Changed return values of Looper.run
Instead of returning a panda dataframe, return both a list of [x0, y0, x1, y1,...] values for all the calculations and the corresponding dict of parameters
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@ -747,15 +747,30 @@ class _PED(_MSCALCULATOR):
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proto_index = i+1
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title = 'Scattering factor at {:.3f} eV'.format(kinetic_energy)
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mini = min(map(np.min, [dset.sf_real, dset.sf_imag, dset.sf_module]))
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maxi = max(map(np.max, [dset.sf_real, dset.sf_imag, dset.sf_module]))
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view = dset.add_view("Proto. atom #{:d}".format(proto_index),
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title=title, projection='polar')
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title=title, projection='polar',
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ylim=[mini, maxi])
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where = "proto_index=={:d}".format(proto_index)
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view.select('theta', 'sf_module', where=where,
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legend=r'$|f(\theta)|$')
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view.select('theta', 'sf_real', where=where,
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legend=r'$\Im(f(\theta))$')
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view.select('theta', 'sf_imag', where=where,
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legend=r'$\Re(f(\theta))$')
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view.select('theta', 'sf_imag', where=where,
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legend=r'$\Im(f(\theta))$')
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if scan_type == 'energy':
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absorber_symbol = self.atoms[self.atoms.absorber].symbol
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title = (r'Energy scan of {}({}) at $\theta$={:.2f}$\degree$ and '
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'$\phi$={:.2f}$\degree$').format(
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absorber_symbol, level, theta, phi)
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xlabel = r'Photoelectron kinetic energy (eV)'
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ylabel = r'Signal (a. u.)'
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view = dset.add_view("EnergyScan".format(ke), title=title,
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xlabel=xlabel, ylabel=ylabel)
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view.select('energy', 'cross_section')
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# save the cluster
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#clusbuf = StringIO()
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@ -922,6 +937,27 @@ class _PED(_MSCALCULATOR):
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malloc={'NPH_M': 8000})
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return data
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def get_energy_scan(self, phi=0, theta=0,
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level=None, kinetic_energy=None, data=None):
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"""Computes an energy scan of the emitted photoelectrons.
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:param phi: All the values of the azimuthal angle to be computed. See
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:ref:`scanparameters-phi`.
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:param theta: The polar angle in degrees. See
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:ref:`scanparameters-theta`.
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:param level: The electronic level. See :ref:`pedparameters-level`.
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:param kinetic_energy: see :ref:`scanparameters-kinetic_energy`.
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:param data: a :py:class:`iodata.Data` object to append the results to
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or None.
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:returns: The modified :py:class:`iodata.Data` object passed as an
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argument or a new :py:class:`iodata.Data` object.
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"""
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data = self._get_scan(scan_type='energy', level=level, theta=theta,
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phi=phi, kinetic_energy=kinetic_energy, data=data)
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return data
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class _EIG(_MSCALCULATOR):
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"""
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@ -236,7 +236,22 @@ class Looper:
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df = pd.DataFrame(dfdata, columns=columns)
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self.data = df
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return df
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#return df
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# return a list of [x0, y0, x1, y1,...xn, yn] and a list
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# of corresponding dict of parameters {'keyA': [val0,...valn],
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# 'keyB': [val0,...valn], ...}
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all_xy = []
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for irow, row in df.iterrows():
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all_xy.append(row.output[0])
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all_xy.append(row.output[1])
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parameters = df.to_dict()
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parameters.pop('output')
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return all_xy, parameters
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@ -282,7 +297,7 @@ if __name__ == "__main__":
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looper = Looper()
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looper.pipeline = bar
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data = looper.run(emitter, emitter_plane, uij, theta, levels, ncpu=1,
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data = looper.run(emitter, emitter_plane, uij, theta, levels, ncpu=4,
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passindex=True)
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print(data[data.emitter_plane.eq(0)].theta.unique())
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print(data)
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#print(data[data.emitter_plane.eq(0)].theta.unique())
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@ -853,8 +853,8 @@ class MuffintinParameters(BaseParameters):
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def __init__(self, phagen_parameters, spec_parameters):
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parameters = (
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Parameter('charge_relaxation', types=bool, default=True, doc="""
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Used to specify wether the charge density of the photoabsorbing atom, which is used
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to construct the potential, is allowaed to relax around the core hole or not.
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Used to specify whether the charge density of the photoabsorbing atom, which is used
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to construct the potential, is allowed to relax around the core hole or not.
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"""),
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Parameter('ionicity', types=dict, default={}, doc="""
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A dictionary to specify the ionicity of each kind of atoms. If empty, the atoms are considered to be
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@ -113,7 +113,7 @@ C
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CST PROGRAM COMP_CURVE
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SUBROUTINE COMP_CURVES()
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C
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PARAMETER (N_SIZE=1000,N_FILES=100,NMAX=9999)
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PARAMETER (N_SIZE=1000,N_FILES=1000,NMAX=9999)
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C
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INTEGER CC_EXP(N_SIZE),CC_CAL(N_SIZE),VALUE,NVALUE
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C
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@ -1634,7 +1634,7 @@ C Author : D. Sébilleau
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C
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C Last modified : 9 Sep 2014
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C
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PARAMETER (N_SIZE=1000,N_FILES=100)
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PARAMETER (N_SIZE=1000,N_FILES=1000)
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C
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REAL*4 X_CAL(N_SIZE),I_CAL,X,Y
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REAL*4 DIFF,STEP1,STEP2
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@ -2955,7 +2955,7 @@ C Author : D. Sébilleau
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C
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C Last modified : 5 Sep 2014
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C
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PARAMETER (N_SIZE=1000,N_FILES=100)
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PARAMETER (N_SIZE=1000,N_FILES=1000)
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C
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REAL*4 EXPE(N_SIZE),CALCULATION(N_SIZE,N_FILES)
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REAL*4 MIN_EXP,MIN_CAL,MINIMUM,SHIFT
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@ -9748,7 +9748,7 @@ C Author : D. Sébilleau
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C
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C Last modified : 19 Aug 2014
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C
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PARAMETER (N_SIZE=1000,N_FILES=100)
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PARAMETER (N_SIZE=1000,N_FILES=1000)
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C
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REAL*4 EXPE(N_SIZE),CALC(N_SIZE),Y_MEAN(N_SIZE)
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real*4 x(N_SIZE)
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