Added the enforcePeriodicBox flag to the C and Fortran wrappers

examples/CMakeLists.txt

@@ -53,7 +53,7 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
 ENDFOREACH(EX_ROOT ${CPP_EXAMPLES})
 
 # Only build wrapper examples if wrappers have been built
-IF(OPENMM_BUILD_API_WRAPPERS)
+IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
     INCLUDE_DIRECTORIES(BEFORE ${PROJECT_BINARY_DIR}/wrappers)
 
     FOREACH(EX_ROOT ${C_EXAMPLES})
@@ -83,7 +83,7 @@ IF(OPENMM_BUILD_API_WRAPPERS)
             ADD_DEPENDENCIES(${EX_STATIC} ApiWrappers)
         ENDIF (BUILD_TESTING_STATIC)
   ENDFOREACH(EX_ROOT ${C_EXAMPLES})
-ENDIF(OPENMM_BUILD_API_WRAPPERS)
+ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
 
 FOREACH(EX_ROOT ${C_EXAMPLES})
   INSTALL(FILES ${EX_ROOT}.c DESTINATION examples)

examples/HelloArgonInC.c

@@ -68,7 +68,7 @@ void simulateArgon()
     /* Simulate. */
    for (frameNum=1; ;++frameNum) {
         /* Output current state information. */
-        OpenMM_State* state    = OpenMM_Context_getState(context, OpenMM_State_Positions);
+        OpenMM_State* state    = OpenMM_Context_getState(context, OpenMM_State_Positions, 0);
         const double  timeInPs = OpenMM_State_getTime(state);
         writePdbFrame(frameNum, state); /*output coordinates*/
         OpenMM_State_destroy(state);

examples/HelloArgonInFortran.f90

@@ -67,7 +67,7 @@ PROGRAM HelloArgon
     frameNum = 1
     do
         ! Output current state information.
-        call OpenMM_Context_getState(context, OpenMM_State_Positions, state)
+        call OpenMM_Context_getState(context, OpenMM_State_Positions, state, 0)
         timeInPs = OpenMM_State_getTime(state)
         call writePdbFrame(frameNum, state) !output coordinates
         call OpenMM_State_destroy(state)

examples/HelloSodiumChlorideInC.c

@@ -289,7 +289,7 @@ myGetOpenMMState(MyOpenMMData* omm, int wantEnergy,
     /* Forces are also available (and cheap). */
 
     /* State object is created here and must be explicitly destroyed below. */
-    state = OpenMM_Context_getState(omm->context, infoMask);
+    state = OpenMM_Context_getState(omm->context, infoMask, 0);
     *timeInPs = OpenMM_State_getTime(state); /* OpenMM time is in ps already. */
 
     /* Positions are maintained as a Vec3Array inside the State. This will give

examples/HelloSodiumChlorideInFortran.f90

@@ -282,7 +282,7 @@ SUBROUTINE myGetOpenMMState(ommHandle, timeInPs, energyInKcal)
     ! Forces are also available (and cheap).
     
     ! Don't forget to destroy this State when you're done with it.
-    call OpenMM_Context_getState(context, infoMask, state) 
+    call OpenMM_Context_getState(context, infoMask, state, 0) 
     timeInPs = OpenMM_State_getTime(state) ! OpenMM time is in ps already.
     
     ! Positions are maintained as a Vec3Array inside the State. This will give

examples/HelloWaterBox.cpp

@@ -356,7 +356,7 @@ myGetOpenMMState(MyOpenMMData* omm, double& timeInPs,
                  std::vector<double>& atomPositionsInAng)
 {
     // We don't calculate energy in this example because it would take most of the time
-    const OpenMM::State state = omm->context->getState(OpenMM::State::Positions);
+    const OpenMM::State state = omm->context->getState(OpenMM::State::Positions, true);
     timeInPs = state.getTime(); // OpenMM time is in ps already
 
     // Copy OpenMM positions into output array and change units from nm to Angstroms.

