Remove code duplication

Author: robertodr

Pipfile

@@ -7,18 +7,18 @@ name = "pypi"
 
 [packages]
 
+docopt = "*"
+pyparsing = "*"
+
+[dev-packages]
+
 Pygments = "*"
 breathe = "*"
-docopt = "*"
 matplotlib = "*"
-pyparsing = "*"
 PyYAML = "*"
 recommonmark = "*"
 Sphinx = "*"
 sphinx_rtd_theme = "*"
 sphinxcontrib-bibtex = "*"
 yapf = "*"
 fprettify = "*"
-
-[dev-packages]
-

Pipfile.lock

@@ -547,10 +547,9 @@ void Meddle::GaussCheck() const {
   Eigen::VectorXd nuclear_mep = computeMEP(input_.molecule(), cavity_->elements());
   Eigen::VectorXd nuclear_asc = K_0_->computeCharge(nuclear_mep);
   double total_nuclear_asc = nuclear_asc.sum() * cavity_->pointGroup().nrIrrep();
-  double gauss_nuclear_asc =
-      detail::GaussEstimate(input_.molecule().charges(),
-                            input_.outsideStaticGreenParams().epsilon,
-                            input_.correction());
+  double gauss_nuclear_asc = GaussEstimate(input_.molecule().charges(),
+                                           input_.outsideStaticGreenParams().epsilon,
+                                           input_.correction());
   double difference = total_nuclear_asc - gauss_nuclear_asc;
   std::stringstream tmp;
   if (!utils::isZero(difference, 1.0e-2)) {
@@ -651,11 +650,5 @@ void print(const PCMInput & inp) {
   std::cout << "outside type " << std::string(inp.outside_type) << std::endl;
   std::cout << "epsilon outside " << inp.outside_epsilon << std::endl;
 }
-
-double GaussEstimate(const Eigen::VectorXd & charges,
-                     double permittivity,
-                     double correction) {
-  return (-charges.sum() * (permittivity - 1) / (permittivity + correction));
-}
 } // namespace detail
 } // namespace pcm

src/interface/Meddle.cpp

@@ -62,15 +62,6 @@ void initSpheresAtoms(const Input &,
                       const Eigen::Matrix3Xd &,
                       std::vector<Sphere> &);
 void print(const PCMInput &);
-
-/*! Gauss' theorem estimate of the total ASC for a set of point charges
- * \param[in] charges Vector of point charges
- * \param[in] permittivity Solvent permittivity
- * \param[in] correction The CPCM correction factor
- */
-double GaussEstimate(const Eigen::VectorXd & charges,
-                     double permittivity,
-                     double correction = 0.0);
 } // namespace detail
 
 /*! \class Meddle

src/interface/Meddle.hpp

@@ -302,4 +302,10 @@ Eigen::VectorXd computeMEP(const std::vector<Element> & el,
   }
   return mep;
 }
+
+double GaussEstimate(const Eigen::VectorXd & charges,
+                     double permittivity,
+                     double correction) {
+  return (-charges.sum() * (permittivity - 1) / (permittivity + correction));
+}
 } // namespace pcm

src/utils/Molecule.cpp

@@ -240,4 +240,13 @@ PCMSolver_EXPORT Eigen::VectorXd computeMEP(const Molecule & mol,
 Eigen::VectorXd computeMEP(const std::vector<cavity::Element> & el,
                            double charge = 1.0,
                            const Eigen::Vector3d & origin = Eigen::Vector3d::Zero());
+
+/*! Gauss' theorem estimate of the total ASC for a set of point charges
+ * \param[in] charges Vector of point charges
+ * \param[in] permittivity Solvent permittivity
+ * \param[in] correction The CPCM correction factor
+ */
+PCMSolver_EXPORT double GaussEstimate(const Eigen::VectorXd & charges,
+                                      double permittivity,
+                                      double correction = 0.0);
 } // namespace pcm

src/utils/Molecule.hpp

@@ -73,15 +73,6 @@ inline Molecule C6H6();
  */
 inline Molecule H2O();
 
-/*! Returns the Gauss' theorem estimate of the total ASC
- * \param[in] charges Vector of molecular charges
- * \param[in] permittivity Solvent permittivity
- * \param[in] correction The CPCM correction factor
- */
-inline double Gauss_ASC(const Eigen::VectorXd & charges,
-                        double permittivity,
-                        double correction = 0.0);
-
 template <int group> Molecule dummy(double radius, const Eigen::Vector3d & center) {
   std::vector<Sphere> spheres;
   Sphere sph1(center, radius);
@@ -546,12 +537,6 @@ Molecule H2O() {
 
   return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
 };
-
-double Gauss_ASC(const Eigen::VectorXd & charges,
-                 double permittivity,
-                 double correction) {
-  return (-charges.sum() * (permittivity - 1) / (permittivity + correction));
-}
 } // namespace pcm
 
 #endif // TESTINGMOLECULES_HPP

tests/TestingMolecules.hpp

@@ -71,7 +71,7 @@ TEST_CASE("Test solver for the C-PCM with H2O molecule and a GePol cavity",
   // for CPCM it will be -Q*(epsilon-1)/(epsilon + correction)
   Eigen::VectorXd fake_asc = Eigen::VectorXd::Zero(size);
   fake_asc = solver.computeCharge(fake_mep);
-  double totalASC = Gauss_ASC(molecule.charges(), permittivity, correction);
+  double totalASC = GaussEstimate(molecule.charges(), permittivity, correction);
   double totalFakeASC = fake_asc.sum();
   CAPTURE(totalASC - totalFakeASC);
   REQUIRE(totalASC == Approx(totalFakeASC).epsilon(1.0e-03));