[WIP] TsLess cavity, take 3

.gitattributes

@@ -41,6 +41,10 @@ src/pedra/*.F90             licensefile=.githooks/LICENSE-Fortran
 src/pedra/*.f90             licensefile=.githooks/LICENSE-Fortran
 src/pedra/pedra_dlapack.f90 !licensefile
 
+# tsless
+src/tsless/*.F90             licensefile=.githooks/LICENSE-Fortran
+src/tsless/*.f90             licensefile=.githooks/LICENSE-Fortran
+
 # solver
 src/solver/*.hpp licensefile=.githooks/LICENSE-C++
 src/solver/*.cpp licensefile=.githooks/LICENSE-C++
@@ -69,6 +73,7 @@ tests/iefpcm/*.cpp               licensefile=.githooks/LICENSE-C++
 tests/input/*.cpp                licensefile=.githooks/LICENSE-C++
 tests/numerical_quadrature/*.cpp licensefile=.githooks/LICENSE-C++
 tests/utils/*.cpp                licensefile=.githooks/LICENSE-C++
+tests/tsless/*.cpp               licensefile=.githooks/LICENSE-C++
 
 # tools
 doc/conf.py               licensefile=.githooks/LICENSE-Python

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### Added
 
+- A new cavity generator using C. S. Pomelli's [TsLess algorithm](http://dx.doi.org/10.1002/jcc.20076)
 - Green’s function for a spherical nanoparticle with **real** permittivity.
   The Green's function is known in analytical form from the work of
   Messina (J. Chem. Phys. 2002, 117 (24), 11062) and

Pipfile

@@ -7,14 +7,15 @@ name = "pypi"
 
 [packages]
 
+PyYAML = "*"
 Pygments = "*"
+Sphinx = "*"
 breathe = "*"
 docopt = "*"
+fprettify = "*"
 matplotlib = "*"
 pyparsing = "*"
-PyYAML = "*"
 recommonmark = "*"
-Sphinx = "*"
 sphinx_rtd_theme = "*"
 sphinxcontrib-bibtex = "*"
 yapf = "*"

default.nix

@@ -3,8 +3,8 @@ let
   nixpkgs = (hostPkgs.fetchFromGitHub {
     owner = "NixOS";
     repo = "nixpkgs-channels";
-    rev = "nixos-unstable";
-    sha256 = "0im8l87nghsp4z7swidgg2qpx9mxidnc0zs7a86qvw8jh7b6sbv2";
+    rev = "nixos-18.03";
+    sha256 = "1qiihxa2qdrij735rglfrx24nhn72kby44lkm1dxph395qy8fg1h";
   });
 in
   with import nixpkgs {

requirements.txt

@@ -1,6 +1,7 @@
 Pygments
 breathe
 docopt
+fprettify
 matplotlib
 pyparsing
 pyyaml

src/CMakeLists.txt

@@ -8,26 +8,28 @@ include_directories(
   SYSTEM ${CMAKE_CURRENT_LIST_DIR}/utils/getkw
   )
 
+add_subdirectory(bi_operators)
 add_subdirectory(cavity)
 add_subdirectory(green)
 add_subdirectory(interface)
 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>
     $<$<BOOL:${ENABLE_Fortran_API}>:$<TARGET_OBJECTS:fortran_bindings>>
+    $<TARGET_OBJECTS:bi_operators>
+    $<TARGET_OBJECTS:cavity>
+    $<TARGET_OBJECTS:getkw>
     $<TARGET_OBJECTS:green>
     $<TARGET_OBJECTS:interface>
     $<TARGET_OBJECTS:metal>
-    $<TARGET_OBJECTS:bi_operators>
     $<TARGET_OBJECTS:pedra>
     $<TARGET_OBJECTS:solver>
+    $<TARGET_OBJECTS:tsless>
     $<TARGET_OBJECTS:utils>
-    $<TARGET_OBJECTS:getkw>
     )
 
 if(NOT STATIC_LIBRARY_ONLY)

src/cavity/CMakeLists.txt

@@ -6,6 +6,7 @@ Element.hpp
 GePolCavity.hpp
 ICavity.hpp
 RestartCavity.hpp
+TsLessCavity.hpp
 )
 
 # List of sources
@@ -14,6 +15,7 @@ Element.cpp
 GePolCavity.cpp
 ICavity.cpp
 RestartCavity.cpp
+TsLessCavity.cpp
 )
 
 add_library(cavity OBJECT ${sources_list} ${headers_list})

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/CavityData.hpp

@@ -42,6 +42,12 @@ 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;
@@ -52,12 +58,16 @@ 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) {}
 };