plugins/amoeba/wrappers/FortranWrapper_Source.xslt

@@ -68,202 +68,6 @@ static string makeString(const char* fsrc, int length) {
 
 extern "C" {
 
-/* OpenMM_Vec3 */
-OPENMM_EXPORT void openmm_vec3_scale_(const OpenMM_Vec3& vec, double const& scale, OpenMM_Vec3& result) {
-    result = OpenMM_Vec3_scale(vec, scale);
-}
-OPENMM_EXPORT void OPENMM_VEC3_SCALE(const OpenMM_Vec3& vec, double const& scale, OpenMM_Vec3& result) {
-    result = OpenMM_Vec3_scale(vec, scale);
-}
-
-/* OpenMM_Vec3Array */
-OPENMM_EXPORT void openmm_vec3array_create_(OpenMM_Vec3Array*& result, const int& size) {
-    result = OpenMM_Vec3Array_create(size);
-}
-OPENMM_EXPORT void OPENMM_VEC3ARRAY_CREATE(OpenMM_Vec3Array*& result, const int& size) {
-    result = OpenMM_Vec3Array_create(size);
-}
-OPENMM_EXPORT void openmm_vec3array_destroy_(OpenMM_Vec3Array*& array) {
-    OpenMM_Vec3Array_destroy(array);
-    array = 0;
-}
-OPENMM_EXPORT void OPENMM_VEC3ARRAY_DESTROY(OpenMM_Vec3Array*& array) {
-    OpenMM_Vec3Array_destroy(array);
-    array = 0;
-}
-OPENMM_EXPORT int openmm_vec3array_getsize_(const OpenMM_Vec3Array* const& array) {
-    return OpenMM_Vec3Array_getSize(array);
-}
-OPENMM_EXPORT int OPENMM_VEC3ARRAY_GETSIZE(const OpenMM_Vec3Array* const& array) {
-    return OpenMM_Vec3Array_getSize(array);
-}
-OPENMM_EXPORT void openmm_vec3array_resize_(OpenMM_Vec3Array* const& array, const int& size) {
-    OpenMM_Vec3Array_resize(array, size);
-}
-OPENMM_EXPORT void OPENMM_VEC3ARRAY_RESIZE(OpenMM_Vec3Array* const& array, const int& size) {
-    OpenMM_Vec3Array_resize(array, size);
-}
-OPENMM_EXPORT void openmm_vec3array_append_(OpenMM_Vec3Array* const& array, const OpenMM_Vec3& vec) {
-    OpenMM_Vec3Array_append(array, vec);
-}
-OPENMM_EXPORT void OPENMM_VEC3ARRAY_APPEND(OpenMM_Vec3Array* const& array, const OpenMM_Vec3& vec) {
-    OpenMM_Vec3Array_append(array, vec);
-}
-OPENMM_EXPORT void openmm_vec3array_set_(OpenMM_Vec3Array* const& array, const int& index, const OpenMM_Vec3& vec) {
-    OpenMM_Vec3Array_set(array, index-1, vec);
-}
-OPENMM_EXPORT void OPENMM_VEC3ARRAY_SET(OpenMM_Vec3Array* const& array, const int& index, const OpenMM_Vec3& vec) {
-    OpenMM_Vec3Array_set(array, index-1, vec);
-}
-OPENMM_EXPORT void openmm_vec3array_get_(const OpenMM_Vec3Array* const& array, const int& index, OpenMM_Vec3& result) {
-    result = *OpenMM_Vec3Array_get(array, index-1);
-}
-OPENMM_EXPORT void OPENMM_VEC3ARRAY_GET(const OpenMM_Vec3Array* const& array, const int& index, OpenMM_Vec3& result) {
-    result = *OpenMM_Vec3Array_get(array, index-1);
-}
-
-/* OpenMM_StringArray */
-OPENMM_EXPORT void openmm_stringarray_create_(OpenMM_StringArray*& result, const int& size) {
-    result = OpenMM_StringArray_create(size);
-}
-OPENMM_EXPORT void OPENMM_STRINGARRAY_CREATE(OpenMM_StringArray*& result, const int& size) {
-    result = OpenMM_StringArray_create(size);
-}
-OPENMM_EXPORT void openmm_stringarray_destroy_(OpenMM_StringArray*& array) {
-    OpenMM_StringArray_destroy(array);
-    array = 0;
-}
-OPENMM_EXPORT void OPENMM_STRINGARRAY_DESTROY(OpenMM_StringArray*& array) {
-    OpenMM_StringArray_destroy(array);
-    array = 0;
-}
-OPENMM_EXPORT int openmm_stringarray_getsize_(const OpenMM_StringArray* const& array) {
-    return OpenMM_StringArray_getSize(array);
-}
-OPENMM_EXPORT int OPENMM_STRINGARRAY_GETSIZE(const OpenMM_StringArray* const& array) {
-    return OpenMM_StringArray_getSize(array);
-}
-OPENMM_EXPORT void openmm_stringarray_resize_(OpenMM_StringArray* const& array, const int& size) {
-    OpenMM_StringArray_resize(array, size);
-}
-OPENMM_EXPORT void OPENMM_STRINGARRAY_RESIZE(OpenMM_StringArray* const& array, const int& size) {
-    OpenMM_StringArray_resize(array, size);
-}
-OPENMM_EXPORT void openmm_stringarray_append_(OpenMM_StringArray* const& array, const char* str, int length) {
-    OpenMM_StringArray_append(array, makeString(str, length).c_str());
-}
-OPENMM_EXPORT void OPENMM_STRINGARRAY_APPEND(OpenMM_StringArray* const& array, const char* str, int length) {
-    OpenMM_StringArray_append(array, makeString(str, length).c_str());
-}
-OPENMM_EXPORT void openmm_stringarray_set_(OpenMM_StringArray* const& array, const int& index, const char* str, int length) {
-  OpenMM_StringArray_set(array, index-1, makeString(str, length).c_str());
-  }
-OPENMM_EXPORT void OPENMM_STRINGARRAY_SET(OpenMM_StringArray* const& array, const int& index, const char* str, int length) {
-  OpenMM_StringArray_set(array, index-1, makeString(str, length).c_str());
-}
-OPENMM_EXPORT void openmm_stringarray_get_(const OpenMM_StringArray* const& array, const int& index, char* result, int length) {
-    const char* str = OpenMM_StringArray_get(array, index-1);
-    copyAndPadString(result, str, length);
-}
-OPENMM_EXPORT void OPENMM_STRINGARRAY_GET(const OpenMM_StringArray* const& array, const int& index, char* result, int length) {
-    const char* str = OpenMM_StringArray_get(array, index-1);
-    copyAndPadString(result, str, length);
-}
-
-/* OpenMM_BondArray */
