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Commit 19d2885a authored by Lee-Ping's avatar Lee-Ping
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Merge github.com:SimTk/openmm

parents 99ef4344 57a6768e
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Showing with 65 additions and 888 deletions
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp
View file @ 19d2885a
......@@ -44,6 +44,9 @@
#include <vector>
using namespace OpenMM;
extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-4;
TorsionTorsionGrid& getTorsionGrid( int gridIndex ) {
......@@ -2683,6 +2686,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestReferenceAmoebaTorsionTorsionForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
//registerAmoebaCudaKernelFactories();
FILE* log = NULL;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp
View file @ 19d2885a
......@@ -51,6 +51,8 @@
using namespace OpenMM;
extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-4;
void testVdw( FILE* log ) {
......@@ -1983,6 +1985,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestReferenceAmoebaVdwForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
FILE* log = NULL;
......
plugins/amoeba/platforms/reference/tests/TestReferenceWcaDispersionForce.cpp
View file @ 19d2885a
......@@ -50,6 +50,9 @@
using namespace OpenMM;
extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-4;
void compareForcesEnergy( std::string& testName, double expectedEnergy, double energy,
......@@ -171,6 +174,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaWcaDispersionForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
FILE* log = NULL;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaAngleForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaAngleForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaAngleForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaAngleForceProxy : public SerializationProxy {
public:
AmoebaAngleForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaBondForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaBondForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaBondForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaBondForceProxy : public SerializationProxy {
public:
AmoebaBondForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaGeneralizedKirkwoodForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaGeneralizedKirkwoodForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaGeneralizedKirkwoodForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaGeneralizedKirkwoodForceProxy : public SerializationProxy {
public:
AmoebaGeneralizedKirkwoodForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaInPlaneAngleForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaInPlaneAngleForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaInPlaneAngleForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaInPlaneAngleForceProxy : public SerializationProxy {
public:
AmoebaInPlaneAngleForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaMultipoleForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaMultipoleForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaMultipoleForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaMultipoleForceProxy : public SerializationProxy {
public:
AmoebaMultipoleForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaOutOfPlaneBendForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaOutOfPlaneBendForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaOutOfPlaneBendForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaOutOfPlaneBendForceProxy : public SerializationProxy {
public:
AmoebaOutOfPlaneBendForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaPiTorsionForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaPiTorsionForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaPiTorsionForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaPiTorsionForceProxy : public SerializationProxy {
public:
AmoebaPiTorsionForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaStretchBendForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaStretchBendForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaStretchBendForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaStretchBendForceProxy : public SerializationProxy {
public:
AmoebaStretchBendForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaTorsionTorsionForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaTorsionTorsionForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaTorsionTorsionForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaTorsionTorsionForceProxy : public SerializationProxy {
public:
AmoebaTorsionTorsionForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaVdwForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaVdwForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaVdwForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaVdwForceProxy : public SerializationProxy {
public:
AmoebaVdwForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaWcaDispersionForceProxy.h
View file @ 19d2885a
......@@ -32,7 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#include "openmm/internal/windowsExportAmoeba.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This is a proxy for serializing AmoebaWcaDispersionForce objects.
*/
class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaWcaDispersionForceProxy : public SerializationProxy {
class OPENMM_EXPORT_AMOEBA AmoebaWcaDispersionForceProxy : public SerializationProxy {
public:
AmoebaWcaDispersionForceProxy();
void serialize(const void* object, SerializationNode& node) const;
......
plugins/amoeba/serialization/include/openmm/serialization/internal/windowsExportAmoebaSerialization.h deleted 100644 → 0
View file @ 99ef4344
#ifndef OPENMM_WINDOWSEXPORTAMOEBASERIALIZATION_H_
#define OPENMM_WINDOWSEXPORTAMOEBASERIALIZATION_H_
/*
* Shared libraries are messy in Visual Studio. We have to distinguish three
* cases:
* (1) this header is being used to build the OpenMM shared library
* (dllexport)
* (2) this header is being used by a *client* of the OpenMM shared
* library (dllimport)
* (3) we are building the OpenMM static library, or the client is
* being compiled with the expectation of linking with the
* OpenMM static library (nothing special needed)
* In the CMake script for building this library, we define one of the symbols
* OPENMM_AMOEBA_SERIALIZATION_BUILDING_{SHARED|STATIC}_LIBRARY
* Client code normally has no special symbol defined, in which case we'll
* assume it wants to use the shared library. However, if the client defines
* the symbol OPENMM_USE_STATIC_LIBRARIES we'll suppress the dllimport so
* that the client code can be linked with static libraries. Note that
* the client symbol is not library dependent, while the library symbols
* affect only the OpenMM library, meaning that other libraries can
* be clients of this one. However, we are assuming all-static or all-shared.
