Added 'other_parameters' keyword to any scan.

This keyword is a dictionary allowing any option
to be passed to Phagen or Spec just before runing
the calculation. It is usefull to pass special options
that are for example set automatically otherwise.

src/msspec/calculator.py

@@ -616,7 +616,7 @@ class _PED(_MSCALCULATOR):
     def _get_scan(self, scan_type='theta', phi=0,
                   theta=np.linspace(-70, 70, 141), level=None,
                   kinetic_energy=None, data=None,
-                  malloc={}):
+                  malloc={}, other_parameters={}):
         LOGGER.info("Computting the %s scan...", scan_type)
         if data:
             self.iodata = data
@@ -651,6 +651,13 @@ class _PED(_MSCALCULATOR):
 
         self.spectroscopy_parameters.set_parameter('level', level)
 
+        # It is still possible to change any parameter right before
+        # runing Phagen or Spec
+        for k, v in other_parameters.items():
+            grp_str, parma_str = k.split('.')
+            grp = getattr(self, grp_str)
+            grp.set_parameter(parma_str, v, force=True)
+
         self.get_tmatrix()
         self.run_spec(malloc)
 
@@ -852,7 +859,7 @@ class _PED(_MSCALCULATOR):
         return self.iodata
 
     def get_scattering_factors(self, level='1s', kinetic_energy=None,
-                               data=None):
+                               data=None, **kwargs):
         """Computes the scattering factors of all prototypical atoms in the
         cluster.
 
@@ -871,11 +878,12 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='scatf', level=level, data=data,
-                              kinetic_energy=kinetic_energy)
+                              kinetic_energy=kinetic_energy, **kwargs)
         return data
 
     def get_theta_scan(self, phi=0, theta=np.linspace(-70, 70, 141),
-                       level=None, kinetic_energy=None, data=None):
+                       level=None, kinetic_energy=None, data=None,
+                       **kwargs):
         """Computes a polar scan of the emitted photoelectrons.
 
         :param phi: The azimuthal angle in degrees. See
@@ -892,11 +900,12 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='theta', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data
 
     def get_phi_scan(self, phi=np.linspace(0, 359, 359), theta=0,
-                     level=None, kinetic_energy=None, data=None):
+                     level=None, kinetic_energy=None, data=None, **kwargs):
         """Computes an azimuthal scan of the emitted photoelectrons.
 
         :param phi: All the values of the azimuthal angle to be computed. See
@@ -913,12 +922,13 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='phi', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data
 
     def get_theta_phi_scan(self, phi=np.linspace(0, 360),
                            theta=np.linspace(0, 90, 45), level=None,
-                           kinetic_energy=None, data=None):
+                           kinetic_energy=None, data=None, **kwargs):
         """Computes a stereographic scan of the emitted photoelectrons.
 
         The azimuth ranges from 0 to 360° and the polar angle ranges from 0 to
@@ -935,11 +945,11 @@ class _PED(_MSCALCULATOR):
         """
         data = self._get_scan(scan_type='theta_phi', level=level, theta=theta,
                               phi=phi, kinetic_energy=kinetic_energy, data=data,
-                              malloc={'NPH_M': 8000})
+                              malloc={'NPH_M': 8000}, **kwargs)
         return data
 
     def get_energy_scan(self, phi=0, theta=0,
-                        level=None, kinetic_energy=None, data=None):
+                        level=None, kinetic_energy=None, data=None, **kwargs):
         """Computes an energy scan of the emitted photoelectrons.
 
         :param phi: All the values of the azimuthal angle to be computed. See
@@ -956,7 +966,8 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='energy', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data
 
 

src/msspec/parameters.py

@@ -1540,7 +1540,7 @@ class CalculationParameters(BaseParameters):
             Parameter('cutoff_factor', types=(int, float),
                       limits=(1e-4, 999.9999), default=0.01, private=False),
             Parameter('mean_free_path', types=(int, float, str),
-                      default='SeahDench', allowed_values=('mono', 'SeahDench'),
+                      default='SeahDench', #allowed_values=('mono', 'SeahDench'),
                       doc="""
             The electron mean free path value. You can either:
             - Enter a value (in Angströms), in this case any value <=0 will disable the damping