Update CHANGELOG.md for v1.1.2

Author: Roberto Di Remigio

CHANGELOG.md

@@ -2,47 +2,67 @@
 
 ## [Unreleased]
 
-## [v1.1.1] (2016-04-09)
+## [v1.1.1] (2016-05-31)
+
+### Fixed
+
+- Signatures for strings in Fortran90 bindings. They have now the proper
+  C interoperable type `character(kind=c_char, len=1) :: label(lbl_size)`.
+  For the host this means that surface function labels will have to be declared
+  as character arrays, for example: `character :: label(7) = (/'T', 'o', 't', 'M', 'E', 'P', char(0)/)`
+
+### Changed
+
+- More informative error messages for runtime crashes caused by access to
+  surface functions.
+- The signatures for the interface functions now accept and/or return `int` (`c_int`)
+  instead of `size_t` (`c_size_t`). This simplifies interfacing with Fortran hosts.
+
+## [v1.1.1] (2016-03-10)
 
 ### Added
 
-- A runtime check to ensure that all atoms have a nonzero radius.
-API kills program execution if this is the case.
+- 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 a feature request from @shofener (Issue #13)
-- The standalone executable `run_pcm` is now tested within the unit tests suite.
-The tests cover the cases where the cavity is given implicitly, explicitly or by substitution of
-radii on chosen atoms.
+  The values in the returned array are in Bohr^2. Addresses a feature request
+  from @shofener (Issue #13)
+- The standalone executable `run_pcm` is now tested within the unit tests
+  suite. The tests cover the cases where the cavity is given implicitly,
+  explicitly or by substitution of radii on chosen atoms.
 
 ### Changed
 
-- Boundary integral operators classes learnt to accept a scaling factor for the diagonal
-elements of the approximate collocation matrices. The change is reflected in the
-Green's funtion classes and in the input parsing. Addresses a feature request from @shofener (Issue #16)
-- GePolCavity learnt to print also the list of spheres used to generate
-the cavity.
+- Boundary integral operators classes learnt to accept a scaling factor for the
+  diagonal elements of the approximate collocation matrices. The change is
+  reflected in the Green's funtion classes and in the input parsing. Addresses
+  a feature request from @shofener (Issue #16)
+- 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, Solvent and Sphere 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)
-- Default types for template paramters `DerivativeTraits`,  `IntegratorPolicy` and `ProfilePolicy`
-are now given for the Green's functions classes. This reduced the verbosity in instatiating
-these objects significantly.
+- Atom, Solvent and Sphere 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)
+- Default types for template paramters `DerivativeTraits`,  `IntegratorPolicy`
+  and `ProfilePolicy` are now given for the Green's functions classes. This
+  reduced the verbosity in instatiating these objects significantly.
 
 ### Known Issues
 
 - The new printer in GePolCavity might not work properly when an explicit list
-of spheres is provided in the input.
-- On Ubuntu 12.10, 32 bit the Intel compiler version 2013.1 produces a faulty library.
-It is possibly a bug in the implementation of `iso_c_binding`, see Issue #25
+  of spheres is provided in the input.
+- On Ubuntu 12.10, 32 bit the Intel compiler version 2013.1 produces a faulty
+  library. It is possibly a bug in the implementation of `iso_c_binding`, see
+  Issue #25
 
 ### Removed
 
-- SurfaceFunction as a class is no longer available. We keep track of surface functions
-at the interface level _via_ a label-vector map.
+- 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)
 

api/pcmsolver.F90

@@ -114,15 +114,15 @@ end subroutine pcmsolver_print
         function pcmsolver_get_cavity_size(context) result(nr_points) bind(C)
             import
             type(c_ptr), value :: context
-            integer(c_size_t)  :: nr_points
+            integer(c_int)  :: nr_points
         end function pcmsolver_get_cavity_size
     end interface pcmsolver_get_cavity_size
 
     interface pcmsolver_get_irreducible_cavity_size
         function pcmsolver_get_irreducible_cavity_size(context) result(nr_points_irr) bind(C)
             import
             type(c_ptr), value :: context
-            integer(c_size_t)  :: nr_points_irr
+            integer(c_int)  :: nr_points_irr
         end function pcmsolver_get_irreducible_cavity_size
     end interface pcmsolver_get_irreducible_cavity_size
 
