Requested adjustments

lib/atom.cpp

@@ -76,6 +76,7 @@ double TransitionMatrix::totalRate() {
  * @param  Z: Atomic number (nuclear charge, can be fractional)
  * @param  m: Mass of the orbiting particle (e.g. electron)
  * @param  A: Atomic mass (amus, ignored if -1)
+ * @param  radius: Solid sphere equivalent radius (fm, ignored if -1)
  * @param  radius_model: Which NuclearRadiusModel to use
  * @param  fc:   Central point of the grid (corresponding to i = 0), as a
  * fraction of 1/(Z*mu), the 1s orbital radius for this atom, or of the nuclear
@@ -112,7 +113,7 @@ Atom::Atom(int Z, double m, int A, double radius, NuclearRadiusModel radius_mode
   // Define radius
   if (A == -1) {
     R = -1;
-  } else if (radius < 0) {
+  } else if (radius == -1) {
     switch (radius_model) {
       case POINT:
         R = -1;
@@ -141,7 +142,7 @@ Atom::Atom(int Z, double m, int A, double radius, NuclearRadiusModel radius_mode
 
   if (radius_model == FERMI2) {
     V_coulomb = new CoulombFermi2Potential(Z, R, A);
-  } else if (radius_model == SPHERE) {
+  } else {
     V_coulomb = new CoulombSpherePotential(Z, R);
   }
 
@@ -327,6 +328,7 @@ double Atom::sphereNuclearModel(int Z, int A) {
  * @param  Z: Atomic number (nuclear charge, can be fractional)
  * @param  m: Mass of the orbiting particle (e.g. electron)
  * @param  A: Atomic mass (amus, ignored if -1)
+ * @param  radius: Solid sphere equivalent radius (fm, ignored if -1)
  * @param  radius_model: Which NuclearRadiusModel to use
  * @param  fc:   Central point of the grid (corresponding to i = 0), as a
  * fraction of 1/(Z*mu), the 1s orbital radius for this atom, or of the nuclear
@@ -337,9 +339,9 @@ double Atom::sphereNuclearModel(int Z, int A) {
  * (default = -1)
  * @retval
  */
-DiracAtom::DiracAtom(int Z, double m, int A, double R, NuclearRadiusModel radius_model,
+DiracAtom::DiracAtom(int Z, double m, int A, double radius, NuclearRadiusModel radius_model,
                      double fc, double dx, int ideal_minshell)
-  : Atom(Z, m, A, R, radius_model, fc, dx) {
+  : Atom(Z, m, A, radius, radius_model, fc, dx) {
   restE = mu * pow(Physical::c, 2);
   LOG(DEBUG) << "Rest energy = " << restE / Physical::eV << " eV\n";
   idshell = ideal_minshell;
@@ -1047,7 +1049,7 @@ TransitionMatrix DiracAtom::getTransitionProbabilities(int n1, int l1, bool s1,
   return tmat;
 }
 
-DiracIdealAtom::DiracIdealAtom(int Z, double m, int A, double R,
+DiracIdealAtom::DiracIdealAtom(int Z, double m, int A, double radius,
                                NuclearRadiusModel radius_model, double fc,
                                double dx)
-  : DiracAtom(Z, m, A, R, radius_model, fc, dx, 1) {}
+  : DiracAtom(Z, m, A, radius, radius_model, fc, dx, 1) {}

lib/atom.hpp

@@ -188,7 +188,7 @@ class DiracAtom : public Atom {
   double in_eps = 1e-5;
   int min_n = 1000;
 
-  DiracAtom(int Z = 1, double m = 1, int A = -1, double R = -1,
+  DiracAtom(int Z = 1, double m = 1, int A = -1, double radius = -1,
             NuclearRadiusModel radius_model = POINT, double fc = 1.0,
             double dx = 0.005, int ideal_minshell = -1);
 
@@ -221,7 +221,7 @@ class DiracAtom : public Atom {
 // the analytical hydrogen-like solution
 class DiracIdealAtom : public DiracAtom {
  public:
-  DiracIdealAtom(int Z = 1, double m = 1, int A = -1, double R = -1,
+  DiracIdealAtom(int Z = 1, double m = 1, int A = -1, double radius = -1,
                  NuclearRadiusModel radius_model = POINT, double fc = 1.0,
                  double dx = 0.005);
 };

lib/config.cpp

@@ -78,7 +78,7 @@ MuDiracInputFile::MuDiracInputFile() : InputFile() {
 DiracAtom MuDiracInputFile::makeAtom() {
   // Now extract the relevant parameters
   int Z = getElementZ(this->getStringValue("element"));
-  double R = this->getDoubleValue("radius");
+  double radius = this->getDoubleValue("radius");
   double t = this->getDoubleValue("tFermi");
   double m = this->getDoubleValue("mass");
   int A = this->getIntValue("isotope");
@@ -103,7 +103,7 @@ DiracAtom MuDiracInputFile::makeAtom() {
 
   // Prepare the DiracAtom
   DiracAtom da;
-  da = DiracAtom(Z, m, A, R, nucmodel, fc, dx, idshell);
+  da = DiracAtom(Z, m, A, radius, nucmodel, fc, dx, idshell);
   da.Etol = this->getDoubleValue("energy_tol");
   da.Edamp = this->getDoubleValue("energy_damp");
   da.max_dE_ratio = this->getDoubleValue("max_dE_ratio");