004.dat")), # 1st shell, longer triangle
    #                       s02    = 'amp',
    #                       e0     = 'enot',
    #                       sigma2 = '2*sso',
    #                       deltar = '2*dro', _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0006.dat")),  # 3rd shell O SS
            degen=1,
            s02='amp*no2',
            #s02    = 'amp*nu*2',
            e0='enot',
            sigma2='sso2',
            deltar='dro2',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0007.dat")
                     ),  # 1st shell, non-forward linear through absorber
            s02='amp',
            e0='enot',
            sigma2='sso2',
            deltar='dro2',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(
                folder, "feff0008.dat")),  # 1st shell forward through absorber
            s02='amp',
            e0='enot',
            sigma2='2*sso',
            deltar='2*dro',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0009.dat")),  # rattle in 1st shell
            s02='amp',
            e0='enot',
            sigma2='2*sso',
            deltar='2*dro',
            _larch=self._larch))

    trans = feffit_transform(kmin=3,
                             kmax=11,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1.25,
                             rmax=4.3,
                             _larch=self._larch)
    dset = feffit_dataset(data=data,
                          pathlist=paths,
                          transform=trans,
                          _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,
                 dset.data.chir_mag + offset,
                 xmax=8,
                 win=2,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_mag + offset,
              label='fit',
              win=2,
              _larch=self._larch)
        _plot(dset.data.r,
              dset.data.chir_re,
              label='data',
              win=2,
              _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_re,
              label='fit',
              win=2,
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    return fit
Esempio n. 13
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    firstshell = False  # no 1st shell fit for this material

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'uranyl.chik'), _larch=self._larch)

    gds = Group(
        amp=Parameter(1, vary=True, _larch=self._larch),
        enot=Parameter(1e-7, vary=True, _larch=self._larch),
        #enot   = Parameter(1e-7,   vary=True,  _larch=self._larch, min=0, max=13),
        enoteq=Parameter(expr='enot', _larch=self._larch),
        deloax=Parameter(1e-7, vary=True, _larch=self._larch),
        deloeq=Parameter(1e-7, vary=True, _larch=self._larch),
        sigoax=Parameter(0.003, vary=True, _larch=self._larch),
        sigoeq=Parameter(0.003, vary=True, _larch=self._larch),
        nax=Parameter(2.0, vary=False, _larch=self._larch),
        neq=Parameter(6, vary=False, _larch=self._larch),  #, min=0, max=12),
        _larch=self._larch)

    paths = list()
    paths.append(
        feffpath(
            realpath(join(folder, "feff0001.dat")),  # axial oxygen
            degen=1,
            s02='amp*nax',
            e0='enot',
            sigma2='sigoax',
            deltar='deloax',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0003.dat")),  # equatorial oxygen
            degen=1,
            s02='amp*neq',
            e0='enoteq',
            sigma2='sigoeq',
            deltar='deloeq',
            _larch=self._larch))

    paths.append(
        feffpath(
            realpath(join(folder, "feff0008.dat")),  # axial oxygen, rattle
            degen=1,
            s02='amp*nax',
            e0='enot',
            sigma2='sigoax*4',
            deltar='deloax*2',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder,
                          "feff0009.dat")),  # axial oxygen, non-forward
            degen=1,
            s02='amp*nax',
            e0='enot',
            sigma2='sigoax',
            deltar='deloax*2',
            _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0010.dat")),  # axial oxygen, forward
            degen=1,
            s02='amp*nax',
            e0='enot',
            sigma2='sigoax',
            deltar='deloax*2',
            _larch=self._larch))

    trans = feffit_transform(kmin=3,
                             kmax=11,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1.0,
                             rmax=3.2,
                             _larch=self._larch)
    dset = feffit_dataset(data=data,
                          pathlist=paths,
                          transform=trans,
                          _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,
                 dset.data.chir_mag + offset,
                 xmax=8,
                 win=2,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_mag + offset,
              label='fit',
              win=2,
              _larch=self._larch)
        _plot(dset.data.r,
              dset.data.chir_re,
              label='data',
              win=2,
              _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_re,
              label='fit',
              win=2,
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells = '_1st'

    write_ascii(join(self.folder, fittest, "fit_" + which + ".k"),
                dset.data.k,
                dset.data.chi,
                dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_" + which + ".r"),
                dset.data.r,
                dset.data.chir_mag,
                dset.model.chir_mag,
                dset.data.chir_re,
                dset.model.chir_re,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_' + which + '.gp'), 'w') as inp:
        inp.write(
            renderer.render_path(
                'plot.mustache',  # gnuplot mustache file
                {
                    'material': 'uranyl',
                    'model': which,
                    'fittest': fittest,
                    'shells': shells,
                    'kmin': 3,
                    'kmax': 11,
                    'rmin': 1.0,
                    'rmax': 3.2,
                    'offset': 1,
                }))

    return fit
Esempio n. 14
0
    def compare(self, nnnn=1, part='feff', use_wrapper=False, _larch=None):
        """
        compare a feffNNNN.dat file from the testrun with the same file from the baseline calculation

            group.compare(N, part, use_wrapper)

        where N is the path index, part is one of 
            feff    :      test the magnitude AND phase of F_eff (default)
            amp     :      test the total amplitude of the path
            phase   :      test the total phase of the path
            lambda  :      test the mean free path
            caps    :      test the central atom phase shift
            redfact :      test the reduction factor
            rep     :      test the real part of the complex wavenumber

        and use_wrapper is True if the test is to use the python interface to the feffpath library
        or False if the test is to use the monolithic feff.

        """
        if self._larch is None:
            raise Warning("cannot do path comparison -- larch broken?")
            
        if not self.feffran:
            print colored("You have not yet run the test Feff calculation", 'magenta', attrs=['bold'])
            return
            
        if not self.available(nnnn):
            print colored("Path %d was not saved from the test Feff calculation" % nnnn, 'magenta', attrs=['bold'])
            return
            
        how='monolithic'
        if use_wrapper: how = 'wrapper'
        nnnndat = "feff%4.4d.dat" % nnnn
        
        blpath = feffpath(join(self.baseline, nnnndat))
        if use_wrapper and self.wrapper_available: # make the f3ffNNNN.dat file on the fly
            self.sp.phpad=join(self.testrun, 'phase.pad')
            self.sp.nnnn=True
            self.sp.index=nnnn
            self.sp.verbose=self.verbose
            self.snarf_geometry(nnnn)
            here = getcwd()
            chdir(self.testrun)
            self.sp.make()
            chdir(here)
            n3nndat = "f3ff%4.4d.dat" % nnnn
            trpath = feffpath(join(self.testrun,  n3nndat))
        else:                   # the feffNNNN.dat file was made by the monolithic feff run
            trpath = feffpath(join(self.testrun,  nnnndat))
        