@@ -155,7 +155,7 @@ end subroutine pcmsolver_get_areas
         subroutine pcmsolver_compute_asc(context, mep_name, asc_name, irrep) bind(C)
             import
             type(c_ptr), value :: context
-            character(c_char), intent(in) :: mep_name, asc_name
+            character(kind=c_char, len=1), intent(in) :: mep_name(*), asc_name(*)
             integer(c_int), value, intent(in) :: irrep
         end subroutine pcmsolver_compute_asc
     end interface pcmsolver_compute_asc
@@ -164,7 +164,7 @@ end subroutine pcmsolver_compute_asc
         subroutine pcmsolver_compute_response_asc(context, mep_name, asc_name, irrep) bind(C)
             import
             type(c_ptr), value :: context
-            character(c_char), intent(in) :: mep_name, asc_name
+            character(kind=c_char, len=1), intent(in) :: mep_name(*), asc_name(*)
             integer(c_int), value, intent(in) :: irrep
         end subroutine pcmsolver_compute_response_asc
     end interface pcmsolver_compute_response_asc
@@ -173,7 +173,7 @@ end subroutine pcmsolver_compute_response_asc
         function pcmsolver_compute_polarization_energy(context, mep_name, asc_name) result(energy) bind(C)
             import
             type(c_ptr), value :: context
-            character(c_char), intent(in) :: mep_name, asc_name
+            character(kind=c_char, len=1), intent(in) :: mep_name(*), asc_name(*)
             real(c_double) :: energy
         end function pcmsolver_compute_polarization_energy
     end interface pcmsolver_compute_polarization_energy
@@ -182,19 +182,19 @@ end function pcmsolver_compute_polarization_energy
         subroutine pcmsolver_get_surface_function(context, f_size, values, name) bind(C)
             import
             type(c_ptr), value :: context
-            integer(c_size_t), value, intent(in) :: f_size
+            integer(c_int), value, intent(in) :: f_size
             real(c_double), intent(inout) :: values(*)
-            character(c_char), intent(in) :: name
+            character(kind=c_char, len=1), intent(in) :: name(*)
         end subroutine pcmsolver_get_surface_function
     end interface pcmsolver_get_surface_function
 
     interface pcmsolver_set_surface_function
         subroutine pcmsolver_set_surface_function(context, f_size, values, name) bind(C)
             import
             type(c_ptr), value :: context
-            integer(c_size_t), value, intent(in) :: f_size
+            integer(c_int), value, intent(in) :: f_size
             real(c_double), intent(in) :: values(*)
-            character(c_char), intent(in) :: name
+            character(kind=c_char, len=1), intent(in) :: name(*)
         end subroutine pcmsolver_set_surface_function
     end interface pcmsolver_set_surface_function
 
@@ -209,15 +209,15 @@ end subroutine pcmsolver_save_surface_functions
         subroutine pcmsolver_save_surface_function(context, name) bind(C)
             import
             type(c_ptr), value :: context
-            character(c_char), intent(in) :: name
+            character(kind=c_char, len=1), intent(in) :: name
         end subroutine pcmsolver_save_surface_function
     end interface pcmsolver_save_surface_function
 
     interface pcmsolver_load_surface_function
         subroutine pcmsolver_load_surface_function(context, name) bind(C)
             import
             type(c_ptr), value :: context
-            character(c_char), intent(in) :: name
+            character(kind=c_char, len=1), intent(in) :: name
         end subroutine pcmsolver_load_surface_function
     end interface pcmsolver_load_surface_function
 

api/pcmsolver.h

@@ -95,7 +95,7 @@ typedef enum
  *  \param[in] message_length length of the passed message
  *  This function **must** be defined by the host program
  */
-void host_writer(const char * message, size_t message_length);
+void host_writer(const char * message, int message_length);
 
