Fix generation of faulty static library

This commit fixes issues #34, #35 and #36 (on GitHub)
and #60, #61 and #62 (on GitLab)
The fix consisted in subscribing **all** subclasses to the factory in
a top-level convenience header that gets included into the `Meddle.cpp`
file.
Namespaces have finally been introduced into the project and some core
abstract base classes have been renamed to signal their ABC status.
Please see the [change log](CHANGELOG.md) for detailed information.

Author: robertodr

.clang-format

@@ -12,8 +12,8 @@ AllowShortLoopsOnASingleLine: false
 AlwaysBreakAfterDefinitionReturnType: false
 AlwaysBreakBeforeMultilineStrings: false
 AlwaysBreakTemplateDeclarations: false
-BinPackArguments: true
-BinPackParameters: true
+BinPackArguments: false
+BinPackParameters: false
 BreakBeforeBinaryOperators: None
 BreakBeforeBraces: Attach
 BreakBeforeTernaryOperators: true

.gitattributes

@@ -4,7 +4,7 @@
 
 # API files
 api/*.h   licensefile=.githooks/LICENSE-C
-api/*.F90 licensefile=.githooks/LICENSE-Fortran
+api/*.f90 licensefile=.githooks/LICENSE-Fortran
 
 # include directory
 include/*.hpp         licensefile=.githooks/LICENSE-C++

.magnum.yml

@@ -17,7 +17,7 @@ before_install:
   - gfortran --version
   - python --version
 script:
-  - python setup.py --cxx=g++ --cc=gcc --fc=gfortran --type=debug --cmake-options='-Hprojects/CMake'
+  - python setup.py --cxx=g++ --cc=gcc --fc=gfortran --type=debug --static --cmake-options='-Hprojects/CMake'
   - cd build
   - cmake --build . -- --jobs=2 VERBOSE=1
   - ctest --parallel 2 --output-on-failure --verbose --dashboard Experimental --track MagnumCI

.travis.yml

@@ -69,6 +69,7 @@ matrix:
         - C_COMPILER='clang-3.6'
         - Fortran_COMPILER='gfortran'
         - BUILD_TYPE='release'
+        - STATIC='--static'
     - os: osx
       osx_image: xcode7.3
       compiler: gcc
@@ -108,6 +109,7 @@ matrix:
         - Fortran_COMPILER='gfortran-4.9'
         - BUILD_TYPE='release'
         - HOMEBREW_GCC='homebrew/versions/gcc49'
+        - STATIC='--static'
     - os: linux
       compiler: clang
       addons: &4
@@ -189,6 +191,7 @@ matrix:
         - C_COMPILER='gcc-4.7'
         - Fortran_COMPILER='gfortran-4.7'
         - BUILD_TYPE='release'
+        - STATIC='--static'
     - os: osx
       osx_image: xcode7.3
       compiler: gcc
@@ -198,6 +201,7 @@ matrix:
         - Fortran_COMPILER='gfortran-5'
         - BUILD_TYPE='release'
         - HOMEBREW_GCC='homebrew/versions/gcc5'
+        - STATIC='--static'
     - os: linux
       compiler: gcc
       addons: &7
@@ -287,7 +291,7 @@ matrix:
         - C_COMPILER='gcc-5'
         - Fortran_COMPILER='gfortran-5'
         - BUILD_TYPE='release'
-        - COVERAGE=true
+        - COVERAGE='--coverage'
   allow_failures:
     - os: linux
       compiler: gcc
@@ -297,7 +301,7 @@ matrix:
         - C_COMPILER='gcc-5'
         - Fortran_COMPILER='gfortran-5'
         - BUILD_TYPE='release'
-        - COVERAGE=true
+        - COVERAGE='--coverage'
 install:
 - |
   if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
@@ -316,12 +320,7 @@ before_script:
 - export FC=${Fortran_COMPILER}
 - ${Fortran_COMPILER} --version
 - python --version
-- |
-  if [[ "${COVERAGE}" = true ]]; then
-    python setup.py --cxx=${CXX_COMPILER} --cc=${C_COMPILER} --fc=${Fortran_COMPILER} --type=${BUILD_TYPE} --cmake-options='-Hprojects/CMake' --coverage
-  else
-    python setup.py --cxx=${CXX_COMPILER} --cc=${C_COMPILER} --fc=${Fortran_COMPILER} --type=${BUILD_TYPE} --cmake-options='-Hprojects/CMake'
-  fi
+- python setup.py --cxx=${CXX_COMPILER} --cc=${C_COMPILER} --fc=${Fortran_COMPILER} --type=${BUILD_TYPE} --cmake-options='-Hprojects/CMake' ${STATIC} ${COVERAGE}
 - cd build
 script:
 - ctest --parallel 2 --output-on-failure --verbose --dashboard Experimental --track TravisCI