        if part=='feff':
            baseline_1 = getattr(blpath._feffdat, 'mag_feff') # + np.random.uniform(0,1,size=1)
            testrun_1  = getattr(trpath._feffdat, 'mag_feff')
            baseline_2 = getattr(blpath._feffdat, 'pha_feff') # + np.random.uniform(0,1,size=1)
            testrun_2  = getattr(trpath._feffdat, 'pha_feff')
            ylabel     = 'magnitude and phase'
            label      = 'magnitude' 
        elif part=='amp':
            baseline_1 = getattr(blpath._feffdat, 'amp')
            testrun_1  = getattr(trpath._feffdat, 'amp')
            ylabel     = 'total amplitude'
            label      = 'amplitude' 
        elif part=='phase':
            baseline_1 = getattr(blpath._feffdat, 'pha')
            testrun_1  = getattr(trpath._feffdat, 'pha')
            ylabel     = 'total phase shift'
            label      = 'phase' 
        elif part=='lambda':
            baseline_1 = getattr(blpath._feffdat, 'lam')
            testrun_1  = getattr(trpath._feffdat, 'lam')
            ylabel     = 'mean free path'
            label      = 'MFP' 
        elif part=='caps':
            baseline_1 = getattr(blpath._feffdat, 'real_phc')
            testrun_1  = getattr(trpath._feffdat, 'real_phc')
            ylabel     = 'central atom phase shift'
            label      = 'CAPS' 
        elif part=='redfact':
            baseline_1 = getattr(blpath._feffdat, 'red_fact')
            testrun_1  = getattr(trpath._feffdat, 'red_fact')
            ylabel     = 'reduction factor'
            label      = 'reduction factor'
        elif part=='rep':
            baseline_1 = getattr(blpath._feffdat, 'rep')
            testrun_1  = getattr(trpath._feffdat, 'rep')
            ylabel     = 'real part of p(k)'
            label      = 'Re[p(k)]'
        else:
            if self.verbose: print colored("Unknown choice of parts \"%s\"\nmust be one of (feff|amp|phase|lambda|caps|redfact|rep)\nusing feff" % part,
                                           'magenta', attrs=['bold'])
            part       = 'feff'
            baseline_1 = getattr(blpath._feffdat, 'mag_feff')
            testrun_1  = getattr(trpath._feffdat, 'mag_feff')
            baseline_2 = getattr(blpath._feffdat, 'pha_feff')
            testrun_2  = getattr(trpath._feffdat, 'pha_feff')
            ylabel     = 'magnitude and phase'
            label      = 'magnitude' 
            
            
        scf="without SCF"
        if self.doscf: scf="with SCF"
        
        self.rfactor_2 = 0
        self.rfactor = sum((baseline_1 - testrun_1)**2) / sum(baseline_1**2)
        if self.verbose: 
            print colored("\nComparing %s of %s (%s) (%s)" % (label, nnnndat, scf, how), 'yellow', attrs=['bold'])
            self.geometry(blpath)
            
        if self.verbose: 
            color = 'green'  if self.rfactor < self.epsilon else 'magenta'
            print label + " R-factor = " + colored("%.3f" % self.rfactor, color, attrs=['bold'])
        if part=='feff':
            self.rfactor_2 = sum((testrun_2 - testrun_2)**2) / sum(baseline_2**2)
            if self.verbose: 
                color = 'green'  if self.rfactor_2 < self.epsilon else 'magenta'
                print "phase R-factor = " + colored("%.3f" % self.rfactor_2, color, attrs=['bold'])
        if self.verbose: print ""
        
        if self.doplot:
            _newplot(blpath._feffdat.k, baseline_1, _larch=self._larch, label=label+' of baseline',
                     xlabel='wavenumber $\AA^{-1}$', ylabel=ylabel, title=nnnndat, show_legend=True, legend_loc='best')
            _plot   (trpath._feffdat.k, testrun_1,  _larch=self._larch, label=label+' of test run')
            if part=='feff':
                _plot(blpath._feffdat.k, np.gradient(baseline_2), _larch=self._larch, label='grad(phase of baseline)')
                _plot(trpath._feffdat.k, np.gradient(testrun_2),  _larch=self._larch, label='grad(phase of test run)')
                
        if use_wrapper and self.wrapper_available:
            unlink(join(self.testrun,  n3nndat))
            self.sp.clear()

        if part=='feff':
            return self.rfactor < self.epsilon and self.rfactor_2 < self.epsilon
        else:
            return self.rfactor < self.epsilon
Esempio n. 15
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    dmt = read_xdi(join(self.path, 'dmt.chik'), _larch=self._larch)
    mmt = read_xdi(join(self.path, 'mmt.chik'), _larch=self._larch)

    gds = Group(amp=Parameter(0.9, vary=True, _larch=self._larch),
                enot=Parameter(1e-7, vary=True, _larch=self._larch),
                delr_c=Parameter(1e-7, vary=True, _larch=self._larch),
                ss_c=Parameter(0.003, vary=True, _larch=self._larch),
                delr_cl=Parameter(1e-7, vary=True, _larch=self._larch),
                ss_cl=Parameter(0.003, vary=True, _larch=self._larch),
                _larch=self._larch)

    paths_dmt = list()
    paths_dmt.append(
        feffpath(realpath(join(folder, "feff0001.dat")),
                 degen=2,
                 s02='amp',
                 e0='enot',
                 sigma2='ss_c',
                 deltar='delr_c',
                 _larch=self._larch))
    paths_dmt.append(
        feffpath(realpath(join(folder, "feff0002.dat")),
                 degen=2,
                 s02='amp',
                 e0='enot',
                 sigma2='ss_cl',
                 deltar='delr_cl',
                 _larch=self._larch))
    paths_mmt = list()
    paths_mmt.append(
        feffpath(realpath(join(folder, "feff0001.dat")),
                 degen=1,
                 s02='amp',
                 e0='enot',
                 sigma2='ss_c',
                 deltar='delr_c',
                 _larch=self._larch))
    paths_mmt.append(
        feffpath(realpath(join(folder, "feff0002.dat")),
                 degen=3,
                 s02='amp',
                 e0='enot',
                 sigma2='ss_cl',
                 deltar='delr_cl',
                 _larch=self._larch))

    trans = feffit_transform(kmin=3,
                             kmax=13,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1.25,
                             rmax=3,
                             _larch=self._larch)
    dset = [
        feffit_dataset(data=dmt,
                       pathlist=paths_dmt,
                       transform=trans,
                       _larch=self._larch),
        feffit_dataset(data=mmt,
                       pathlist=paths_mmt,
                       transform=trans,
                       _larch=self._larch)
    ]
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset[0].data.chir_mag) / 2
        _newplot(dset[0].data.r,
                 dset[0].data.chir_mag + offset,
                 xmax=5,
                 win=1,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='dimethyltin',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset[0].model.r,
              dset[0].model.chir_mag + offset,
              label='fit',
              win=1,
              _larch=self._larch)
        _plot(dset[0].data.r,
              dset[0].data.chir_re,
              label='dimethyltin',
              win=1,
              _larch=self._larch)
        _plot(dset[0].model.r,
              dset[0].model.chir_re,
              label='fit',
              win=1,
              _larch=self._larch)

