Let host manage lifetime of host input struct

Author: robertodr

api/pcmsolver.F90

@@ -1,6 +1,6 @@
 module pcmsolver
-
-    use, intrinsic :: iso_c_binding, only: c_bool, c_char, c_double, c_int
+ 
+    use, intrinsic :: iso_c_binding
 
     implicit none
 
@@ -24,32 +24,26 @@ module pcmsolver
     public pcmsolver_load_surface_function
     public pcmsolver_write_timings
 
-    type, public, bind(C) :: cavityInput
+    type, public, bind(C) :: PCMInput
+        character(kind=c_char, len=1) :: cavity_type(8)
         integer(c_int)                :: patch_level
         real(c_double)                :: coarsity
         real(c_double)                :: area
         real(c_double)                :: min_distance
         integer(c_int)                :: der_order
-        character(kind=c_char, len=1) :: cavity_type(8)
         logical(c_bool)               :: scaling
+        character(kind=c_char, len=1) :: radii_set(8)
         character(kind=c_char, len=1) :: restart_name(20)
         real(c_double)                :: min_radius
-        character(kind=c_char, len=1) :: radii_set(8)
-    end type
-
-    type, public, bind(C) :: solverInput
         character(kind=c_char, len=1) :: solver_type(7)
-        real(c_double)                :: correction
         character(kind=c_char, len=1) :: solvent(16)
-        real(c_double)                :: probe_radius
         character(kind=c_char, len=1) :: equation_type(11)
-    end type
-
-    type, public, bind(C) :: greenInput
+        real(c_double)                :: correction
+        real(c_double)                :: probe_radius
         character(kind=c_char, len=1) :: inside_type(7)
         real(c_double)                :: outside_epsilon
         character(kind=c_char, len=1) :: outside_type(22)
-    end type
+    end type PCMInput
 
     public PCMSOLVER_READER_OWN
     public PCMSOLVER_READER_HOST
@@ -59,65 +53,66 @@ module pcmsolver
     end enum
 
     interface pcmsolver_new
-        function pcmsolver_new(input_reading, nr_nuclei, charges, coordinates, symmetry_info) result(context) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_int, c_double, c_ptr
+        function pcmsolver_new(input_reading, nr_nuclei, charges, coordinates, symmetry_info, host_input) result(context) bind(C)
+            import
             integer(c_int), value :: input_reading
             integer(c_int), value :: nr_nuclei
-            real(c_double), intent(out) :: charges(*)
-            real(c_double), intent(out) :: coordinates(*)
-            integer(c_int), intent(out) :: symmetry_info(*)
+            real(c_double), intent(in) :: charges(*)
+            real(c_double), intent(in) :: coordinates(*)
+            integer(c_int), intent(in) :: symmetry_info(*)
+            type(PCMInput), intent(in) :: host_input 
             type(c_ptr) :: context
         end function pcmsolver_new
     end interface pcmsolver_new
 
     interface pcmsolver_delete
         subroutine pcmsolver_delete(context) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr
+            import
             type(c_ptr), value :: context
         end subroutine pcmsolver_delete
     end interface pcmsolver_delete
 
     interface pcmsolver_is_compatible_library
         function pcmsolver_is_compatible_library() result(compatible) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_bool
+            import
             logical(c_bool) :: compatible
         end function pcmsolver_is_compatible_library
     end interface pcmsolver_is_compatible_library
 
     interface pcmsolver_print
         subroutine pcmsolver_print(context) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr
+            import
             type(c_ptr), value :: context
         end subroutine pcmsolver_print
     end interface pcmsolver_print
 
     interface pcmsolver_get_cavity_size
         function pcmsolver_get_cavity_size(context) result(nr_points) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_size_t
+            import
             type(c_ptr), value :: context
             integer(c_size_t)  :: 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)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_size_t
+            import
             type(c_ptr), value :: context
             integer(c_size_t)  :: nr_points_irr
         end function pcmsolver_get_irreducible_cavity_size
     end interface pcmsolver_get_irreducible_cavity_size
 