CHANGELOG.md

@@ -1,5 +1,61 @@
 # Change Log
 
+## [Unreleased]
+
+### Added
+
+- Namespaces for all of the internal code have been introduced.
+  The top-level namespace is `pcm`. At finer levels the namespaces have the same
+  names as the respective subdirectories. Read the programmers' documentation
+  for further details on the use of namespaces in the project.
+  Related to issue #34 on [GitHub] and #60 on [GitLab].
+- The top-level, convenience header `BoundaryIntegralOperator.hpp` includes all
+  subclasses and utility headers in the `bi_operators` subdirectory.
+  Related to issue #34 on [GitHub] and #60 on [GitLab].
+- The top-level, convenience header `Cavity.hpp` includes all subclasses and
+  utility headers in the `cavity` subdirectory.
+  Related to issue #34 on [GitHub] and #60 on [GitLab].
+- The top-level, convenience header `Green.hpp` includes all subclasses and
+  utility headers in the `green` subdirectory.
+  Related to issue #34 on [GitHub] and #60 on [GitLab].
+- The top-level, convenience header `Solver.hpp` includes all subclasses and
+  utility headers in the `solver` subdirectory.
+  Related to issue #34 on [GitHub] and #60 on [GitLab].
+
+### Changed
+
+- The abstract base class for the boundary integral operator integrators has
+  been renamed `IBoundaryIntegralOperator`.
+  The relevant factory is bootstrapped upon creation of the `Meddle` object,
+  i.e. at library initialization.
+  Related to issue #34 on [GitHub] and #60 on [GitLab].
+- The abstract base class for the cavities has been renamed `ICavity`.
+  The relevant factory is bootstrapped upon creation of the `Meddle` object,
+  i.e. at library initialization.
+  Related to issue #34 on [GitHub] and #60 on [GitLab].
+- The abstract base class for the solvers has been renamed `ISolver`.
+  The relevant factory is bootstrapped upon creation of the `Meddle` object,
+  i.e. at library initialization.
+  Related to issue #34 on [GitHub] and #60 on [GitLab].
+- The `typedef` for numerical differentiation in the Green's function classes
+  has been renamed `Stencil` to avoid name clashes with the `Numerical`
+  boundary integral operator type.
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+- A bug in the selection of the extended diagnostics flags for the GNU C++
+  compiler. These flags are now enabled only for versions >= 5.1.0 and when the
+  C++11 standard is enable. Fixes issue #36 on [GitHub] and #62 on [GitLab].
+- A bug in the initialization of the factory for the cavity classes was fixed.
+  The bug manifested only in the static library `libpcm.a`
+  Fixes issue #34 on [GitHub] and #60 on [GitLab].
+
+### Security
+
 ## [Version 1.1.7] - 2016-12-01
 
 ### Added
@@ -247,3 +303,6 @@
 [Version 1.1.2]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.1...v1.1.3
 [Version 1.1.1]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.0...v1.1.1
 [Version 1.1.0]: https://github.com/PCMSolver/pcmsolver/releases/tag/v1.1.0
+
+[GitHub]: https://github.com/PCMSolver/pcmsolver
+[GitLab]: https://gitlab.com/PCMSolver/pcmsolver

api/PCMInput.h

@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2017 Roberto Di Remigio, Luca Frediani and collaborators.
  *
  * This file is part of PCMSolver.
  *

api/pcmsolver.f90

@@ -1,6 +1,6 @@
 !
 ! PCMSolver, an API for the Polarizable Continuum Model
-! Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
+! Copyright (C) 2017 Roberto Di Remigio, Luca Frediani and collaborators.
 !
 ! This file is part of PCMSolver.
 !

api/pcmsolver.h

@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2017 Roberto Di Remigio, Luca Frediani and collaborators.
  *
  * This file is part of PCMSolver.
  *
@@ -94,7 +94,8 @@ typedef void (*HostWriter)(const char * message);
  *  respectively. Generators map to integers as in table :ref:`symmetry-ops`
  */
 PCMSolver_API pcmsolver_context_t * pcmsolver_new(pcmsolver_reader_t input_reading,
-                                                  int nr_nuclei, double charges[],
+                                                  int nr_nuclei,
+                                                  double charges[],
                                                   double coordinates[],
                                                   int symmetry_info[],
                                                   struct PCMInput * host_input,
@@ -145,7 +146,8 @@ PCMSolver_API void pcmsolver_get_centers(pcmsolver_context_t * context,
  *  \param[in] its index of the finite element
  *  \param[out] center array holding the coordinates of the finite element center
  */
-PCMSolver_API void pcmsolver_get_center(pcmsolver_context_t * context, int its,
+PCMSolver_API void pcmsolver_get_center(pcmsolver_context_t * context,
+                                        int its,
                                         double center[]);
 