        _plot(dset[1].data.r,
              dset[1].data.chir_mag + 7 * offset,
              label='monomethyltin',
              win=1,
              _larch=self._larch)
        _plot(dset[1].model.r,
              dset[1].model.chir_mag + 7 * offset,
              label='fit',
              win=1,
              _larch=self._larch)
        _plot(dset[1].data.r,
              dset[1].data.chir_re + 6 * offset,
              label='monomethyltin',
              win=1,
              _larch=self._larch)
        _plot(dset[1].model.r,
              dset[1].model.chir_re + 6 * offset,
              label='fit',
              win=1,
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells = '_1st'

    write_ascii(join(self.folder, fittest, "fit_" + which + ".k"),
                dset.data[0].k,
                dset.data[0].chi,
                dset.model[0].chi,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_" + which + ".r"),
                dset.data[0].r,
                dset.data[0].chir_mag,
                dset.model[0].chir_mag,
                dset.data[0].chir_re,
                dset.model[0].chir_re,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_' + which + '.gp'), 'w') as inp:
        inp.write(
            renderer.render_path(
                'plot.mustache',  # gnuplot mustache file
                {
                    'material': 'methyltin',
                    'model': which,
                    'fittest': fittest,
                    'shells': shells,
                    'kmin': 3,
                    'kmax': 13,
                    'rmin': 1.25,
                    'rmax': 3,
                    'offset': 1,
                }))

    return fit
Esempio n. 16
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'Copper.chik'), _larch=self._larch)

    gds = Group(amp    = Parameter(1,     vary=True,  _larch=self._larch),
                enot   = Parameter(1e-7,  vary=True,  _larch=self._larch),
                ss1    = Parameter(0.003, vary=True,  _larch=self._larch), _larch=self._larch  )

    if firstshell:
        gds.delr   = Parameter(1e-7,   vary=True, _larch=self._larch)
        dr1param   = 'delr'
    else:
        gds.thetad = Parameter(500,   vary=True,  _larch=self._larch)
        gds.temp   = Parameter(10,    vary=False, _larch=self._larch)
        gds.alpha  = Parameter(1e-7,  vary=True,  _larch=self._larch)
        dr1param   = 'alpha*reff'

    imax = 16
    if firstshell: imax = 2
    paths = list()
    for index in range(1,imax):
        nnnn = realpath(join(folder, "feff%4.4d.dat" % index))
        if not exists(nnnn):
            continue
        #end if
        if index > 1:
            sigsqr = 'sigma2_debye(temp, thetad)' 
        else:
            sigsqr = 'ss1'
        #end if
        paths.append(feffpath(nnnn,
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = sigsqr,
                              deltar = dr1param, _larch=self._larch))
    #end for

    rx  = 5.0
    if firstshell: rx  = 2.8

    trans = feffit_transform(kmin=3, kmax=15, kw=(2,1,3), dk=1, window='hanning', rmin=1, rmax=rx, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8,
              xlabel=r'$R \rm\,(\AA)$', label='data',
              ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
              title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells='_1st'

    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".k"), dset.data.k, dset.data.chi, dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
                dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_'+which+shells+'.gp'), 'w') as inp:
        inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
                                        {'material': 'Copper',
                                         'model': which,
                                         'fittest': fittest,
                                         'shells': shells,
                                         'kmin': 3,
                                         'kmax': 15,
                                         'rmin': 1,
                                         'rmax': rx,
                                         'offset': 2,
                                     } ))

    return fit
Esempio n. 17
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    dmt = read_xdi(join(self.path, 'dmt.chik'), _larch=self._larch)
    mmt = read_xdi(join(self.path, 'mmt.chik'), _larch=self._larch)

    gds = Group(amp     = Parameter(0.9,       vary=True,  _larch=self._larch),
                enot    = Parameter(1e-7,      vary=True,  _larch=self._larch),
                delr_c  = Parameter(1e-7,      vary=True,  _larch=self._larch),
                ss_c    = Parameter(0.003,     vary=True,  _larch=self._larch),
                delr_cl = Parameter(1e-7,      vary=True,  _larch=self._larch),
                ss_cl   = Parameter(0.003,     vary=True,  _larch=self._larch),
                _larch=self._larch  )

    paths_dmt = list()
    paths_dmt.append(feffpath(realpath(join(folder, "feff0001.dat")),
                              degen  = 2,
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ss_c',
                              deltar = 'delr_c', _larch=self._larch))
    paths_dmt.append(feffpath(realpath(join(folder, "feff0002.dat")),
                              degen  = 2,
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ss_cl',
                              deltar = 'delr_cl', _larch=self._larch))
    paths_mmt = list()
    paths_mmt.append(feffpath(realpath(join(folder, "feff0001.dat")),
                              degen  = 1,
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ss_c',
                              deltar = 'delr_c', _larch=self._larch))
    paths_mmt.append(feffpath(realpath(join(folder, "feff0002.dat")),
                              degen  = 3,
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ss_cl',
                              deltar = 'delr_cl', _larch=self._larch))


    trans = feffit_transform(kmin=3, kmax=13, kw=(2,1,3), dk=1, window='hanning', rmin=1.25, rmax=3, _larch=self._larch)
    dset  = [feffit_dataset(data=dmt, pathlist=paths_dmt, transform=trans, _larch=self._larch),
             feffit_dataset(data=mmt, pathlist=paths_mmt, transform=trans, _larch=self._larch)]
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset[0].data.chir_mag)/2
        _newplot(dset[0].data.r,  dset[0].data.chir_mag+offset, xmax=5, win=1,
                 xlabel=r'$R \rm\,(\AA)$', label='dimethyltin',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset[0].model.r, dset[0].model.chir_mag+offset,   label='fit',  win=1, _larch=self._larch)
        _plot(dset[0].data.r,  dset[0].data.chir_re,            label='dimethyltin', win=1, _larch=self._larch)
        _plot(dset[0].model.r, dset[0].model.chir_re,           label='fit',  win=1, _larch=self._larch)