     interface pcmsolver_get_centers
         subroutine pcmsolver_get_centers(context, centers) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_double
+            import
             type(c_ptr), value :: context
             real(c_double), intent(inout) :: centers(*)
         end subroutine pcmsolver_get_centers
     end interface pcmsolver_get_centers
 
     interface pcmsolver_get_center
         subroutine pcmsolver_get_center(context, its, center) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_int, c_double
+            import
             type(c_ptr), value :: context
             integer(c_int), value, intent(in) :: its
             real(c_double), intent(inout) :: center(*)
@@ -126,7 +121,7 @@ end subroutine pcmsolver_get_center
 
     interface pcmsolver_compute_asc
         subroutine pcmsolver_compute_asc(context, mep_name, asc_name, irrep) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_char, c_int
+            import
             type(c_ptr), value :: context
             character(c_char), intent(in) :: mep_name, asc_name
             integer(c_int), value, intent(in) :: irrep
@@ -135,7 +130,7 @@ end subroutine pcmsolver_compute_asc
 
     interface pcmsolver_compute_response_asc
         subroutine pcmsolver_compute_response_asc(context, mep_name, asc_name, irrep) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_char, c_int
+            import
             type(c_ptr), value :: context
             character(c_char), intent(in) :: mep_name, asc_name
             integer(c_int), value, intent(in) :: irrep
@@ -144,16 +139,16 @@ end subroutine pcmsolver_compute_response_asc
 
     interface pcmsolver_compute_polarization_energy
         function pcmsolver_compute_polarization_energy(context, mep_name, asc_name) result(energy) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_char, c_double
+            import
             type(c_ptr), value :: context
             character(c_char), intent(in) :: mep_name, asc_name
             real(c_double) :: energy
         end function pcmsolver_compute_polarization_energy
     end interface pcmsolver_compute_polarization_energy
-
+    
     interface pcmsolver_get_surface_function
         subroutine pcmsolver_get_surface_function(context, f_size, values, name) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_char, c_size_t, c_double
+            import
             type(c_ptr), value :: context
             integer(c_size_t), value, intent(in) :: f_size
             real(c_double), intent(inout) :: values(*)
@@ -163,7 +158,7 @@ end subroutine pcmsolver_get_surface_function
 
     interface pcmsolver_set_surface_function
         subroutine pcmsolver_set_surface_function(context, f_size, values, name) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_char, c_size_t, c_double
+            import
             type(c_ptr), value :: context
             integer(c_size_t), value, intent(in) :: f_size
             real(c_double), intent(in) :: values(*)
@@ -173,30 +168,30 @@ end subroutine pcmsolver_set_surface_function
 
     interface pcmsolver_save_surface_functions
         subroutine pcmsolver_save_surface_functions(context) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr
+            import
             type(c_ptr), value :: context
         end subroutine pcmsolver_save_surface_functions
     end interface pcmsolver_save_surface_functions
 
     interface pcmsolver_save_surface_function
         subroutine pcmsolver_save_surface_function(context, name) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_char
+            import
             type(c_ptr), value :: context
             character(c_char), 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)
-            use, intrinsic :: iso_c_binding, only: c_ptr, c_char
+            import
             type(c_ptr), value :: context
             character(c_char), intent(in) :: name
         end subroutine pcmsolver_load_surface_function
     end interface pcmsolver_load_surface_function
 
     interface pcmsolver_write_timings
         subroutine pcmsolver_write_timings(context) bind(C)
-            use, intrinsic :: iso_c_binding, only: c_ptr
+            import
             type(c_ptr), value :: context
         end subroutine pcmsolver_write_timings
     end interface pcmsolver_write_timings

api/pcmsolver.h

@@ -25,9 +25,7 @@
 extern "C" {
 #endif
 
-struct cavityInput;
-struct solverInput;
-struct greenInput;
+struct PCMInput;
 
 struct pcmsolver_context_s;
 typedef struct pcmsolver_context_s pcmsolver_context_t;
@@ -39,13 +37,13 @@ typedef enum
 } pcmsolver_reader_t;
 
 void host_writer(const char *);
-void host_input(cavityInput *, solverInput *, greenInput *);
 