 /*! \brief Getter for the areas/weights of the finite elements
@@ -166,7 +168,8 @@ PCMSolver_API void pcmsolver_get_areas(pcmsolver_context_t * context,
  */
 PCMSolver_API void pcmsolver_compute_asc(pcmsolver_context_t * context,
                                          const char * mep_name,
-                                         const char * asc_name, int irrep);
+                                         const char * asc_name,
+                                         int irrep);
 
 /*! \brief Computes response ASC given a MEP and the desired irreducible
  * representation
@@ -181,7 +184,8 @@ PCMSolver_API void pcmsolver_compute_asc(pcmsolver_context_t * context,
  */
 PCMSolver_API void pcmsolver_compute_response_asc(pcmsolver_context_t * context,
                                                   const char * mep_name,
-                                                  const char * asc_name, int irrep);
+                                                  const char * asc_name,
+                                                  int irrep);
 
 /*! \brief Computes the polarization energy
  *  \param[in, out] context the PCM context object
@@ -191,7 +195,9 @@ PCMSolver_API void pcmsolver_compute_response_asc(pcmsolver_context_t * context,
  *  This function calculates the dot product of the given MEP and ASC vectors.
  */
 PCMSolver_API double pcmsolver_compute_polarization_energy(
-    pcmsolver_context_t * context, const char * mep_name, const char * asc_name);
+    pcmsolver_context_t * context,
+    const char * mep_name,
+    const char * asc_name);
 
 /*! \brief Getter for the ASC dipole
  *  \param[in, out] context the PCM context object
@@ -210,7 +216,8 @@ PCMSolver_API double pcmsolver_get_asc_dipole(pcmsolver_context_t * context,
  *  \param[in] name label of the surface function
  */
 PCMSolver_API void pcmsolver_get_surface_function(pcmsolver_context_t * context,
-                                                  int size, double values[],
+                                                  int size,
+                                                  double values[],
                                                   const char * name);
 
 /*! \brief Sets a surface function given data and label
@@ -220,7 +227,8 @@ PCMSolver_API void pcmsolver_get_surface_function(pcmsolver_context_t * context,
  *  \param[in] name label of the surface function
  */
 PCMSolver_API void pcmsolver_set_surface_function(pcmsolver_context_t * context,
-                                                  int size, double values[],
+                                                  int size,
+                                                  double values[],
                                                   const char * name);
 
 /*! \brief Prints surface function contents to host output

cmake/custom/compilers/GNU.CXX.cmake

@@ -15,8 +15,8 @@ if(NOT DEFINED ENV{CXXFLAGS})
 
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_STANDARD_FLAG}")
     set(EXDIAG_CXX_FLAGS -Wsuggest-attribute=pure -Wsuggest-attribute=const -Wsuggest-attribute=noreturn -Wsuggest-final-types -Wsuggest-final-methods -Wsuggest-override -Wuseless-cast -Wunsafe-loop-optimizations)
-    if(CXX_COMPILER_VERSION VERSION_LESS 4.9.0)
-      message(STATUS "Old GNU C++ compiler. Turning off extended diagnostic flags.")
+    if(CXX_COMPILER_VERSION VERSION_LESS 4.9.0 OR NOT ENABLE_CXX11_SUPPORT)
+      message(STATUS "Turning off extended diagnostic flags.")
       set(EXDIAG_CXX_FLAGS)
     endif()
     set(CMAKE_CXX_FLAGS_DEBUG   "-O0 -g3 -DDEBUG -Wall -Wextra -Winit-self -Woverloaded-virtual -Wuninitialized -Wmissing-declarations -Wwrite-strings -Wno-sign-compare")

doc/code-reference/cavities.rst

@@ -10,9 +10,9 @@ implemented through the generic Factory class.
    :scale: 70 %
    :align: center
 
-Cavity
-------
-.. doxygenclass:: Cavity
+ICavity
+-------
+.. doxygenclass:: ICavity
    :project: PCMSolver
    :members:
    :protected-members: