[WIP] Tessellationless integration grid

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Change Log
 
+## [Unreleased]
+
+### Added
+
+- A new cavity generator using the C. S. Pomelli's [TsLess algorithm](http://dx.doi.org/10.1002/jcc.20076)
+
 ## [Version 1.1.11] - 2017-10-25
 
 ### Added
@@ -352,7 +358,6 @@
 ## v1.0.0 - 2014-09-30 [YANKED]
 
 [Unreleased]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.10...HEAD
-[Version 1.1.11]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.10...v1.1.11
 [Version 1.1.10]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.9...v1.1.10
 [Version 1.1.9]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.8...v1.1.9
 [Version 1.1.8]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.7...v1.1.8

include/Citation.hpp

@@ -52,6 +52,7 @@ inline std::string citation_message() {
   rest << "     U. Ekstroem        (automatic differentiation library)" << std::endl;
   rest << "     J. Juselius        (input parsing library and CMake framework)"
        << std::endl;
+  rest << "     C. S. Pomelli      (TsLess cavity library)" << std::endl;
   rest << "   Theory: - J. Tomasi, B. Mennucci and R. Cammi:" << std::endl;
   rest << "            \"Quantum Mechanical Continuum Solvation Models\", Chem. "
           "Rev., 105 (2005) 2999"

src/CMakeLists.txt

@@ -10,6 +10,7 @@ add_subdirectory(metal)
 add_subdirectory(bi_operators)
 add_subdirectory(pedra)
 add_subdirectory(solver)
+add_subdirectory(tsless)
 add_subdirectory(utils)
 
 list(APPEND _objects $<TARGET_OBJECTS:cavity>
@@ -19,6 +20,7 @@ list(APPEND _objects $<TARGET_OBJECTS:cavity>
                      $<TARGET_OBJECTS:bi_operators>
                      $<TARGET_OBJECTS:pedra>
                      $<TARGET_OBJECTS:solver>
+                     $<TARGET_OBJECTS:tsless>
                      $<TARGET_OBJECTS:utils>
                      $<TARGET_OBJECTS:getkw>
     )

src/cavity/CMakeLists.txt

@@ -1,8 +1,8 @@
 # List of headers
-list(APPEND headers_list Cavity.hpp ICavity.hpp CavityData.hpp Element.hpp GePolCavity.hpp RestartCavity.hpp)
+list(APPEND headers_list Cavity.hpp ICavity.hpp CavityData.hpp Element.hpp GePolCavity.hpp RestartCavity.hpp TsLessCavity.hpp)
 
 # List of sources
-list(APPEND sources_list ICavity.cpp Element.cpp GePolCavity.cpp RestartCavity.cpp)
+list(APPEND sources_list ICavity.cpp Element.cpp GePolCavity.cpp RestartCavity.cpp TsLessCavity.cpp)
 
 add_library(cavity OBJECT ${sources_list} ${headers_list})
 set_target_properties(cavity PROPERTIES POSITION_INDEPENDENT_CODE 1 )

src/cavity/Cavity.hpp

@@ -28,6 +28,7 @@
 #include "GePolCavity.hpp"
 #include "ICavity.hpp"
 #include "RestartCavity.hpp"
+#include "TsLessCavity.hpp"
 #include "utils/Factory.hpp"
 
 /*!
@@ -51,6 +52,7 @@ inline Factory<detail::CreateCavity> bootstrapFactory() {
 
   factory_.subscribe("GEPOL", createGePolCavity);
   factory_.subscribe("RESTART", createRestartCavity);
+  factory_.subscribe("TSLESS", createTsLessCavity);
 
   return factory_;
 }

src/cavity/GePolCavity.cpp

@@ -81,12 +81,9 @@ void GePolCavity::build(const std::string & suffix,
                         int maxsph,
                         int maxvert) {
 
-  // This is a wrapper for the generatecavity_cpp function defined in the Fortran
-  // code PEDRA.
-  // Here we allocate the necessary arrays to be passed to PEDRA, in particular we
-  // allow
-  // for the insertion of additional spheres as in the most general formulation of
-  // the
+  // This is a wrapper for the generatecavity_cpp function defined in the Fortran code PEDRA.
+  // Here we allocate the necessary arrays to be passed to PEDRA, in particular we allow
+  // for the insertion of additional spheres as in the most general formulation of the
   // GePol algorithm.
 