        _plot(dset[1].data.r,  dset[1].data.chir_mag+7*offset,  label='monomethyltin', win=1, _larch=self._larch)
        _plot(dset[1].model.r, dset[1].model.chir_mag+7*offset, label='fit',  win=1, _larch=self._larch)
        _plot(dset[1].data.r,  dset[1].data.chir_re+6*offset,   label='monomethyltin', win=1, _larch=self._larch)
        _plot(dset[1].model.r, dset[1].model.chir_re+6*offset,  label='fit',  win=1, _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells='_1st'

    write_ascii(join(self.folder, fittest, "fit_"+which+".k"), dset.data[0].k, dset.data[0].chi, dset.model[0].chi,
                labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_"+which+".r"), dset.data[0].r, dset.data[0].chir_mag, dset.model[0].chir_mag,
                dset.data[0].chir_re, dset.model[0].chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_'+which+'.gp'), 'w') as inp:
        inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
                                        {'material': 'methyltin',
                                         'model': which,
                                         'fittest': fittest,
                                         'shells': shells,
                                         'kmin': 3,
                                         'kmax': 13,
                                         'rmin': 1.25,
                                         'rmax': 3,
                                         'offset': 1,
                                     } ))

    return fit
Esempio n. 18
0
def do_fit(self, which):

    if which == "testrun":
        folder = self.testrun
    else:
        folder = self.baseline

    data = read_xdi(join(self.path, "UO2.chik"), _larch=self._larch)

    gds = Group(
        amp=Parameter(1, vary=True, _larch=self._larch),
        enot=Parameter(0.01, vary=True, _larch=self._larch),
        sso=Parameter(0.003, vary=True, _larch=self._larch),
        ssu=Parameter(0.003, vary=True, _larch=self._larch),
        sso2=Parameter(0.003, vary=True, _larch=self._larch),
        dro=Parameter(0.0001, vary=True, _larch=self._larch),
        dru=Parameter(0.0001, vary=True, _larch=self._larch),
        dro2=Parameter(0.0001, vary=True, _larch=self._larch),
        nu=Parameter(12, vary=True, _larch=self._larch),
        no2=Parameter(expr="2*nu", _larch=self._larch),
        _larch=self._larch,
    )

    paths = list()
    paths.append(
        feffpath(
            realpath(join(folder, "feff0001.dat")),  # 1st shell O SS
            s02="amp",
            e0="enot",
            sigma2="sso",
            deltar="dro",
            _larch=self._larch,
        )
    )
    # paths.append(feffpath(realpath(join(folder, "feff0002.dat")), # triangle in first shell
    #                       s02    = 'amp',
    #                       e0     = 'enot',
    #                       sigma2 = 'sso*1.5',
    #                       deltar = 'dro*(1+sqrt(2))/2', _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0003.dat")),  # 2nd shell U SS
            degen=1,
            s02="amp*nu",
            e0="enot",
            sigma2="ssu",
            deltar="dru",
            _larch=self._larch,
        )
    )
    # paths.append(feffpath(realpath(join(folder, "feff0004.dat")), # 1st shell, longer triangle
    #                       s02    = 'amp',
    #                       e0     = 'enot',
    #                       sigma2 = '2*sso',
    #                       deltar = '2*dro', _larch=self._larch))
    paths.append(
        feffpath(
            realpath(join(folder, "feff0006.dat")),  # 3rd shell O SS
            degen=1,
            s02="amp*no2",
            # s02    = 'amp*nu*2',
            e0="enot",
            sigma2="sso2",
            deltar="dro2",
            _larch=self._larch,
        )
    )
    paths.append(
        feffpath(
            realpath(join(folder, "feff0007.dat")),  # 1st shell, non-forward linear through absorber
            s02="amp",
            e0="enot",
            sigma2="sso2",
            deltar="dro2",
            _larch=self._larch,
        )
    )
    paths.append(
        feffpath(
            realpath(join(folder, "feff0008.dat")),  # 1st shell forward through absorber
            s02="amp",
            e0="enot",
            sigma2="2*sso",
            deltar="2*dro",
            _larch=self._larch,
        )
    )
    paths.append(
        feffpath(
            realpath(join(folder, "feff0009.dat")),  # rattle in 1st shell
            s02="amp",
            e0="enot",
            sigma2="2*sso",
            deltar="2*dro",
            _larch=self._larch,
        )
    )

    trans = feffit_transform(
        kmin=3, kmax=11, kw=(2, 1, 3), dk=1, window="hanning", rmin=1.25, rmax=4.3, _larch=self._larch
    )
    dset = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(
            dset.data.r,
            dset.data.chir_mag + offset,
            xmax=8,
            win=2,
            xlabel=r"$R \rm\,(\AA)$",
            label="data",
            ylabel=r"$|\chi(R)| \rm\,(\AA^{-3})$",
            title="Fit to " + self.folder,
            show_legend=True,
            _larch=self._larch,
        )
        _plot(dset.model.r, dset.model.chir_mag + offset, label="fit", win=2, _larch=self._larch)
        _plot(dset.data.r, dset.data.chir_re, label="data", win=2, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label="fit", win=2, _larch=self._larch)
    # end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    # end if

    return fit
Esempio n. 19
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'UO2.chik'), _larch=self._larch)

    gds = Group(amp    = Parameter(1,      vary=True, _larch=self._larch),
                enot   = Parameter(1e-7,   vary=True, _larch=self._larch),
                sso    = Parameter(0.003,  vary=True, _larch=self._larch),
                dro    = Parameter(1e-7,   vary=True, _larch=self._larch), _larch=self._larch  )

    if not firstshell:
        gds.ssu    = Parameter(0.003,  vary=True, _larch=self._larch)
        gds.sso2   = Parameter(0.003,  vary=True, _larch=self._larch)
        gds.dru    = Parameter(1e-7,   vary=True, _larch=self._larch)
        gds.dro2   = Parameter(1e-7,   vary=True, _larch=self._larch)
        gds.nu     = Parameter(12,     vary=True, _larch=self._larch)
        gds.no2    = Parameter(expr='2*nu',       _larch=self._larch)

    paths = list() 
    paths.append(feffpath(realpath(join(folder, "feff0001.dat")), # 1st shell O SS
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'sso',
                          deltar = 'dro', _larch=self._larch))