*/
#ifdef _MSC_VER
// We don't want to hear about how sprintf is "unsafe".
#pragma warning(disable:4996)
// Keep MS VC++ quiet about lack of dll export of private members.
#pragma warning(disable:4251)
#if defined(OPENMM_AMOEBA_SERIALIZATION_BUILDING_SHARED_LIBRARY)
#define OPENMM_EXPORT_AMOEBA_SERIALIZATION __declspec(dllexport)
#elif defined(OPENMM_AMOEBA_SERIALIZATION_BUILDING_STATIC_LIBRARY) || defined(OPENMM_AMOEBA_SERIALIZATION_USE_STATIC_LIBRARIES)
#define OPENMM_EXPORT_AMOEBA_SERIALIZATION
#else
#define OPENMM_EXPORT_AMOEBA_SERIALIZATION __declspec(dllimport) // i.e., a client of a shared library
#endif
#else
#define OPENMM_EXPORT_AMOEBA_SERIALIZATION // Linux, Mac
#endif
#endif // OPENMM_WINDOWSEXPORTAMOEBASERIALIZATION_H_
plugins/amoeba/serialization/src/AmoebaSerializationProxyRegistration.cpp
View file @ 19d2885a
......@@ -65,11 +65,10 @@
#include "openmm/serialization/AmoebaTorsionTorsionForceProxy.h"
#include "openmm/serialization/AmoebaVdwForceProxy.h"
#include "openmm/serialization/AmoebaWcaDispersionForceProxy.h"
#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
#if defined(WIN32)
#include <windows.h>
extern "C" OPENMM_EXPORT_AMOEBA_SERIALIZATION void registerAmoebaSerializationProxies();
extern "C" OPENMM_EXPORT_AMOEBA void registerAmoebaSerializationProxies();
BOOL WINAPI DllMain(HANDLE hModule, DWORD ul_reason_for_call, LPVOID lpReserved) {
if (ul_reason_for_call == DLL_PROCESS_ATTACH)
registerAmoebaSerializationProxies();
......@@ -81,7 +80,7 @@
using namespace OpenMM;
extern "C" OPENMM_EXPORT_AMOEBA_SERIALIZATION void registerAmoebaSerializationProxies() {
extern "C" OPENMM_EXPORT_AMOEBA void registerAmoebaSerializationProxies() {
SerializationProxy::registerProxy(typeid(AmoebaGeneralizedKirkwoodForce), new AmoebaGeneralizedKirkwoodForceProxy());
SerializationProxy::registerProxy(typeid(AmoebaBondForce), new AmoebaBondForceProxy());
SerializationProxy::registerProxy(typeid(AmoebaAngleForce), new AmoebaAngleForceProxy());
......
plugins/amoeba/serialization/tests/CMakeLists.txt
View file @ 19d2885a
......@@ -11,7 +11,8 @@ FOREACH(TEST_PROG ${TEST_PROGS})
# All tests use shared libraries
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} ${OPENMM_AMOEBA_LIBRARY_NAME})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET})
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
plugins/amoeba/wrappers/CMakeLists.txt
View file @ 19d2885a
#set(GCCXML_EXTRA_ARGS "" CACHE STRING "Additional arguments to gccxml, such as '--gccxml-compiler;msvc8'")
#SET(GCCXML_ARGS) # start empty
#FOREACH(subdir ${API_INCLUDE_DIRS})
# SET(GCCXML_ARGS ${GCCXML_ARGS} -I${subdir})
#ENDFOREACH(subdir)
#SET(GCCXML_ARGS ${GCCXML_ARGS} ${GCCXML_EXTRA_ARGS})
SET(SAXON_JAR ${CMAKE_SOURCE_DIR}/wrappers/saxonb9-1-0-7j/saxon9.jar)
# OpenMMAmoeba
ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMApi.xml COMMAND ${GCCXML_PATH} ${GCCXML_ARGS} -I${CMAKE_SOURCE_DIR}/openmmapi/include -I${CMAKE_SOURCE_DIR}/olla/include ${CMAKE_SOURCE_DIR}/plugins/amoeba/openmmapi/include/OpenMMAmoeba.h -fxml=AmoebaOpenMMApi.xml)
ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMCWrapper.h COMMAND ${JAVA_RUNTIME} -jar ${SAXON_JAR} -t -s:AmoebaOpenMMApi.xml
-xsl:${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/CWrapper_Header.xslt -o:AmoebaOpenMMCWrapper.h DEPENDS AmoebaOpenMMApi.xml)
#
ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMCWrapper.cpp COMMAND ${JAVA_RUNTIME} -jar ${SAXON_JAR} -t -s:AmoebaOpenMMApi.xml
-xsl:${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/CWrapper_Source.xslt -o:AmoebaOpenMMCWrapper.cpp DEPENDS AmoebaOpenMMApi.xml)
ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMFortranModule.f90 COMMAND ${JAVA_RUNTIME} -jar ${SAXON_JAR} -t -s:AmoebaOpenMMApi.xml
-xsl:${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/FortranWrapper_Header.xslt -o:AmoebaOpenMMFortranModule.f90 DEPENDS AmoebaOpenMMApi.xml ${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/FortranWrapper_Header.xslt)
ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMFortranWrapper.cpp COMMAND ${JAVA_RUNTIME} -jar ${SAXON_JAR} -t -s:AmoebaOpenMMApi.xml
-xsl:${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/FortranWrapper_Source.xslt -o:AmoebaOpenMMFortranWrapper.cpp DEPENDS AmoebaOpenMMApi.xml)
ADD_CUSTOM_TARGET(AmoebaApiWrappers DEPENDS AmoebaOpenMMCWrapper.h AmoebaOpenMMCWrapper.cpp AmoebaOpenMMFortranModule.f90 AmoebaOpenMMFortranWrapper.cpp)
INSTALL_FILES(/include FILES AmoebaOpenMMCWrapper.h AmoebaOpenMMFortranModule.f90 )
# WRAPPER_DOXYGEN_DIR is a workspace directory where wrapper files will be created
set(WRAPPER_DOXYGEN_DIR "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
file(MAKE_DIRECTORY "${WRAPPER_DOXYGEN_DIR}")
# Step 1 - Create Doxyfile to point to OpenMM headers
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
${WRAPPER_DOXYGEN_DIR}/Doxyfile
@ONLY
)
# Step 2 - Run doxygen to analyze the headers
add_custom_command(
OUTPUT "${WRAPPER_DOXYGEN_DIR}/xml/index.xml"
COMMAND "${DOXYGEN_EXECUTABLE}"
DEPENDS "${WRAPPER_DOXYGEN_DIR}/Doxyfile"
WORKING_DIRECTORY "${WRAPPER_DOXYGEN_DIR}"
COMMENT "Parsing OpenMM header files with Doxygen..."
)
# Step 3 - Generate the wrappers
ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMCWrapper.h AmoebaOpenMMCWrapper.cpp AmoebaOpenMMFortranModule.f90 AmoebaOpenMMFortranWrapper.cpp
COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/generateAmoebaWrappers.py" "${WRAPPER_DOXYGEN_DIR}/xml" "${CMAKE_CURRENT_BINARY_DIR}"
DEPENDS "${WRAPPER_DOXYGEN_DIR}/xml/index.xml" "${CMAKE_CURRENT_SOURCE_DIR}/generateAmoebaWrappers.py")
ADD_CUSTOM_TARGET(AmoebaApiWrappers DEPENDS AmoebaOpenMMCWrapper.h AmoebaOpenMMCWrapper.cpp AmoebaOpenMMFortranModule.f90 AmoebaOpenMMFortranWrapper.cpp)
INSTALL_FILES(/include FILES AmoebaOpenMMCWrapper.h AmoebaOpenMMFortranModule.f90)
plugins/amoeba/wrappers/CWrapper_Header.xslt deleted 100644 → 0
View file @ 99ef4344
<?xml version="1.0" encoding="ISO-8859-1"?>
<xsl:stylesheet version="2.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output method="text" omit-xml-declaration="yes"/>
<xsl:variable name="std_namespace_id" select="/GCC_XML/Namespace[@name='std']/@id"/>
<xsl:variable name="openmm_namespace_id" select="/GCC_XML/Namespace[@name='OpenMM']/@id"/>
<xsl:variable name="bool_type_id" select="/GCC_XML/FundamentalType[@name='bool']/@id"/>
<xsl:variable name="double_type_id" select="/GCC_XML/FundamentalType[@name='double']/@id"/>
<xsl:variable name="string_type_id" select="/GCC_XML/*[@name='string' and @context=$std_namespace_id]/@id"/>
<xsl:variable name="const_string_type_id" select="/GCC_XML/CvQualifiedType[@type=$string_type_id]/@id"/>
<xsl:variable name="const_ref_string_type_id" select="/GCC_XML/ReferenceType[@type=$const_string_type_id]/@id"/>
<xsl:variable name="vector_string_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::basic_string')]/@id"/>
<xsl:variable name="vector_vec3_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;OpenMM::Vec3')]/@id"/>
<xsl:variable name="vector_bond_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::pair&lt;int, int')]/@id"/>
<xsl:variable name="vector_2d_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::vector&lt;int')]/@id"/>