   double * xtscor = new double[maxts];
@@ -173,7 +170,7 @@ void GePolCavity::build(const std::string & suffix,
   int len_f_pedra = std::strlen(pedra.str().c_str());
   // Go PEDRA, Go!
   TIMER_ON("GePolCavity::generatecavity_cpp");
-  generatecavity_cpp(&maxts,
+  pedra_driver(&maxts,
                      &maxsph,
                      &maxvert,
                      xtscor,
@@ -416,7 +413,7 @@ std::ostream & GePolCavity::printCavity(std::ostream & os) {
     os << boost::format("      %s") % "Du";
     os << boost::format("%9.4f") % (sphereRadius_(idx) * bohrToAngstrom());
     os << boost::format("   %1.2f   ") % 1.00;
-    os << boost::format("%10.6f  ") % (sphereCenter_(0, idx) * bohrToAngstrom());
+    os << boost::format("%10.6f  ")  % (sphereCenter_(0, idx) * bohrToAngstrom());
     os << boost::format(" %10.6f  ") % (sphereCenter_(1, idx) * bohrToAngstrom());
     os << boost::format(" %10.6f  ") % (sphereCenter_(2, idx) * bohrToAngstrom());
     os << std::endl;

src/cavity/GePolCavity.hpp

@@ -28,6 +28,7 @@
 #include <vector>
 
 #include "Config.hpp"
+#include "FCMangle.hpp"
 
 namespace pcm {
 struct CavityData;
@@ -94,18 +95,7 @@ class GePolCavity __final : public ICavity {
   void writeOFF(const std::string & suffix);
 };
 
-/*! \fn extern "C" void generatecavity_cpp(int * maxts, int * maxsph, int * maxvert,
- *                                 double * xtscor, double * ytscor, double * ztscor,
- * double * ar,
- *                                 double * xsphcor, double * ysphcor, double *
- * zsphcor, double * rsph,
- *                                 int * nts, int * ntsirr, int * nesfp, int *
- * addsph,
- *                                 double * xe, double * ye, double * ze, double *
- * rin,
- *                                 double * avgArea, double * rsolv, double * ret,
- *                                 int * nr_gen, int * gen1, int * gen2, int * gen3,
- *                                 int * nvert, double * vert, double * centr)
+/*! \brief Interface to the Fortran PEDRA code
  *  \param[in] maxts maximum number of tesserae allowed
  *  \param[in] maxsph maximum number of spheres allowed
  *  \param[in] maxvert maximum number of vertices allowed
@@ -144,39 +134,40 @@ class GePolCavity __final : public ICavity {
  *  \param[out] vert coordinates of tesserae vertices
  *  \param[out] centr centers of arcs defining the edges of the tesserae
  */
-extern "C" void generatecavity_cpp(int * maxts,
-                                   int * maxsph,
-                                   int * maxvert,
-                                   double * xtscor,
-                                   double * ytscor,
-                                   double * ztscor,
-                                   double * ar,
-                                   double * xsphcor,
-                                   double * ysphcor,
-                                   double * zsphcor,
-                                   double * rsph,
-                                   int * nts,
-                                   int * ntsirr,
-                                   int * nesfp,
-                                   int * addsph,
-                                   double * xe,
-                                   double * ye,
-                                   double * ze,
-                                   double * rin,
-                                   double * masses,
-                                   double * avgArea,
-                                   double * rsolv,
-                                   double * ret,
-                                   int * nr_gen,
-                                   int * gen1,
-                                   int * gen2,
-                                   int * gen3,
-                                   int * nvert,
-                                   double * vert,
-                                   double * centr,
-                                   int * isphe,
-                                   const char * pedra,
-                                   int * len_f_pedra);
+#define pedra_driver FortranCInterface_GLOBAL_(pedra_driver, PEDRA_DRIVER)
+extern "C" void pedra_driver(int * maxts,
+                             int * maxsph,
+                             int * maxvert,
+                             double * xtscor,
+                             double * ytscor,
+                             double * ztscor,
+                             double * ar,
+                             double * xsphcor,
+                             double * ysphcor,
+                             double * zsphcor,
+                             double * rsph,
+                             int * nts,
+                             int * ntsirr,
+                             int * nesfp,
+                             int * addsph,
+                             double * xe,
+                             double * ye,
+                             double * ze,
+                             double * rin,
+                             double * masses,
+                             double * avgArea,
+                             double * rsolv,
+                             double * ret,
+                             int * nr_gen,
+                             int * gen1,
+                             int * gen2,
+                             int * gen3,
+                             int * nvert,
+                             double * vert,
+                             double * centr,
+                             int * isphe,
+                             const char * pedra,
+                             int * len_f_pedra);
 
 ICavity * createGePolCavity(const CavityData & data);
 } // namespace cavity