    if not firstshell:
        # paths.append(feffpath(realpath(join(folder, "feff0002.dat")), # triangle in first shell
        #                       s02    = 'amp',
        #                       e0     = 'enot',
        #                       sigma2 = 'sso*(1+sqrt(3))**2',
        #                       deltar = 'dro*(1+sqrt(3))/2', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0003.dat")), # 2nd shell U SS
                              degen  = 1,
                              s02    = 'amp*nu',
                              e0     = 'enot',
                              sigma2 = 'ssu',
                              deltar = 'dru', _larch=self._larch))
        # paths.append(feffpath(realpath(join(folder, "feff0004.dat")), # 1st shell, longer triangle
        #                       s02    = 'amp',
        #                       e0     = 'enot',
        #                       sigma2 = 'sso*(1+sqrt(2/3))**2',
        #                       deltar = '(1+sqrt(2/3))*dro', _larch=self._larch))
        # paths.append(feffpath(realpath(join(folder, "feff0005.dat")), # 1st shell, longer U-O-U triangle
        #                       degen  = 1,
        #                       s02    = 'amp*nu',
        #                       e0     = 'enot',
        #                       sigma2 = 'sso*ssu/2',
        #                       deltar = '(1+sqrt(2/3))*dro', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0006.dat")), # 3rd shell O SS
                              degen  = 1,
                              s02    = 'amp*no2',
                              e0     = 'enot',
                              sigma2 = 'sso2',
                              deltar = 'dro2', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0007.dat")), # 1st shell, non-forward linear through absorber
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = '2*sso2',
                              deltar = '2*dro2', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0008.dat")), # 1st shell forward through absorber
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = '2*sso',
                              deltar = '2*dro', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0009.dat")), # rattle in 1st shell
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = '2*sso',
                              deltar = '2*dro', _larch=self._larch))

    rx  = 4.3
    if firstshell: rx  = 2.5

    trans = feffit_transform(kmin=3, kmax=11, kw=(2,1,3), dk=1, window='hanning', rmin=1.25, rmax=rx, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8,
              xlabel=r'$R \rm\,(\AA)$', label='data',
              ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
              title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells='_1st'

    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".k"), dset.data.k, dset.data.chi, dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
                dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_'+which+shells+'.gp'), 'w') as inp:
        inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
                                        {'material': 'UO2',
                                         'model': which,
                                         'fittest': fittest,
                                         'shells': shells,
                                         'kmin': 3,
                                         'kmax': 11,
                                         'rmin': 1.25,
                                         'rmax': rx,
                                         'offset': 0.75,
                                     } ))

    return fit
Esempio n. 20
0
    def compare(self, nnnn=1, part='feff', use_wrapper=False, _larch=None):
        """
        Compare a feffNNNN.dat file from the testrun with the same file
        from the baseline calculation

            group.compare(N, part, use_wrapper)

        where N is the path index, part is one of 
            feff    :      test the magnitude AND phase of F_eff (default)
            amp     :      test the total amplitude of the path
            phase   :      test the total phase of the path
            lambda  :      test the mean free path
            caps    :      test the central atom phase shift
            redfact :      test the reduction factor
            rep     :      test the real part of the complex wavenumber

        and use_wrapper is True if the test is to use the python interface to
        the feffpath library or False if the test is to use the feffrunner and
        the Feff executables.  (Currently, only feffrunner is working...)

        Sets self.rfactor (and self.rfactor_2).

        """
        if self._larch is None:
            raise Warning("cannot do path comparison -- larch broken?")

        if not self.feffran:
            print colored("You have not yet run the test Feff calculation",
                          'magenta',
                          attrs=['bold'])
            return

        if not self.available(nnnn):
            print colored(
                "Path %d was not saved from the test Feff calculation" % nnnn,
                'magenta',
                attrs=['bold'])
            return

        how = 'wrapper' if use_wrapper else 'executables'
        nnnndat = "feff%4.4d.dat" % nnnn

        blpath = feffpath(join(self.baseline, nnnndat))
        if use_wrapper and self.wrapper_available:  # make the f3ffNNNN.dat file on the fly
            self.sp.phpad = join(self.testrun, 'phase.pad')
            self.sp.nnnn = True
            self.sp.index = nnnn
            self.sp.verbose = self.verbose
            self.__snarf_geometry(nnnn)
            owd = getcwd()
            try:
                chdir(self.testrun)
                self.sp.make()
            finally:
                chdir(owd)
            n3nndat = "f3ff%4.4d.dat" % nnnn
            trpath = feffpath(join(self.testrun, n3nndat))
        else:  # the feffNNNN.dat file was made by the monolithic feff run
            trpath = feffpath(join(self.testrun, nnnndat))

        if part == 'feff':
            baseline_1 = getattr(blpath._feffdat,
                                 'mag_feff')  # + np.random.uniform(0,1,size=1)
            testrun_1 = getattr(trpath._feffdat, 'mag_feff')
            baseline_2 = getattr(blpath._feffdat,
                                 'pha_feff')  # + np.random.uniform(0,1,size=1)
            testrun_2 = getattr(trpath._feffdat, 'pha_feff')
            ylabel = 'magnitude and phase'
            label = 'magnitude'
        elif part == 'amp':
            baseline_1 = getattr(blpath._feffdat, 'amp')
            testrun_1 = getattr(trpath._feffdat, 'amp')
            ylabel = 'total amplitude'
            label = 'amplitude'
        elif part == 'phase':
            baseline_1 = getattr(blpath._feffdat, 'pha')
            testrun_1 = getattr(trpath._feffdat, 'pha')
            ylabel = 'total phase shift'
            label = 'phase'
        elif part == 'lambda':
            baseline_1 = getattr(blpath._feffdat, 'lam')
            testrun_1 = getattr(trpath._feffdat, 'lam')
            ylabel = 'mean free path'
            label = 'MFP'
        elif part == 'caps':
            baseline_1 = getattr(blpath._feffdat, 'real_phc')
            testrun_1 = getattr(trpath._feffdat, 'real_phc')
            ylabel = 'central atom phase shift'
            label = 'CAPS'
        elif part == 'redfact':
            baseline_1 = getattr(blpath._feffdat, 'red_fact')
            testrun_1 = getattr(trpath._feffdat, 'red_fact')
            ylabel = 'reduction factor'
            label = 'reduction factor'
        elif part == 'rep':
            baseline_1 = getattr(blpath._feffdat, 'rep')
            testrun_1 = getattr(trpath._feffdat, 'rep')
            ylabel = 'real part of p(k)'
            label = 'Re[p(k)]'
        else:
            if self.verbose:
                print colored(
                    "Unknown choice of parts \"%s\"\nmust be one of (feff|amp|phase|lambda|caps|redfact|rep)\nusing feff"
                    % part,
                    'magenta',
                    attrs=['bold'])
            part = 'feff'
            baseline_1 = getattr(blpath._feffdat, 'mag_feff')
            testrun_1 = getattr(trpath._feffdat, 'mag_feff')
            baseline_2 = getattr(blpath._feffdat, 'pha_feff')
            testrun_2 = getattr(trpath._feffdat, 'pha_feff')
            ylabel = 'magnitude and phase'
            label = 'magnitude'

        self.rfactor_2 = 0
        self.rfactor = sum((baseline_1 - testrun_1)**2) / sum(baseline_1**2)
        if self.verbose:
            print colored("\nComparing %s of %s (%s) (using %s)" %
                          (label, nnnndat,
                           "with SCF" if self.doscf else "without SCF", how),
                          'yellow',
                          attrs=['bold'])
            self.print_geometry(blpath)

