Add TsLess sources

Author: robertodr

CHANGELOG.md

@@ -2,13 +2,15 @@
 
 ## [Unreleased]
 
-## [Version 2.0.0-alpha1] - 2019-04-XY
-
 We have introduced a number of breaking changes, motivated by the need to
 modernize the library.
 
 - The version 1 release series is available in the archived repository [PCMSolver/pcmsolver_v1]
 
+### Added
+
+- A new cavity generator using C. S. Pomelli's [TsLess algorithm](http://dx.doi.org/10.1002/jcc.20076)
+
 ### Changed
 
 - **BREAKING** We require a fully compliant C++14 compiler.

src/CMakeLists.txt

@@ -65,6 +65,7 @@ add_subdirectory(interface)
 add_subdirectory(pedra)
 add_subdirectory(solver)
 add_subdirectory(utils)
+add_subdirectory(tsless)
 
 add_library(pcm $<TARGET_OBJECTS:pcm-object>)
 

src/cavity/CMakeLists.txt

@@ -4,6 +4,7 @@ target_sources(pcm-object
     ${CMAKE_CURRENT_LIST_DIR}/GePolCavity.cpp
     ${CMAKE_CURRENT_LIST_DIR}/ICavity.cpp
     ${CMAKE_CURRENT_LIST_DIR}/RestartCavity.cpp
+    ${CMAKE_CURRENT_LIST_DIR}/TsLessCavity.cpp
   )
 
 # List of headers
@@ -14,6 +15,7 @@ list(APPEND headers_list
   GePolCavity.hpp
   ICavity.hpp
   RestartCavity.hpp
+  TsLessCavity.hpp
   )
 # Sets install directory for all the headers in the list
 foreach(_header IN LISTS headers_list)

src/cavity/Cavity.hpp

@@ -26,6 +26,7 @@
 #include "GePolCavity.hpp"
 #include "ICavity.hpp"
 #include "RestartCavity.hpp"
+#include "TsLessCavity.hpp"
 #include "utils/Factory.hpp"
 
 /*!
@@ -49,6 +50,7 @@ inline Factory<detail::CreateCavity> bootstrapFactory() {
 
   factory_.subscribe("GEPOL", createGePolCavity);
   factory_.subscribe("RESTART", createRestartCavity);
+  factory_.subscribe("TSLESS", createTsLessCavity);
 
   return factory_;
 }

src/cavity/CavityData.hpp

@@ -40,6 +40,12 @@ struct CavityData {
   double area;
   /*! The radius of the spherical probe representing the solvent */
   double probeRadius;
+  /*! The minimal distance between two sampling points on different spheres. Relevant
+   * for TsLessCavity */
+  double minDistance;
+  /*! The maximum derivative order to be used in the definition of the smoothing
+   * function. Relevant for TsLessCavity */
+  int derOrder;
   /*! Triggers the addition of spheres not centered on atoms, relevant for
    * GePolCavity */
   double minimalRadius;
@@ -50,12 +56,16 @@ struct CavityData {
              const Molecule & _molec,
              double _area,
              double _probeRadius,
+             double _minDistance,
+             int _derOrder,
              double _minRadius,
              const std::string & _fname)
       : cavityType(type),
         molecule(_molec),
         area(_area),
         probeRadius(_probeRadius),
+        minDistance(_minDistance),
+        derOrder(_derOrder),
         minimalRadius(_minRadius),
         filename(_fname) {}
 };

src/cavity/GePolCavity.cpp

@@ -81,7 +81,7 @@ void GePolCavity::build(const std::string & suffix,
                         int maxsph,
                         int maxvert) {
 
-  // This is a wrapper for the generatecavity_cpp function defined in the Fortran
+  // This is a wrapper for the pedra_driver function defined in the Fortran
   // code PEDRA.
   // Here we allocate the necessary arrays to be passed to PEDRA, in particular we
   // allow
@@ -172,41 +172,41 @@ void GePolCavity::build(const std::string & suffix,
   pedra << "PEDRA.OUT_" << suffix << "_" << getpid();
   int len_f_pedra = std::strlen(pedra.str().c_str());
   // Go PEDRA, Go!
-  timer::timerON("GePolCavity::generatecavity_cpp");
-  generatecavity_cpp(&maxts,
-                     &maxsph,
-                     &maxvert,
-                     xtscor,
-                     ytscor,
-                     ztscor,
-                     ar,
-                     xsphcor,
-                     ysphcor,
-                     zsphcor,
-                     rsph,
-                     &nts,
-                     &ntsirr,
-                     &nSpheres_,
-                     &addedSpheres,
-                     xe,
-                     ye,
-                     ze,
-                     rin,
-                     mass,
-                     &averageArea,
-                     &probeRadius,
-                     &minimalRadius,
-                     &nr_gen,
-                     &gen1,
-                     &gen2,
-                     &gen3,
-                     nvert,
-                     vert,
-                     centr,
-                     isphe,
-                     pedra.str().c_str(),
-                     &len_f_pedra);
-  timer::timerOFF("GePolCavity::generatecavity_cpp");
+  timer::timerON("GePolCavity::pedra_driver");
+  pedra_driver(&maxts,
+               &maxsph,
+               &maxvert,
+               xtscor,
+               ytscor,
+               ztscor,
+               ar,
+               xsphcor,
+               ysphcor,
+               zsphcor,
+               rsph,
+               &nts,
+               &ntsirr,
+               &nSpheres_,
+               &addedSpheres,
+               xe,
+               ye,
+               ze,
+               rin,
+               mass,
+               &averageArea,
+               &probeRadius,
+               &minimalRadius,
+               &nr_gen,
+               &gen1,
+               &gen2,
+               &gen3,
+               nvert,
+               vert,
+               centr,
+               isphe,
+               pedra.str().c_str(),
+               &len_f_pedra);
+  timer::timerOFF("GePolCavity::pedra_driver");
 
   // The "intensive" part of updating the spheres related class data members will be
   // of course

src/cavity/GePolCavity.hpp

@@ -89,18 +89,7 @@ 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
@@ -139,39 +128,39 @@ 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);
+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