Add a Getkw data member in Input class. Include only those headers from Eigen that are actually used

Author: Roberto Di Remigio

src/utils/Atom.cpp

@@ -29,7 +29,7 @@
 
 #include "Config.hpp"
 
-#include <Eigen/Dense>
+#include <Eigen/Core>
 
 std::vector<Atom> & Atom::initBondi()
 {

src/utils/Atom.hpp

@@ -31,7 +31,7 @@
 
 #include "Config.hpp"
 
-#include <Eigen/Dense>
+#include <Eigen/Core>
 
 /*! \file Atom.hpp
  *  \class Atom

src/utils/GreenData.hpp

@@ -30,7 +30,7 @@
 
 #include "Config.hpp"
 
-#include <Eigen/Dense>
+#include <Eigen/Core>
 
 /*! @struct greenData
  *  @brief Contains all data defined from user input in the green section.

src/utils/Input.cpp

@@ -33,7 +33,7 @@
 
 #include "Config.hpp"
 
-#include <Eigen/Dense>
+#include <Eigen/Core>
 #include "Getkw.h"
 
 #include <boost/algorithm/string.hpp>
@@ -49,28 +49,25 @@
 
 using boost::algorithm::to_upper_copy;
 
-Input::Input(const std::string & filename)
+Input::Input(const std::string & filename) : input_(Getkw(filename, false, true))
 {
-    reader(filename.c_str());
+    reader();
     semanticCheck();
 }
 
 Input::Input(const cavityInput & cav, const solverInput & solv,
-             const greenInput & green)
+             const greenInput & green) : input_(Getkw())
 {
     reader(cav, solv, green);
     semanticCheck();
 }
 
-void Input::reader(const char * pythonParsed)
+void Input::reader()
 {
-    // Create a Getkw object from input file.
-    Getkw input = Getkw(pythonParsed, false, true);
+    units_      = input_.getStr("UNITS");
+    CODATAyear_ = input_.getInt("CODATA");
 
-    units_      = input.getStr("UNITS");
-    CODATAyear_ = input.getInt("CODATA");
-
-    const Section & cavity = input.getSect("CAVITY");
+    const Section & cavity = input_.getSect("CAVITY");
 
     type_ = cavity.getStr("TYPE");
     area_ = cavity.getDbl("AREA");
@@ -105,7 +102,7 @@ void Input::reader(const char * pythonParsed)
     }
 
     // Get the contents of the Medium section
-    const Section & medium = input.getSect("MEDIUM");
+    const Section & medium = input_.getSect("MEDIUM");
     // Get the name of the solvent
     std::string name = medium.getStr("SOLVENT");
     if (name == "EXPLICIT" || name == "E") {

src/utils/Input.hpp

@@ -120,9 +120,9 @@ class Input
     friend std::ostream & operator<<(std::ostream &os, const Input &input);
     /// @}
 private:
-    /*! Read Python-parsed input (API-side syntactic input parsing) into Input object
-     */
-    void reader(const char * pythonParsed);
+    /*! Contains all input information (API-side syntactic input parsing) */
+    Getkw input_;
+    void reader();
     /*! Read host data structures (host-side syntactic input parsing) into Input object.
      *  It provides access to a **limited** number of options only, basically the ones
      *  that can be filled into the cavityInput, solverInput and greenInput data structures.
@@ -138,8 +138,7 @@ class Input
      */
     void reader(const cavityInput & cav, const solverInput & solv,
                 const greenInput & green);
-    /*! Perform semantic input parsing aka sanity check
-     */
+    /*! Perform semantic input parsing aka sanity check */
     void semanticCheck();
 
     /// Units of measure

src/utils/MathUtils.hpp

@@ -37,6 +37,7 @@
 #include "Config.hpp"
 
 #include <Eigen/Core>
+#include <Eigen/Geometry>
 
 #include "SplineFunction.hpp"
 #include "Symmetry.hpp"
@@ -306,7 +307,7 @@ inline double splineInterpolation(const double point, const std::vector<double>
     size_t index = std::distance(grid.begin(), std::lower_bound(grid.begin(), grid.end(), point)) - 1;
 
     // Parameters for the interpolating spline
-    Eigen::Vector3d x, y; 
+    Eigen::Vector3d x, y;
     x << grid[index-1], grid[index], grid[index+1];
     y << function[index-1], function[index], function[index+1];
     SplineFunction s(x, y);

src/utils/Molecule.cpp

@@ -33,7 +33,8 @@
 
 #include "Config.hpp"
 
-#include <Eigen/Dense>
+#include <Eigen/Core>
+#include <Eigen/Eigenvalues>
 
 #include "Atom.hpp"
 #include "MathUtils.hpp"

src/utils/Molecule.hpp

@@ -32,7 +32,7 @@
 
 #include "Config.hpp"
 
-#include <Eigen/Dense>
+#include <Eigen/Core>
 
 #include "Atom.hpp"
 #include "Sphere.hpp"

src/utils/Sphere.cpp

@@ -31,7 +31,7 @@
 
 #include "Config.hpp"
 
-#include <Eigen/Dense>
+#include <Eigen/Core>
 
 #include "Exception.hpp"
 

src/utils/Sphere.hpp

@@ -32,7 +32,7 @@
 
 #include "Config.hpp"
 
-#include <Eigen/Dense>
+#include <Eigen/Core>
 
 /*! \file Sphere.hpp
  *  \class Sphere