        if self.verbose:
            print label + " R-factor = " + colored(
                "%.3f" % self.rfactor,
                'green' if self.rfactor < self.epsilon else 'magenta',
                attrs=['bold'])
        if part == 'feff':
            self.rfactor_2 = sum(
                (testrun_2 - testrun_2)**2) / sum(baseline_2**2)
            if self.verbose:
                color = 'green' if self.rfactor_2 < self.epsilon else 'magenta'
                print "phase R-factor = " + colored(
                    "%.3f" % self.rfactor_2, color, attrs=['bold'])
        if self.verbose: print ""

        if self.doplot:
            _newplot(blpath._feffdat.k,
                     baseline_1,
                     _larch=self._larch,
                     label=label + ' of baseline',
                     xlabel='wavenumber $\AA^{-1}$',
                     ylabel=ylabel,
                     title=nnnndat,
                     show_legend=True,
                     legend_loc='best')
            _plot(trpath._feffdat.k,
                  testrun_1,
                  _larch=self._larch,
                  label=label + ' of test run')
            if part == 'feff':
                _plot(blpath._feffdat.k,
                      np.gradient(baseline_2),
                      _larch=self._larch,
                      label='grad(phase of baseline)')
                _plot(trpath._feffdat.k,
                      np.gradient(testrun_2),
                      _larch=self._larch,
                      label='grad(phase of test run)')

        if use_wrapper and self.wrapper_available:
            unlink(join(self.testrun, n3nndat))
            self.sp.clear()

        if part == 'feff':
            return self.rfactor < self.epsilon and self.rfactor_2 < self.epsilon
        else:
            return self.rfactor < self.epsilon
Esempio n. 21
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'bromoadamantane.chik'), _larch=self._larch)

    gds = Group(amp     = Parameter(0.9,       vary=True,  _larch=self._larch),
                enot    = Parameter(4.01,      vary=True,  _larch=self._larch),
                delr    = Parameter(1e-7  ,    vary=True,  units='AA',   decimals=3, _larch=self._larch),
                ss      = Parameter(0.003,     vary=True,  units='AA^2', _larch=self._larch),
                c3      = Parameter(1e-7,      vary=False, _larch=self._larch),
                _larch=self._larch  )
    if not firstshell:
        gds.brc     = Parameter(expr = '1.9521+delr',  units='AA',  _larch=self._larch)
        #gds.phir    = Parameter(109.29960 * 3.141592653589793 / 180,   vary=False, _larch=self._larch)
        gds.cc      = Parameter(1.53780,   vary=False, _larch=self._larch)
        #gds.tanbeta = Parameter(expr = '(brc+cc)*tan(phir/2) / (brc-cc)', _larch=self._larch)
        #gds.beta    = Parameter(expr = 'atan(tanbeta)', _larch=self._larch)
        #gds.brc2    = Parameter(expr = '(brc-cc)*cos(phir/2)/cos(beta)',  units='AA', _larch=self._larch)
        gds.drh     = Parameter(0.04,      vary=True,  units='AA', decimals=3, _larch=self._larch)
        gds.ssh     = Parameter(0.005,     vary=True,  units='AA^2', _larch=self._larch)
        gds.ss2     = Parameter(expr = 'ss*(brc2/brc)**2', units ='AA^2', _larch=self._larch)
        gds.drc     = Parameter(0.04,      vary=True,  units='AA', decimals=3, _larch=self._larch)
        gds.brc2    = Parameter(expr = '2.8565+drc',   units='AA', decimals=3, _larch=self._larch)
        
    paths = list()
    paths.append(feffpath(realpath(join(folder, "feff0001.dat")),
                          s02    = 'amp',
                          e0     = 'enot',
                          sigma2 = 'ss',
                          deltar = 'delr',
                          third  = 'c3', _larch=self._larch))

    if not firstshell:
        paths.append(feffpath(realpath(join(folder, "feff0002.dat")),
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ss2',
                              #deltar = 'brc2-2.8565',
                              deltar = 'drc',_larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0003.dat")),
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = 'ssh',
                              deltar = 'drh', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0004.dat")),
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = '(ss+ss2)/2',
                              deltar = '(brc+brc2+cc)/2 - 3.173', _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0005.dat")),
                              s02    = 'amp',
                              e0     = 'enot',
                              sigma2 = '(ss+ss2)/2',
                              deltar = '(brc+brc2+cc)/2 - 3.173', _larch=self._larch))

    rx  = 3
    if firstshell: rx  = 1.83

    trans = feffit_transform(kmin=3, kmax=11, kw=(2,1,3), dk=1, window='hanning', rmin=1, rmax=3, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8,
                 xlabel=r'$R \rm\,(\AA)$', label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells='_1st'

    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".k"), dset.data.k, dset.data.chi, dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
                dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest,'fit_'+which+shells+'.gp'), 'w') as inp:
        inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
                                        {'material': 'bromoadamantane',
                                         'model': which,
                                         'fittest': fittest,
                                         'shells': shells,
                                         'kmin': 3,
                                         'kmax': 13,
                                         'rmin': 1,
                                         'rmax': rx,
                                         'offset': 0.2,
                                     } ))

    return fit
Esempio n. 22
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'BaZrO3.chik'), _larch=self._larch)

    gds = Group(amp    = Parameter(0.95,    vary=True,  _larch=self._larch),
                enot   = Parameter(1e-7,    vary=True,  _larch=self._larch),
                sso    = Parameter(0.003,   vary=True,  _larch=self._larch),
                czr    = Parameter(0.,      vary=False, _larch=self._larch), _larch=self._larch  )

    if firstshell:
        gds.delr   = Parameter(1e-7,    vary=True,  _larch=self._larch)
        dr1param   = 'delr'
    else:
        gds.alpha  = Parameter(0.00001, vary=True,  _larch=self._larch)
        gds.ssba   = Parameter(0.003,   vary=True,  _larch=self._larch)
        gds.sszr   = Parameter(0.003,   vary=True,  _larch=self._larch)
        gds.eba    = Parameter(1e-7,    vary=True,  _larch=self._larch)
        gds.ezr    = Parameter(1e-7,    vary=True,  _larch=self._larch)
        #gds.eba    = Parameter(expr='enot',          _larch=self._larch)
        #gdsezr    = Parameter(expr='enot',         _larch=self._larch)
        gds.sso2   = Parameter(0.003,   vary=True,  _larch=self._larch)
        dr1param   = 'alpha*reff'

    paths = list()
    paths.append(feffpath(realpath(join(folder, "feff0001.dat")),
                          s02    = 'amp',
                          deltar = dr1param,
                          e0     = 'enot',
                          sigma2 = 'sso',
                          _larch=self._larch))
    if not firstshell:
        paths.append(feffpath(realpath(join(folder, "feff0002.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = 'enot',
                              sigma2 = 'sso*1.5',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0003.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = 'eba',
                              sigma2 = 'ssba',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0004.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = 'ezr',
                              sigma2 = 'sszr',
                              third  = 'czr',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0005.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = 'enot',
                              sigma2 = 'sso*2',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0006.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = '(enot+ezr)/2',
                              sigma2 = 'sszr',
                              third  = 'czr',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0007.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = 'enot',
                              sigma2 = 'sso*2',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0009.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = '(2*enot+ezr)/3',
                              sigma2 = 'sszr',
                              third  = 'czr',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0008.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = 'enot',
                              sigma2 = 'sso*4',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0011.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = '(enot+eba)/2',
                              sigma2 = 'ssba+sso',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0012.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = 'enot',
                              sigma2 = 'sso2',
                              _larch=self._larch))
        paths.append(feffpath(realpath(join(folder, "feff0013.dat")),
                              s02    = 'amp',
                              deltar = 'alpha*reff',
                              e0     = 'enot',
                              sigma2 = 'sso+sso2',
                              _larch=self._larch))

    rx  = 4.5
    if firstshell: rx  = 1.95

    trans = feffit_transform(kmin=3, kmax=14.5, kw=(2,1,3), dk=1, window='hanning', rmin=1.2, rmax=rx, _larch=self._larch)
    dset  = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
    fit   = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,  dset.data.chir_mag+offset, xmax=8,
              xlabel=r'$R \rm\,(\AA)$', label='data',
              ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
              title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_mag+offset, label='fit', _larch=self._larch)
        _plot(dset.data.r,  dset.data.chir_re, label='data', _larch=self._larch)
        _plot(dset.model.r, dset.model.chir_re, label='fit', _larch=self._larch)
    #end if
    
    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells='_1st'

    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".k"), dset.data.k, dset.data.chi, dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_"+which+shells+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
                dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_'+which+shells+'.gp'), 'w') as inp:
        inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
                                        {'material': 'BaZrO3',
                                         'model': which,
                                         'fittest': fittest,
                                         'shells': shells,
                                         'kmin': 3,
                                         'kmax': 14.5,
                                         'rmin': 1.2,
                                         'rmax': rx,
                                         'offset': 1,
                                     } ))

    return fit
Esempio n. 23
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'Copper.chik'), _larch=self._larch)

    gds = Group(amp=Parameter(1, vary=True, _larch=self._larch),
                enot=Parameter(1e-7, vary=True, _larch=self._larch),
                ss1=Parameter(0.003, vary=True, _larch=self._larch),
                _larch=self._larch)

    if firstshell:
        gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
        dr1param = 'delr'
    else:
        gds.thetad = Parameter(500, vary=True, _larch=self._larch)
        gds.temp = Parameter(10, vary=False, _larch=self._larch)
        gds.alpha = Parameter(1e-7, vary=True, _larch=self._larch)
        dr1param = 'alpha*reff'

    imax = 16
    if firstshell: imax = 2
    paths = list()
    for index in range(1, imax):
        nnnn = realpath(join(folder, "feff%4.4d.dat" % index))
        if not exists(nnnn):
            continue
        #end if
        if index > 1:
            sigsqr = 'sigma2_debye(temp, thetad)'
        else:
            sigsqr = 'ss1'
        #end if
        paths.append(
            feffpath(nnnn,
                     s02='amp',
                     e0='enot',
                     sigma2=sigsqr,
                     deltar=dr1param,
                     _larch=self._larch))
    #end for

    rx = 5.0
    if firstshell: rx = 2.8

    trans = feffit_transform(kmin=3,
                             kmax=15,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1,
                             rmax=rx,
                             _larch=self._larch)
    dset = feffit_dataset(data=data,
                          pathlist=paths,
                          transform=trans,
                          _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = max(dset.data.chir_mag)
        _newplot(dset.data.r,
                 dset.data.chir_mag + offset,
                 xmax=8,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_mag + offset,
              label='fit',
              _larch=self._larch)
        _plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_re,
              label='fit',
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells = '_1st'

    write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".k"),
                dset.data.k,
                dset.data.chi,
                dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".r"),
                dset.data.r,
                dset.data.chir_mag,
                dset.model.chir_mag,
                dset.data.chir_re,
                dset.model.chir_re,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_' + which + shells + '.gp'),
              'w') as inp:
        inp.write(
            renderer.render_path(
                'plot.mustache',  # gnuplot mustache file
                {
                    'material': 'Copper',
                    'model': which,
                    'fittest': fittest,
                    'shells': shells,
                    'kmin': 3,
                    'kmax': 15,
                    'rmin': 1,
                    'rmax': rx,
                    'offset': 2,
                }))

    return fit
Esempio n. 24
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'NiO.chik'), _larch=self._larch)
    if hasattr(data, 'wavenumber'):
        data.k = data.wavenumber

    gds = Group(amp=Parameter(1, vary=True, _larch=self._larch),
                enot=Parameter(1e-7, vary=True, _larch=self._larch),
                sso=Parameter(0.003, vary=True, _larch=self._larch),
                _larch=self._larch)

    if firstshell:
        gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
        dr1param = 'delr'
    else:
        gds.alpha = Parameter(1e-7, vary=True, _larch=self._larch)
        gds.ssni = Parameter(0.003, vary=True, _larch=self._larch)
        gds.sso2 = Parameter(0.003, vary=True, _larch=self._larch)
        #gds.sso3   = Parameter(0.003,  vary=True, _larch=self._larch)
        gds.ssni2 = Parameter(0.003, vary=True, _larch=self._larch)
        #gds.ssni3  = Parameter(0.003,  vary=True, _larch=self._larch)
        #gds.ssni4  = Parameter(0.003,  vary=True, _larch=self._larch)
        dr1param = 'alpha*reff'

