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

src/msspec/calculator.py

@@ -747,15 +747,30 @@ class _PED(_MSCALCULATOR):
                 proto_index = i+1
                 title = 'Scattering factor at {:.3f} eV'.format(kinetic_energy)
 
+                mini = min(map(np.min, [dset.sf_real, dset.sf_imag, dset.sf_module]))
+                maxi = max(map(np.max, [dset.sf_real, dset.sf_imag, dset.sf_module]))
                 view = dset.add_view("Proto. atom #{:d}".format(proto_index),
-                                     title=title, projection='polar')
+                                     title=title, projection='polar',
+                                     ylim=[mini, maxi])
                 where = "proto_index=={:d}".format(proto_index)
                 view.select('theta', 'sf_module', where=where,
                             legend=r'$|f(\theta)|$')
                 view.select('theta', 'sf_real', where=where,
-                            legend=r'$\Im(f(\theta))$')
-                view.select('theta', 'sf_imag', where=where,
                             legend=r'$\Re(f(\theta))$')
+                view.select('theta', 'sf_imag', where=where,
+                            legend=r'$\Im(f(\theta))$')
+
+        if scan_type == 'energy':
+            absorber_symbol = self.atoms[self.atoms.absorber].symbol
+            title = (r'Energy scan of {}({}) at $\theta$={:.2f}$\degree$ and '
+                      '$\phi$={:.2f}$\degree$').format(
+                     absorber_symbol, level, theta, phi)
+            xlabel = r'Photoelectron kinetic energy (eV)'
+            ylabel = r'Signal (a. u.)'
+
+            view = dset.add_view("EnergyScan".format(ke), title=title,
+                                 xlabel=xlabel, ylabel=ylabel)
+            view.select('energy', 'cross_section')
 
         # save the cluster
         #clusbuf = StringIO()
@@ -922,6 +937,27 @@ class _PED(_MSCALCULATOR):
                               malloc={'NPH_M': 8000})
         return data
 
+    def get_energy_scan(self, phi=0, theta=0,
+                        level=None, kinetic_energy=None, data=None):
+        """Computes an energy scan of the emitted photoelectrons.
+
+        :param phi: All the values of the azimuthal angle to be computed. See
+            :ref:`scanparameters-phi`.
+        :param theta: The polar angle in degrees. See
+            :ref:`scanparameters-theta`.
+        :param level: The electronic level. See :ref:`pedparameters-level`.
+        :param kinetic_energy: see :ref:`scanparameters-kinetic_energy`.
+        :param data: a :py:class:`iodata.Data` object to append the results to
+            or None.
+
+        :returns: The modified :py:class:`iodata.Data` object passed as an
+            argument or a new :py:class:`iodata.Data` object.
+
+        """
+        data = self._get_scan(scan_type='energy', level=level, theta=theta,
+                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+        return data
+
 
 class _EIG(_MSCALCULATOR):
     """

src/msspec/looper.py

@@ -236,7 +236,22 @@ class Looper:
         df = pd.DataFrame(dfdata, columns=columns)
 
         self.data = df
-        return df
+
+        #return df
+        # return a list of [x0, y0, x1, y1,...xn, yn] and a list
+        # of corresponding dict of parameters {'keyA': [val0,...valn],
+        # 'keyB': [val0,...valn], ...}
+
+        all_xy = []
+        for irow, row in df.iterrows():
+            all_xy.append(row.output[0])
+            all_xy.append(row.output[1])
+        parameters = df.to_dict()
+        parameters.pop('output')
+
+        return all_xy, parameters
+
+
 
 
 
@@ -282,7 +297,7 @@ if __name__ == "__main__":
 
     looper = Looper()
     looper.pipeline = bar
-    data = looper.run(emitter, emitter_plane, uij, theta, levels, ncpu=1,
+    data = looper.run(emitter, emitter_plane, uij, theta, levels, ncpu=4,
                       passindex=True)
-
+    print(data)
-    print(data[data.emitter_plane.eq(0)].theta.unique())
+    #print(data[data.emitter_plane.eq(0)].theta.unique())

src/msspec/parameters.py

@@ -853,8 +853,8 @@ class MuffintinParameters(BaseParameters):
     def __init__(self, phagen_parameters, spec_parameters):
         parameters = (
             Parameter('charge_relaxation', types=bool, default=True, doc="""
-            Used to specify wether the charge density of the photoabsorbing atom, which is used
+            Used to specify whether the charge density of the photoabsorbing atom, which is used
-            to construct the potential, is allowaed to relax around the core hole or not.
+            to construct the potential, is allowed to relax around the core hole or not.
             """),
             Parameter('ionicity', types=dict, default={}, doc="""
             A dictionary to specify the ionicity of each kind of atoms. If empty, the atoms are considered to be

src/msspec/spec/fortran/treatment/comp_curves.f

@@ -113,7 +113,7 @@ C
 CST      PROGRAM COMP_CURVE
       SUBROUTINE COMP_CURVES()
 C
-      PARAMETER (N_SIZE=1000,N_FILES=100,NMAX=9999)
+      PARAMETER (N_SIZE=1000,N_FILES=1000,NMAX=9999)
 C
       INTEGER CC_EXP(N_SIZE),CC_CAL(N_SIZE),VALUE,NVALUE
 C
@@ -1634,7 +1634,7 @@ C   Author :  D. Sébilleau
 C  
 C                                           Last modified : 9 Sep 2014
 C
-      PARAMETER (N_SIZE=1000,N_FILES=100)
+      PARAMETER (N_SIZE=1000,N_FILES=1000)
 C
       REAL*4 X_CAL(N_SIZE),I_CAL,X,Y
       REAL*4 DIFF,STEP1,STEP2
@@ -2955,7 +2955,7 @@ C   Author :  D. Sébilleau
 C  
 C                                           Last modified :  5 Sep 2014
 C
-      PARAMETER (N_SIZE=1000,N_FILES=100)
+      PARAMETER (N_SIZE=1000,N_FILES=1000)
 C
       REAL*4 EXPE(N_SIZE),CALCULATION(N_SIZE,N_FILES)
       REAL*4 MIN_EXP,MIN_CAL,MINIMUM,SHIFT
@@ -9748,7 +9748,7 @@ C   Author :  D. Sébilleau
 C              
 C                                          Last modified : 19 Aug 2014
 C
-      PARAMETER (N_SIZE=1000,N_FILES=100)
+      PARAMETER (N_SIZE=1000,N_FILES=1000)
 C
       REAL*4 EXPE(N_SIZE),CALC(N_SIZE),Y_MEAN(N_SIZE)
       real*4 x(N_SIZE)