<xsl:variable name="map_parameter_type_id" select="/GCC_XML/Class[starts-with(@name, 'map&lt;std::basic_string') and contains(@name, 'double')]/@id"/>
<xsl:variable name="map_property_type_id" select="/GCC_XML/Class[starts-with(@name, 'map&lt;std::basic_string') and not(contains(@name, 'double'))]/@id"/>
<xsl:variable name="vector_double_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;double')]/@id"/>
<xsl:variable name="vector_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;int')]/@id"/>
<xsl:variable name="vector_tortor_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::vector&lt;std::vector&lt;double')]/@id"/>
<!-- Do not generate functions for the following classes -->
<xsl:variable name="skip_classes" select="('Vec3', 'Context', 'Kernel', 'System', 'Stream', 'KernelImpl', 'StreamImpl', 'KernelFactory', 'StreamFactory', 'ContextImpl', 'OpenMMException', 'Force', 'ForceImpl')"/>
<!-- Do not generate the following functions -->
<xsl:variable name="skip_methods" select="('OpenMM_Context_getState', 'OpenMM_Platform_loadPluginsFromDirectory')"/>
<!-- Suppress any function which references any of the following classes -->
<xsl:variable name="hide_classes" select="('Kernel', 'Stream', 'KernelImpl', 'StreamImpl', 'KernelFactory', 'StreamFactory', 'ContextImpl')"/>
<!-- Main loop over all classes in the OpenMM namespace -->
<xsl:template match="/GCC_XML">
#ifndef AMOEBA_OPENMM_CWRAPPER_H_
#define AMOEBA_OPENMM_CWRAPPER_H_
#ifndef OPENMM_EXPORT_AMOEBA
#define OPENMM_EXPORT_AMOEBA
#endif
/* Global Constants */
<xsl:for-each select="Variable[@context=$openmm_namespace_id]">
static <xsl:call-template name="wrap_type"><xsl:with-param name="type_id" select="@type"/></xsl:call-template><xsl:value-of select="concat(' OpenMM_', @name, ' = ', number(@init), ';')"/>
</xsl:for-each>
/* Type Declarations */
<xsl:for-each select="(Class | Struct)[@context=$openmm_namespace_id and empty(index-of($skip_classes, @name))]">
typedef struct OpenMM_<xsl:value-of select="concat(@name, '_struct OpenMM_', @name, ';')"/>
</xsl:for-each>
typedef struct OpenMM_2D_IntArray_struct OpenMM_2D_IntArray;
typedef struct OpenMM_3D_DoubleArray_struct OpenMM_3D_DoubleArray;
#if defined(__cplusplus)
extern "C" {
#endif
/* OpenMM_3D_DoubleArray */
OPENMM_EXPORT_AMOEBA OpenMM_3D_DoubleArray* OpenMM_3D_DoubleArray_create(int size1, int size2, int size3);
OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array, int index1, int index2, OpenMM_DoubleArray* values);
OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy( OpenMM_3D_DoubleArray* array);
<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>
<!-- Class members -->
<xsl:for-each select="Class[@context=$openmm_namespace_id and empty(index-of($skip_classes, @name))]">
<xsl:call-template name="class"/>
</xsl:for-each>
#if defined(__cplusplus)
}
#endif
#endif /*AMOEBA_OPENMM_CWRAPPER_H_*/
</xsl:template>
<!-- Print out the declarations for a (Primitive)Array type -->
<xsl:template name="primitive_array">
<xsl:param name="element_type"/>
<xsl:param name="name"/>
/* <xsl:value-of select="$name"/> */
extern OPENMM_EXPORT_AMOEBA <xsl:value-of select="$name"/>* <xsl:value-of select="$name"/>_create(int size);
extern OPENMM_EXPORT_AMOEBA void <xsl:value-of select="$name"/>_destroy(<xsl:value-of select="$name"/>* array);
extern OPENMM_EXPORT_AMOEBA int <xsl:value-of select="$name"/>_getSize(const <xsl:value-of select="$name"/>* array);
extern OPENMM_EXPORT_AMOEBA void <xsl:value-of select="$name"/>_resize(<xsl:value-of select="$name"/>* array, int size);