    paths = list()
    paths.append(
        feffpath(
            realpath(join(folder, "feff0001.dat")),  # 1st shell O SS
            s02='amp',
            e0='enot',
            sigma2='sso',
            deltar=dr1param,
            _larch=self._larch))
    if not firstshell:
        paths.append(
            feffpath(
                realpath(join(folder, "feff0002.dat")),  # 2nd shell Ni SS
                s02='amp',
                e0='enot',
                sigma2='ssni',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0003.dat")),  # O-O triangle
                s02='amp',
                e0='enot',
                sigma2='1.5*sso',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0004.dat")),  # O-Ni triangle
                s02='amp',
                e0='enot',
                sigma2='sso+ssni/2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0005.dat")),  # 3rd shell O SS
                s02='amp',
                e0='enot',
                sigma2='sso2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0006.dat")),  # 4th shell Ni SS
                s02='amp',
                e0='enot',
                sigma2='ssni2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder,
                              "feff0007.dat")),  # O-O non-forward linear
                s02='amp',
                e0='enot',
                sigma2='sso*2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder,
                              "feff0008.dat")),  # O-Ni forward scattering
                s02='amp',
                e0='enot',
                sigma2='ssni2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder,
                              "feff0009.dat")),  # O-O forward through absorber
                s02='amp',
                e0='enot',
                sigma2='sso*2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder,
                              "feff0011.dat")),  # O-Ni-O double forward
                s02='amp',
                e0='enot',
                sigma2='ssni2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(
                    join(folder, "feff0010.dat")
                ),  # O-O rattle (the order of 10 and 11 is different in Demeter's pathfinder!)
                s02='amp',
                e0='enot',
                sigma2='sso*4',
                deltar='alpha*reff',
                _larch=self._larch))

    rx = 4.2
    if firstshell: rx = 1.95

    trans = feffit_transform(kmin=3,
                             kmax=15.938,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1.0,
                             rmax=rx,
                             _larch=self._larch)
    dset = feffit_dataset(data=data,
                          pathlist=paths,
                          transform=trans,
                          _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = 0.6 * max(dset.data.chir_mag)
        _newplot(dset.data.r,
                 dset.data.chir_mag + offset,
                 xmax=8,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_mag + offset,
              label='fit',
              _larch=self._larch)
        _plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_re,
              label='fit',
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells = '_1st'

    write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".k"),
                dset.data.k,
                dset.data.chi,
                dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".r"),
                dset.data.r,
                dset.data.chir_mag,
                dset.model.chir_mag,
                dset.data.chir_re,
                dset.model.chir_re,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_' + which + shells + '.gp'),
              'w') as inp:
        inp.write(
            renderer.render_path(
                'plot.mustache',  # gnuplot mustache file
                {
                    'material': 'NiO',
                    'model': which,
                    'fittest': fittest,
                    'shells': shells,
                    'kmin': 3,
                    'kmax': 15.938,
                    'rmin': 1.0,
                    'rmax': rx,
                    'offset': 1,
                }))

    return fit
Esempio n. 25
0
def do_fit(self, which, firstshell=False, fittest='baseline'):

    if which == 'testrun':
        folder = self.testrun
    elif which == 'baseline':
        folder = self.baseline
    else:
        folder = realpath(join(self.folder, fittest, which))
    #endif

    data = read_xdi(join(self.path, 'FeS2.chik'), _larch=self._larch)

    gds = Group(amp=Parameter(1, vary=True, _larch=self._larch),
                enot=Parameter(1e-7, vary=True, _larch=self._larch),
                ss=Parameter(0.003, vary=True, _larch=self._larch),
                _larch=self._larch)

    if firstshell:
        gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
        dr1param = 'delr'
    else:
        gds.alpha = Parameter(1e-7, vary=True, _larch=self._larch)
        gds.ss2 = Parameter(0.003, vary=True, _larch=self._larch)
        gds.ss3 = Parameter(expr='ss2', _larch=self._larch)
        gds.ssfe = Parameter(0.003, vary=True, _larch=self._larch)
        dr1param = 'alpha*reff'

    paths = list()
    paths.append(
        feffpath(
            realpath(join(folder, "feff0001.dat")),  # 1st shell S SS
            s02='amp',
            e0='enot',
            sigma2='ss',
            deltar=dr1param,
            _larch=self._larch))
    if not firstshell:
        paths.append(
            feffpath(
                realpath(join(folder, "feff0002.dat")),  # 2nd shell S SS
                s02='amp',
                e0='enot',
                sigma2='ss2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0003.dat")),  # 3rd shell S SS
                s02='amp',
                e0='enot',
                sigma2='ss3',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0004.dat")),  # 4th shell Fe SS
                s02='amp',
                e0='enot',
                sigma2='ssfe',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0005.dat")),  # S-S triangle
                s02='amp',
                e0='enot',
                sigma2='ss*1.5',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0006.dat")),  # S-Fe triangle
                s02='amp',
                e0='enot',
                sigma2='ss/2+ssfe',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder,
                              "feff0012.dat")),  # S-S non-forward linear
                s02='amp',
                e0='enot',
                sigma2='ss*2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder,
                              "feff0013.dat")),  # S-S forward scattering
                s02='amp',
                e0='enot',
                sigma2='ss*2',
                deltar='alpha*reff',
                _larch=self._larch))
        paths.append(
            feffpath(
                realpath(join(folder, "feff0014.dat")),  # S-S rattle
                s02='amp',
                e0='enot',
                sigma2='ss*4',
                deltar='alpha*reff',
                _larch=self._larch))

    rx = 4.2
    if firstshell: rx = 2.3

    trans = feffit_transform(kmin=3,
                             kmax=12.956,
                             kw=(2, 1, 3),
                             dk=1,
                             window='hanning',
                             rmin=1.2,
                             rmax=rx,
                             _larch=self._larch)
    dset = feffit_dataset(data=data,
                          pathlist=paths,
                          transform=trans,
                          _larch=self._larch)
    fit = feffit(gds, dset, _larch=self._larch)

    if self.doplot:
        offset = 0.6 * max(dset.data.chir_mag)
        _newplot(dset.data.r,
                 dset.data.chir_mag + offset,
                 xmax=8,
                 xlabel=r'$R \rm\,(\AA)$',
                 label='data',
                 ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
                 title='Fit to ' + self.folder,
                 show_legend=True,
                 _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_mag + offset,
              label='fit',
              _larch=self._larch)
        _plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
        _plot(dset.model.r,
              dset.model.chir_re,
              label='fit',
              _larch=self._larch)
    #end if

    if self.verbose:
        print feffit_report(fit, _larch=self._larch)
    #end if

    shells = ''
    if firstshell: shells = '_1st'

    write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".k"),
                dset.data.k,
                dset.data.chi,
                dset.model.chi,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)
    write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".r"),
                dset.data.r,
                dset.data.chir_mag,
                dset.model.chir_mag,
                dset.data.chir_re,
                dset.model.chir_re,
                labels="r data_mag fit_mag data_re fit_re",
                _larch=self._larch)

    renderer = pystache.Renderer()
    with open(join(self.folder, fittest, 'fit_' + which + shells + '.gp'),
              'w') as inp:
        inp.write(
            renderer.render_path(
                'plot.mustache',  # gnuplot mustache file
                {
                    'material': 'FeS2',
                    'model': which,
                    'fittest': fittest,
                    'shells': shells,
                    'kmin': 3,
                    'kmax': 12.956,
                    'rmin': 1.2,
                    'rmax': rx,
                    'offset': 1,
                }))

    return fit