 PCMSOLVER_API pcmsolver_context_t * pcmsolver_new(pcmsolver_reader_t input_reading,
                                         int nr_nuclei,
                                         double charges[],
                                         double coordinates[],
-                                        int symmetry_info[]);
+                                        int symmetry_info[],
+					PCMInput * host_input);
 
 PCMSOLVER_API void pcmsolver_delete(pcmsolver_context_t * context);
 

cmake/autocmake.cfg

@@ -1,6 +1,7 @@
 [project]
 name: PCMSolver
 min_cmake_version: 2.8.3
+setup_script: setup.py
 
 [cxx]
 source: https://github.com/scisoft/autocmake/raw/master/modules/cxx.cmake

cmake/downloaded/autocmake_boost.cmake

@@ -63,8 +63,8 @@ set(BOOST_ARCHIVE boost_${BOOSTVER}.zip)
 set(Boost_USE_STATIC_LIBS    ON)
 set(Boost_USE_MULTITHREADED  ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
-set(Boost_DEBUG ON)
-set(Boost_DETAILED_FAILURE_MESSAGE ON)
+set(Boost_DEBUG OFF)
+set(Boost_DETAILED_FAILURE_MESSAGE OFF)
 
 set(BUILD_CUSTOM_BOOST FALSE)
 if(FORCE_CUSTOM_BOOST)
@@ -107,7 +107,7 @@ if(BUILD_CUSTOM_BOOST)
     include(${CMAKE_CURRENT_LIST_DIR}/boost_unpack.cmake)
     include(${CMAKE_CURRENT_LIST_DIR}/boost_userconfig.cmake)
 
-    if(NOT BOOST_COMPONENTS_REQUIRED STREQUAL "")
+    if(NOT "${BOOST_COMPONENTS_REQUIRED}" STREQUAL "")
         # Non-empty list. Compiled libraries needed
         # Transform the ;-separated list to a ,-separated list (digested by the Boost build toolchain!)
         string(REPLACE ";" "," b2_needed_components "${BOOST_COMPONENTS_REQUIRED}")

cmake/update.py

@@ -128,9 +128,9 @@ def autogenerated_notice():
 # ------------------------------------------------------------------------------
 
 
-def gen_setup(config, relative_path):
+def gen_setup(config, relative_path, setup_script_name):
     """
-    Generate setup.py script.
+    Generate setup script.
     """
     s = []
     s.append('#!/usr/bin/env python')
@@ -145,8 +145,8 @@ def gen_setup(config, relative_path):
 
     s.append('\n\noptions = """')
     s.append('Usage:')
-    s.append('  ./setup.py [options] [<builddir>]')
-    s.append('  ./setup.py (-h | --help)')
+    s.append('  ./{0} [options] [<builddir>]'.format(setup_script_name))
+    s.append('  ./{0} (-h | --help)'.format(setup_script_name))
     s.append('\nOptions:')
 
     options = []
@@ -334,7 +334,7 @@ def main(argv):
         sys.stderr.write("Step 1: Update or create infrastructure files\n")
         sys.stderr.write("        which will be needed to configure and build the project:\n")
         sys.stderr.write("        $ %s --self\n\n" % argv[0])
-        sys.stderr.write("Step 2: Create CMakeLists.txt and setup.py in PROJECT_ROOT:\n")
+        sys.stderr.write("Step 2: Create CMakeLists.txt and setup script in PROJECT_ROOT:\n")
         sys.stderr.write("        $ %s <PROJECT_ROOT>\n" % argv[0])
         sys.stderr.write("        example:\n")
         sys.stderr.write("        $ %s ..\n" % argv[0])
@@ -343,7 +343,7 @@ def main(argv):
     if argv[1] in ['-h', '--help']:
         print('Usage:')
         print('  python update.py --self         Update this script and fetch or update infrastructure files under lib/.')
-        print('  python update.py <builddir>     (Re)generate CMakeLists.txt and setup.py and fetch or update CMake modules.')
+        print('  python update.py <builddir>     (Re)generate CMakeLists.txt and setup script and fetch or update CMake modules.')
         print('  python update.py (-h | --help)  Show this help text.')
         sys.exit(0)
 