 /*! \brief Creates a new PCM context object
  *  \param[in] input_reading input processing strategy
@@ -138,13 +138,13 @@ PCMSOLVER_API void pcmsolver_print(pcmsolver_context_t * context);
  *  \param[in, out] context the PCM context object
  *  \return the size of the cavity
  */
-PCMSOLVER_API size_t pcmsolver_get_cavity_size(pcmsolver_context_t * context);
+PCMSOLVER_API int pcmsolver_get_cavity_size(pcmsolver_context_t * context);
 
 /*! \brief Getter for the number of irreducible finite elements composing the molecular cavity
  *  \param[in, out] context the PCM context object
  *  \return the number of irreducible finite elements
  */
-PCMSOLVER_API size_t pcmsolver_get_irreducible_cavity_size(pcmsolver_context_t * context);
+PCMSOLVER_API int pcmsolver_get_irreducible_cavity_size(pcmsolver_context_t * context);
 
 /*! \brief Getter for the centers of the finite elements composing the molecular cavity
  *  \param[in, out] context the PCM context object
@@ -211,7 +211,7 @@ PCMSOLVER_API double pcmsolver_compute_polarization_energy(pcmsolver_context_t *
  *  \param[in] name label of the surface function
  */
 PCMSOLVER_API void pcmsolver_get_surface_function(pcmsolver_context_t * context,
-                                                 size_t size,
+                                                 int size,
                                                  double values[],
                                                  const char * name);
 
@@ -222,7 +222,7 @@ 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,
-                                                 size_t size,
+                                                 int size,
                                                  double values[],
                                                  const char * name);
 

cmake/custom/compilers/Clang.C.cmake

@@ -1,7 +1,7 @@
 if(NOT DEFINED ENV{CFLAGS})
   if(CMAKE_C_COMPILER_ID MATCHES Clang)
     set(CMAKE_C_FLAGS         "${CMAKE_C_FLAGS} -std=c99 -DRESTRICT=restrict -DFUNDERSCORE=1 -Qunused-arguments -fcolor-diagnostics")
-    set(CMAKE_C_FLAGS_DEBUG   "-O0 -DDEBUG -g3 -Wall -Wextra -Winit-self -Wuninitialized -Wmissing-declarations -Wwrite-strings ")
+    set(CMAKE_C_FLAGS_DEBUG   "-O0 -DDEBUG -g3 -Wall -Wextra -Winit-self -Wuninitialized -Wmissing-declarations -Wwrite-strings -Wno-sign-compare")
     set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG")
   endif()
 endif()

cmake/custom/compilers/Clang.CXX.cmake

@@ -8,7 +8,7 @@ if(NOT DEFINED ENV{CXXFLAGS})
     endif()
 
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_STANDARD_FLAG} -Qunused-arguments -fcolor-diagnostics")
-    set(CMAKE_CXX_FLAGS_DEBUG    "-O0 -DDEBUG -Wall -Wextra -Winit-self -Woverloaded-virtual -Wuninitialized -Wmissing-declarations -Wwrite-strings -Weffc++ -Wdocumentation")
+    set(CMAKE_CXX_FLAGS_DEBUG    "-O0 -DDEBUG -Wall -Wextra -Winit-self -Woverloaded-virtual -Wuninitialized -Wmissing-declarations -Wwrite-strings -Weffc++ -Wdocumentation -Wno-sign-compare")
     set(CMAKE_CXX_FLAGS_RELEASE  "-O3 -DNDEBUG -Wno-unused")
   endif()
 endif()

