A better printer for GePolCavity + address feature request #13.

The printer for GePolCavity can possibly report wrong values for explicitly
specified lists of spheres

Author: Roberto Di Remigio

CHANGELOG.md

@@ -4,17 +4,30 @@
 ### Added
 - A runtime check to ensure that all atoms have a nonzero radius.
 API kills program execution if this is the case.
+- An API function to retrieve the areas/weights of the cavity finite elements.
+The values in the returned array are in Bohr^2.
+Addresses feature request from @shofener (Issue #13)
 
 ### Changed
+- GePolCavity learnt to print also the list of spheres used to generate
+the cavity.
+- Different internal handling of conversion factors from Bohr to Angstrom.
 - CMake minimum required version is 2.8.10
-- Atom is now a POD
+- Atom and Solvent are now PODs. The radii and solvent lists are free functions.
 - `PCMSOLVER_ERROR ` kills program execution when an error arises but does
 not use C++ exceptions.
 - `include`-s are now specified on a per-directory basis (see programmers' manual
 for a more detailed explanation)
 
-## [v1.1.0](https://github.com/PCMSolver/pcmsolver/tree/v1.1.0) (2016-02-07)
-[Full Changelog](https://github.com/PCMSolver/pcmsolver/compare/v1.0.4...v1.1.0)
+### Known Issues
+- The new printer in GePolCavity might not work properly when an explicit list
+of spheres is provided in the input.
+
+### Removed
+- SurfaceFunction as a class is no longer available. We keep track of surface functions
+at the interface level _via_ a label-vector map.
+
+## [v1.1.0] (2016-02-07)
 
 ### Added
 - Green's function for diffuse interfaces in spherical symmetry
@@ -23,19 +36,20 @@ for a more detailed explanation)
 - CMake minimum required version is 2.8.8 (2016-01-08)
 - Documentation is now served [here](http://pcmsolver.readthedocs.org/)
 
-## [v1.0.4](https://github.com/PCMSolver/pcmsolver/tree/v1.0.4) (2015-07-22)
-[Full Changelog](https://github.com/PCMSolver/pcmsolver/compare/v1.0.3...v1.0.4)
-
-## [v1.0.3](https://github.com/PCMSolver/pcmsolver/tree/v1.0.3) (2015-03-29)
-[Full Changelog](https://github.com/PCMSolver/pcmsolver/compare/v1.0.2...v1.0.3)
+## [v1.0.4] (2015-07-22)
 
-## [v1.0.2](https://github.com/PCMSolver/pcmsolver/tree/v1.0.2) (2015-03-28)
-[Full Changelog](https://github.com/PCMSolver/pcmsolver/compare/v1.0.1...v1.0.2)
+## [v1.0.3] (2015-03-29)
 
-## [v1.0.1](https://github.com/PCMSolver/pcmsolver/tree/v1.0.1) (2015-01-06)
-[Full Changelog](https://github.com/PCMSolver/pcmsolver/compare/1.0.0...v1.0.1)
+## [v1.0.2] (2015-03-28)
 
-## [1.0.0](https://github.com/PCMSolver/pcmsolver/tree/1.0.0) (2014-09-30)
+## [v1.0.1] (2015-01-06)
 
+## [1.0.0] (2014-09-30)
 
-\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*
+[Unreleased]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.0...HEAD
+[v1.1.0]: https://github.com/PCMSolver/pcmsolver/compare/v1.0.4...v1.1.0
+[v1.0.4]: https://github.com/PCMSolver/pcmsolver/compare/v1.0.3...v1.0.4
+[v1.0.3]: https://github.com/PCMSolver/pcmsolver/compare/v1.0.2...v1.0.3
+[v1.0.2]: https://github.com/PCMSolver/pcmsolver/compare/v1.0.1...v1.0.2
+[v1.0.1]: https://github.com/PCMSolver/pcmsolver/compare/1.0.0...v1.0.1
+[1.0.0]: https://github.com/PCMSolver/pcmsolver/tree/1.0.0

api/pcmsolver.F90

@@ -1,22 +1,22 @@
 !pcmsolver_copyright_start
 !       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/>
 !pcmsolver_copyright_end
@@ -37,6 +37,7 @@ module pcmsolver
     public pcmsolver_get_irreducible_cavity_size
     public pcmsolver_get_centers
     public pcmsolver_get_center
+    public pcmsolver_get_areas
     public pcmsolver_compute_asc
     public pcmsolver_compute_response_asc
     public pcmsolver_compute_polarization_energy
@@ -142,6 +143,14 @@ subroutine pcmsolver_get_center(context, its, center) bind(C)
         end subroutine pcmsolver_get_center
     end interface pcmsolver_get_center
 
+    interface pcmsolver_get_areas
+        subroutine pcmsolver_get_areas(context, areas) bind(C)
+            import
+            type(c_ptr), value :: context
+            real(c_double), intent(inout) :: areas(*)
+        end subroutine pcmsolver_get_areas
+    end interface pcmsolver_get_areas
+
     interface pcmsolver_compute_asc
         subroutine pcmsolver_compute_asc(context, mep_name, asc_name, irrep) bind(C)
             import

api/pcmsolver.h

@@ -159,6 +159,12 @@ PCMSOLVER_API void pcmsolver_get_centers(pcmsolver_context_t * context, double c
  */
 PCMSOLVER_API void pcmsolver_get_center(pcmsolver_context_t * context, int its, double center[]);
 
+/*! \brief Getter for the areas/weights of the finite elements
+ *  \param[in, out] context the PCM context object
+ *  \param[out] areas array holding the weights/areas of the finite elements
+ */
+PCMSOLVER_API void pcmsolver_get_areas(pcmsolver_context_t * context, double areas[]);
+
 /*! \brief Computes ASC given a MEP and the desired irreducible representation
  *  \param[in, out] context the PCM context object
  *  \param[in] mep_name label of the MEP surface function