-OPENMM_EXPORT void openmm_bondarray_create_(OpenMM_BondArray*& result, const int& size) {
-    result = OpenMM_BondArray_create(size);
-}
-OPENMM_EXPORT void OPENMM_BONDARRAY_CREATE(OpenMM_BondArray*& result, const int& size) {
-    result = OpenMM_BondArray_create(size);
-}
-OPENMM_EXPORT void openmm_bondarray_destroy_(OpenMM_BondArray*& array) {
-    OpenMM_BondArray_destroy(array);
-    array = 0;
-}
-OPENMM_EXPORT void OPENMM_BONDARRAY_DESTROY(OpenMM_BondArray*& array) {
-    OpenMM_BondArray_destroy(array);
-    array = 0;
-}
-OPENMM_EXPORT int openmm_bondarray_getsize_(const OpenMM_BondArray* const& array) {
-    return OpenMM_BondArray_getSize(array);
-}
-OPENMM_EXPORT int OPENMM_BONDARRAY_GETSIZE(const OpenMM_BondArray* const& array) {
-    return OpenMM_BondArray_getSize(array);
-}
-OPENMM_EXPORT void openmm_bondarray_resize_(OpenMM_BondArray* const& array, const int& size) {
-    OpenMM_BondArray_resize(array, size);
-}
-OPENMM_EXPORT void OPENMM_BONDARRAY_RESIZE(OpenMM_BondArray* const& array, const int& size) {
-    OpenMM_BondArray_resize(array, size);
-}
-OPENMM_EXPORT void openmm_bondarray_append_(OpenMM_BondArray* const& array, const int& particle1, const int& particle2) {
-    OpenMM_BondArray_append(array, particle1, particle2);
-}
-OPENMM_EXPORT void OPENMM_BONDARRAY_APPEND(OpenMM_BondArray* const& array, const int& particle1, const int& particle2) {
-    OpenMM_BondArray_append(array, particle1, particle2);
-}
-OPENMM_EXPORT void openmm_bondarray_set_(OpenMM_BondArray* const& array, const int& index, const int& particle1, const int& particle2) {
-    OpenMM_BondArray_set(array, index-1, particle1, particle2);
-}
-OPENMM_EXPORT void OPENMM_BONDARRAY_SET(OpenMM_BondArray* const& array, const int& index, const int& particle1, const int& particle2) {
-    OpenMM_BondArray_set(array, index-1, particle1, particle2);
-}
-OPENMM_EXPORT void openmm_bondarray_get_(const OpenMM_BondArray* const& array, const int& index, int* particle1, int* particle2) {
-    OpenMM_BondArray_get(array, index-1, particle1, particle2);
-}
-OPENMM_EXPORT void OPENMM_BONDARRAY_GET(const OpenMM_BondArray* const& array, const int& index, int* particle1, int* particle2) {
-    OpenMM_BondArray_get(array, index-1, particle1, particle2);
-}
-
-/* OpenMM_ParameterArray */
-OPENMM_EXPORT int openmm_parameterarray_getsize_(const OpenMM_ParameterArray* const& array) {
-    return OpenMM_ParameterArray_getSize(array);
-}
-OPENMM_EXPORT int OPENMM_PARAMETERARRAY_GETSIZE(const OpenMM_ParameterArray* const& array) {
-    return OpenMM_ParameterArray_getSize(array);
-}
-OPENMM_EXPORT double openmm_parameterarray_get_(const OpenMM_ParameterArray* const& array, const char* name, int length) {
-    return OpenMM_ParameterArray_get(array, makeString(name, length).c_str());
-}
-OPENMM_EXPORT double OPENMM_PARAMETERARRAY_GET(const OpenMM_ParameterArray* const& array, const char* name, int length) {
-    return OpenMM_ParameterArray_get(array, makeString(name, length).c_str());
-}
-
-/* OpenMM_PropertyArray */
-OPENMM_EXPORT int openmm_propertyarray_getsize_(const OpenMM_PropertyArray* const& array) {
-    return OpenMM_PropertyArray_getSize(array);
-}
-OPENMM_EXPORT int OPENMM_PROPERTYARRAY_GETSIZE(const OpenMM_PropertyArray* const& array) {
-    return OpenMM_PropertyArray_getSize(array);
-}
-OPENMM_EXPORT const char* openmm_propertyarray_get_(const OpenMM_PropertyArray* const& array, const char* name, int length) {
-    return OpenMM_PropertyArray_get(array, makeString(name, length).c_str());
-}
-OPENMM_EXPORT const char* OPENMM_PROPERTYARRAY_GET(const OpenMM_PropertyArray* const& array, const char* name, int length) {
-    return OpenMM_PropertyArray_get(array, makeString(name, length).c_str());
-}
-
-<xsl:call-template name="primitive_array">
- <xsl:with-param name="element_type" select="'int'"/>
- <xsl:with-param name="name" select="'OpenMM_IntArray'"/>
-</xsl:call-template>
-
-/* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
-   Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
-OPENMM_EXPORT void openmm_context_getstate_(const OpenMM_Context*&amp; target, int const&amp; types, OpenMM_State*&amp; result) {
-    result = OpenMM_Context_getState(target, types);
-};
-OPENMM_EXPORT void OPENMM_CONTEXT_GETSTATE(const OpenMM_Context*&amp; target, int const&amp; types, OpenMM_State*&amp; result) {
-    result = OpenMM_Context_getState(target, types);
-};
-OPENMM_EXPORT void openmm_platform_loadpluginsfromdirectory_(const char* directory, OpenMM_StringArray*&amp; result, int length) {
-    result = OpenMM_Platform_loadPluginsFromDirectory(makeString(directory, length).c_str());
-};
-OPENMM_EXPORT void OPENMM_PLATFORM_LOADPLUGINSFROMDIRECTORY(const char* directory, OpenMM_StringArray*&amp; result, int length) {
-    result = OpenMM_Platform_loadPluginsFromDirectory(makeString(directory, length).c_str());
-};
-
  <!-- Class members -->
  <xsl:for-each select="Class[@context=$openmm_namespace_id and empty(index-of($skip_classes, @name))]">
   <xsl:call-template name="class"/>