cmake/custom/compilers/GNU.C.cmake

@@ -1,7 +1,7 @@
 if(NOT DEFINED ENV{CFLAGS})
   if(CMAKE_C_COMPILER_ID MATCHES GNU)
     set(CMAKE_C_FLAGS         "${CMAKE_C_FLAGS} -std=c99 -DRESTRICT=restrict -DFUNDERSCORE=1 -fPIC")
-    set(CMAKE_C_FLAGS_DEBUG   "-O0 -g3 -DDEBUG -Wall -Wextra -Winit-self -Wuninitialized -Wmissing-declarations -Wwrite-strings ")
+    set(CMAKE_C_FLAGS_DEBUG   "-O0 -g3 -DDEBUG -Wall -Wextra -Winit-self -Wuninitialized -Wmissing-declarations -Wwrite-strings -Wno-sign-compare")
     set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG")
   endif()
 endif()

cmake/custom/compilers/GNU.CXX.cmake

@@ -14,7 +14,7 @@ if(NOT DEFINED ENV{CXXFLAGS})
     endif()
 
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_STANDARD_FLAG} ${EXDIAG_CXX_FLAGS}")
-    set(CMAKE_CXX_FLAGS_DEBUG   "-O0 -g3 -DDEBUG -Wall -Wextra -Winit-self -Woverloaded-virtual -Wuninitialized -Wmissing-declarations -Wwrite-strings")
+    set(CMAKE_CXX_FLAGS_DEBUG   "-O0 -g3 -DDEBUG -Wall -Wextra -Winit-self -Woverloaded-virtual -Wuninitialized -Wmissing-declarations -Wwrite-strings -Wno-sign-compare")
     set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG -Wno-unused")
   endif()
 endif()

cmake/custom/compilers/Intel.C.cmake

@@ -1,7 +1,7 @@
 if(NOT DEFINED ENV{CFLAGS})
     if(CMAKE_C_COMPILER_ID MATCHES Intel)
         set(CMAKE_C_FLAGS         "${CMAKE_C_FLAGS} -restrict -DRESTRICT=restrict -std=c99 -fPIC")
-        set(CMAKE_C_FLAGS_DEBUG   "-O0 -DDEBUG -g -w3 -Wall -Wuninitialized")
+        set(CMAKE_C_FLAGS_DEBUG   "-O0 -DDEBUG -g -w3 -Wall -Wuninitialized -Wno-sign-compare")
         set(CMAKE_C_FLAGS_RELEASE "-O3 -ip -DNDEBUG")
         # FIXME Not sure this is really needed
         set(CMAKE_C_LINK_FLAGS    "-shared-intel -fPIC")

cmake/custom/compilers/Intel.CXX.cmake

@@ -14,7 +14,7 @@ if(NOT DEFINED ENV{CXXFLAGS})
     endif()
 
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_STANDARD_FLAG}")
-    set(CMAKE_CXX_FLAGS_DEBUG   "-O0 -debug -DDEBUG -Wall -Wuninitialized -Wno-unknown-pragmas")
+    set(CMAKE_CXX_FLAGS_DEBUG   "-O0 -debug -DDEBUG -Wall -Wuninitialized -Wno-unknown-pragmas -Wno-sign-compare")
     set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
     # FIXME not sure this is actually needed...
     set(CMAKE_CXX_LINK_FLAGS    "-shared-intel")

doc/pcmsolver.bib

@@ -283,3 +283,19 @@ @Article{Frediani2004a
   Publisher                = {AIP},
   Timestamp                = {2013.03.02}
 }
+
+@ARTICLE{DiRemigio2016-nn,
+  title       = {{A Polarizable Continuum Model for Molecules at Spherical Diffuse Interfaces}},
+  author      = "Di Remigio, Roberto and Mozgawa, Krzysztof and Cao, Hui and
+                 Weijo, Ville and Frediani, Luca",
+  journal     = "J. Chem. Phys.",
+  volume      =  144,
+  number      =  12,
+  pages       = "124103",
+  month       =  "28~" # mar,
+  year        =  2016,
+  issn        = "0021-9606, 1089-7690",
+  pmid        = "27036423",
+  doi         = "10.1063/1.4943782",
+  addendum        = "Times cited: 0"
+}