def plotkk(self):
"""
Make a quick-n-dirty plot of the output of the KK transform.
"""
if not HASPLOT: return
_newplot(self.energy, self.f2, _larch=self._larch, label='$f_2$', xlabel='Energy (eV)', ylabel='scattering factors',
show_legend=True, legend_loc='lr')
_plot(self.energy, self.fpp, _larch=self._larch, label="$f''(E)$")
_plot(self.energy, self.f1, _larch=self._larch, label='$f_1$')
_plot(self.energy, self.fp, _larch=self._larch, label="$f'(E)$")
def plotkk(self):
"""
Make a quick-n-dirty plot of the output of the KK transform.
"""
if not HASPLOT: return
_newplot(self.energy, self.f2, _larch=self._larch, label='$f_2$', xlabel='Energy (eV)', ylabel='scattering factors',
show_legend=True, legend_loc='lr')
_plot(self.energy, self.fpp, _larch=self._larch, label="$f''(E)$")
_plot(self.energy, self.f1, _larch=self._larch, label='$f_1$')
_plot(self.energy, self.fp, _larch=self._larch, label="$f'(E)$")
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
lam : test the mean free path
caps : test the central atom phase shift
red_fact: 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_error("You have not yet run the test Feff calculation")
return
if not self.available(nnnn):
print_error("Path %d was not saved from the test Feff calculation" % nnnn)
return
how = 'wrapper' if use_wrapper else 'executables'
nnnndat = "feff%4.4d.dat" % nnnn
blpath = feffpath(join(self.baseline, nnnndat), _larch=self._larch)
if use_wrapper: # make the feffNNNN.dat file on the fly
self.sp.phase_file = 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.calculate_xafs()
finally:
chdir(owd)
n3nndat = "feff%4.4d.dat" % nnnn
trpath = feffpath(join(self.testrun, n3nndat), _larch=self._larch)
else: # the feffNNNN.dat file was made by the monolithic feff run
trpath = feffpath(join(self.testrun, nnnndat), _larch=self._larch)
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 = np.sin(getattr(blpath._feffdat, 'pha_feff')) # + np.random.uniform(0,1,size=1)
testrun_2 = np.sin(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 = np.sin(getattr(blpath._feffdat, 'pha'))
testrun_1 = np.sin(getattr(trpath._feffdat, 'pha'))
ylabel = 'total phase shift'
label = 'phase'
elif part=='lam':
baseline_1 = getattr(blpath._feffdat, 'lam')
testrun_1 = getattr(trpath._feffdat, 'lam')
ylabel = 'mean free path'
label = 'lambda'
elif part=='phc':
baseline_1 = getattr(blpath._feffdat, 'real_phc')
testrun_1 = getattr(trpath._feffdat, 'real_phc')
ylabel = 'central atom phase shift'
label = 'phc'
elif part=='red_fact':
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_error("Unknown choice of parts \"%s\"\nmust be one of (feff|amp|phase|lam|phc|red_fact|rep)\nusing feff" % part)
part = 'feff'
baseline_1 = getattr(blpath._feffdat, 'mag_feff')
testrun_1 = getattr(trpath._feffdat, 'mag_feff')
baseline_2 = np.sin(getattr(blpath._feffdat, 'pha_feff'))
testrun_2 = np.sin(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_warn("\nComparing %s of %s (%s) (using %s)" % (label, nnnndat, "with SCF" if self.doscf else "without SCF", how))
self.print_geometry(blpath)
print_warn("%s: %f v %f " % (blpath, sum(baseline_1**2) , sum(testrun_1**2)))
if self.verbose:
print label + " R-factor = " + test_text("%.9g" % self.rfactor, (self.rfactor < self.epsilon))
if part=='feff':
self.rfactor_2 = sum((baseline_2 - testrun_2)**2) / sum(baseline_2**2)
if self.verbose:
print(" -- ",self.epsilon, sum((baseline_2 - testrun_2)**2), sum(baseline_2**2))
print "phase R-factor = " + test_text("%.9g" % self.rfactor_2, self.rfactor_2 < self.epsilon)
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 WRAPPER_AVAILABLE:
self.sp.reset()
if part=='feff':
return self.rfactor < self.epsilon and self.rfactor_2 < self.epsilon
else:
return self.rfactor < self.epsilon