@@ -398,7 +398,12 @@ def main(argv):
         sys.exit(-1)
     min_cmake_version = config.get('project', 'min_cmake_version')
 
-    # get relative path from setup.py script to this directory
+    if config.has_option('project', 'setup_script'):
+        setup_script_name = config.get('project', 'setup_script')
+    else:
+        setup_script_name = 'setup'
+
+    # get relative path from setup script to this directory
     relative_path = os.path.relpath(os.path.abspath('.'), project_root)
 
     # fetch modules from the web or from relative paths
@@ -410,10 +415,10 @@ def main(argv):
     with open(os.path.join(project_root, 'CMakeLists.txt'), 'w') as f:
         f.write('%s\n' % '\n'.join(s))
 
-    # create setup.py
-    print('- generating setup.py')
-    s = gen_setup(config, relative_path)
-    file_path = os.path.join(project_root, 'setup.py')
+    # create setup script
+    print('- generating setup script')
+    s = gen_setup(config, relative_path, setup_script_name)
+    file_path = os.path.join(project_root, setup_script_name)
     with open(file_path, 'w') as f:
         f.write('%s\n' % '\n'.join(s))
     if sys.platform != 'win32':

src/interface/Meddle.cpp

@@ -38,13 +38,13 @@
 #include "Cavity.hpp"
 #include "RegisterCavityToFactory.hpp"
 #include "IGreensFunction.hpp"
-#include "InputManager.hpp"
 #include "RegisterGreensFunctionToFactory.hpp"
 #include "PCMSolver.hpp"
 #include "RegisterSolverToFactory.hpp"
 #include "Atom.hpp"
 #include "Citation.hpp"
 #include "cnpy.hpp"
+#include "PCMInput.hpp"
 #include "PhysicalConstants.hpp"
 #include "Solvent.hpp"
 #include "Sphere.hpp"
@@ -58,9 +58,9 @@
 #endif
 
 PCMSOLVER_API
-pcmsolver_context_t * pcmsolver_new(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[])
+pcmsolver_context_t * pcmsolver_new(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[], PCMInput * host_input)
 {
-    return AS_TYPE(pcmsolver_context_t, new pcm::Meddle(input_reading, nr_nuclei, charges, coordinates, symmetry_info));
+    return AS_TYPE(pcmsolver_context_t, new pcm::Meddle(input_reading, nr_nuclei, charges, coordinates, symmetry_info, *host_input));
 }
 
 PCMSOLVER_API
@@ -172,10 +172,10 @@ void pcmsolver_write_timings(pcmsolver_context_t * context)
 }
 
 namespace pcm {
-    Meddle::Meddle(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[])
+    Meddle::Meddle(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[], const PCMInput & host_input)
         : hasDynamic_(false)
     {
-        initInput(input_reading, nr_nuclei, charges, coordinates, symmetry_info);
+        initInput(input_reading, nr_nuclei, charges, coordinates, symmetry_info, host_input);
         initCavity();
         initStaticSolver();
         if (input_.isDynamic()) initDynamicSolver();
@@ -351,22 +351,11 @@ namespace pcm {
         TIMER_DONE("pcmsolver.timer.dat");
     }
 
-    void Meddle::initInput(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[])
+    void Meddle::initInput(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[], const PCMInput & host_input)
     {
         if (input_reading) {
-            cavityInput cav;
-            init(cav);
-            solverInput solv;
-            init(solv);
-            greenInput green;
-            init(green);
-
-            host_input(&cav, &solv, &green);
-
-            trim(cav);
-            trim(solv);
-            trim(green);
-            input_ = Input(cav, solv, green);
+	    //trim(host_input);
+            input_ = Input(host_input);
         } else {
             input_ = Input("@pcmsolver.inp");
         }