From 925d69409922aa9db6dc3d9d8a74237fcdb04305 Mon Sep 17 00:00:00 2001
From: Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>
Date: Tue, 30 Nov 2021 16:26:10 +0100
Subject: [PATCH] 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 | 33 ++++++++++++++++++++++-----------
 src/msspec/parameters.py |  2 +-
 2 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/src/msspec/calculator.py b/src/msspec/calculator.py
index 9f9ef2b..d78a1c9 100644
--- a/src/msspec/calculator.py
+++ b/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
 
 
diff --git a/src/msspec/parameters.py b/src/msspec/parameters.py
index 51a3817..8a682f4 100644
--- a/src/msspec/parameters.py
+++ b/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