wrappers/CWrapper_Header.xslt

@@ -100,7 +100,7 @@ extern OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyA
 
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
-extern OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types);
+extern OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types, int enforcePeriodicBox);
 extern OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_loadPluginsFromDirectory(const char* directory);
 
  <!-- Class members -->

wrappers/CWrapper_Source.xslt

@@ -150,8 +150,8 @@ OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyArray* a
 
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
-OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types) {
-    State result = reinterpret_cast<const Context*>(target)->getState(types);
+OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types, int enforcePeriodicBox) {
+    State result = reinterpret_cast<const Context*>(target)->getState(types, enforcePeriodicBox);
     return reinterpret_cast<OpenMM_State*>(new State(result));
 };
 OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_loadPluginsFromDirectory(const char* directory) {

wrappers/FortranWrapper_Source.xslt

@@ -245,11 +245,11 @@ OPENMM_EXPORT const char* OPENMM_PROPERTYARRAY_GET(const OpenMM_PropertyArray* c
 
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
-OPENMM_EXPORT void openmm_context_getstate_(const OpenMM_Context*& target, int const& types, OpenMM_State*& result) {
-    result = OpenMM_Context_getState(target, types);
+OPENMM_EXPORT void openmm_context_getstate_(const OpenMM_Context*& target, int const& types, int const& enforcePeriodicBox, OpenMM_State*& result) {
+    result = OpenMM_Context_getState(target, types, enforcePeriodicBox);
 };
-OPENMM_EXPORT void OPENMM_CONTEXT_GETSTATE(const OpenMM_Context*& target, int const& types, OpenMM_State*& result) {
-    result = OpenMM_Context_getState(target, types);
+OPENMM_EXPORT void OPENMM_CONTEXT_GETSTATE(const OpenMM_Context*& target, int const& types, int const& enforcePeriodicBox, OpenMM_State*& result) {
+    result = OpenMM_Context_getState(target, types, enforcePeriodicBox);
 };
 OPENMM_EXPORT void openmm_platform_loadpluginsfromdirectory_(const char* directory, OpenMM_StringArray*& result, int length) {
     result = OpenMM_Platform_loadPluginsFromDirectory(makeString(directory, length).c_str());