Move one header file from utils directory

Author: Roberto Di Remigio

include/CMakeLists.txt

@@ -1,4 +1,11 @@
-list(APPEND headers_list Citation.hpp Cxx11Workarounds.hpp ErrorHandling.hpp LoggerInterface.hpp TimerInterface.hpp)
+list(APPEND headers_list Citation.hpp
+                         Cxx11Workarounds.hpp
+                         ErrorHandling.hpp
+                         LoggerInterface.hpp
+                         PhysicalConstants.hpp
+                         STLUtils.hpp
+                         TimerInterface.hpp
+                         )
 
 # Sets install directory for all the headers in the list
 foreach(_header ${headers_list})

src/utils/GeneralPurpose.hpp renamed to include/STLUtils.hpp

@@ -70,20 +70,4 @@ inline void PRINT_MAPPED_ELEMENTS (const T& coll,
     std::cout << std::endl;
 }
 
-template <typename Derived>
-inline void print_eigen_matrix(const Eigen::MatrixBase<Derived> & matrix, const std::string & fname)
-{
-    std::ofstream fout;
-    fout.open(fname.c_str());
-    fout << " Row index " << '\t' << " Column index " << '\t' << " Matrix entry " << std::endl;
-    int rows = matrix.rows();
-    int cols = matrix.cols();
-    for (int i = 0; i < rows; ++i) {
-        for (int j = 0; j < cols; ++j) {
-            fout << i << '\t' << j << '\t' << matrix(i, j) << std::endl;
-        }
-    }
-    fout.close();
-}
-
 #endif /*GENERALPURPOSE_HPP*/

src/bin/plot_green_spherical.cpp

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013-2015 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
+ *
  *     PCMSolver is free software: you can redistribute it and/or modify
  *     it under the terms of the GNU Lesser General Public License as published by
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
- *     
+ *
  *     PCMSolver is distributed in the hope that it will be useful,
  *     but WITHOUT ANY WARRANTY; without even the implied warranty of
  *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *     GNU Lesser General Public License for more details.
- *     
+ *
  *     You should have received a copy of the GNU Lesser General Public License
  *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
+ *
  *     For information on the complete list of contributors to the
  *     PCMSolver API, see: <http://pcmsolver.readthedocs.org/>
  */
@@ -33,7 +33,7 @@
 
 #include "CollocationIntegrator.hpp"
 #include "DerivativeTypes.hpp"
-#include "GeneralPurpose.hpp"
+#include "STLUtils.hpp"
 #include "OneLayerTanh.hpp"
 #include "SphericalDiffuse.hpp"
 #include "UniformDielectric.hpp"

src/utils/MathUtils.hpp

@@ -294,6 +294,31 @@ inline double splineInterpolation(const double point, const std::vector<double>
     return s(point);
 }
 
+/*! \brief Prints Eigen object (matrix or vector) to file
+ *  \param[in] matrix Eigen object
+ *  \param[in] fname  name of the file
+ *  \tparam Derived template parameters of the MatrixBase object
+ *
+ *  \note This is for debugging only, the format is in fact rather ugly.
+ *      Row index     Column index      Matrix entry
+ *         0               0              0.0000
+ */
+template <typename Derived>
+inline void print_eigen_matrix(const Eigen::MatrixBase<Derived> & matrix, const std::string & fname)
+{
+  std::ofstream fout;
+  fout.open(fname.c_str());
+  fout << " Row index " << '\t' << " Column index " << '\t' << " Matrix entry " << std::endl;
+  int rows = matrix.rows();
+  int cols = matrix.cols();
+  for (int i = 0; i < rows; ++i) {
+    for (int j = 0; j < cols; ++j) {
+      fout << i << '\t' << j << '\t' << matrix(i, j) << std::endl;
+    }
+  }
+  fout.close();
+}
+
 namespace cnpy
 {
   /*!