extern OPENMM_EXPORT_AMOEBA void <xsl:value-of select="$name"/>_append(<xsl:value-of select="$name"/>* array, <xsl:value-of select="$element_type"/> value);
extern OPENMM_EXPORT_AMOEBA void <xsl:value-of select="$name"/>_set(<xsl:value-of select="$name"/>* array, int index, <xsl:value-of select="$element_type"/> value);
extern OPENMM_EXPORT_AMOEBA <xsl:value-of select="concat($element_type, ' ', $name)"/>_get(const <xsl:value-of select="$name"/>* array, int index);
</xsl:template>
<!-- Print out information for a class -->
<xsl:template name="class">
<xsl:variable name="class_name" select="@name"/>
<xsl:variable name="class_id" select="@id"/>
/* OpenMM::<xsl:value-of select="concat(@name, '*/')"/>
<!-- Enumerations -->
<xsl:for-each select="/GCC_XML/Enumeration[@context=$class_id and @access='public']">
<xsl:call-template name="enumeration">
<xsl:with-param name="class_name" select="$class_name"/>
</xsl:call-template>
</xsl:for-each>
<!-- Constructors and destructor -->
<xsl:if test="not(@abstract=1)">
<xsl:variable name="constructors" select="/GCC_XML/Constructor[@context=$class_id and @access='public' and not(@artificial='1')]"/>
<xsl:for-each select="$constructors">
<xsl:call-template name="constructor">
<xsl:with-param name="suffix" select="if (position() > 1) then concat('_', position()) else ''"/>
</xsl:call-template>
</xsl:for-each>
</xsl:if>
extern OPENMM_EXPORT_AMOEBA void OpenMM_<xsl:value-of select="concat(@name, '_destroy(OpenMM_', @name, '* target);')"/>
<!-- Methods -->
<xsl:variable name="methods" select="/GCC_XML/Method[@context=$class_id and @access='public']"/>
<xsl:for-each select="$methods">
<xsl:variable name="node" select="."/>
<!-- The next line is to deal with overloaded methods that have a const and a non-const version. -->
<xsl:if test="not(@const=1) or empty($methods[@name=$node/@name and not(@const=1)])">
<xsl:variable name="hide">
<xsl:call-template name="should_hide"/>
</xsl:variable>
<xsl:if test="string-length($hide)=0">
<xsl:call-template name="method">
<xsl:with-param name="class_name" select="$class_name"/>
</xsl:call-template>
</xsl:if>
</xsl:if>
</xsl:for-each>
</xsl:template>
<!-- Print out the declaration for an enumeration -->
<xsl:template name="enumeration">
<xsl:param name="class_name"/>
typedef enum {
<xsl:for-each select="EnumValue">
<xsl:value-of select="concat('OpenMM_', $class_name, '_', @name, ' = ', @init)"/>
<xsl:if test="position() &lt; last()">, </xsl:if>
</xsl:for-each>
} OpenMM_<xsl:value-of select="concat($class_name, '_', @name, ';')"/>
</xsl:template>
<!-- Print out the declaration for a constructor -->
<xsl:template name="constructor">
<xsl:param name="suffix"/>
extern OPENMM_EXPORT_AMOEBA OpenMM_<xsl:value-of select="concat(@name, '* OpenMM_', @name, '_create', $suffix, '(')"/>
<xsl:for-each select="Argument">
<xsl:if test="position() > 1">, </xsl:if>
<xsl:call-template name="wrap_type"><xsl:with-param name="type_id" select="@type"/></xsl:call-template>
<xsl:value-of select="concat(' ', @name)"/>
</xsl:for-each>
<xsl:value-of select="');'"/>
</xsl:template>
<!-- Print out the declaration for a method -->
<xsl:template name="method">
<xsl:param name="class_name"/>
extern OPENMM_EXPORT_AMOEBA <xsl:call-template name="wrap_type"><xsl:with-param name="type_id" select="@returns"/></xsl:call-template><xsl:value-of select="concat(' OpenMM_', $class_name, '_', @name, '(')"/>
<xsl:if test="not(@static='1')">
<xsl:if test="@const='1'">
<xsl:value-of select="'const '"/>
</xsl:if>
<xsl:value-of select="concat('OpenMM_', $class_name, '* target')"/>
</xsl:if>
<xsl:variable name="static" select="@static"/>
<xsl:for-each select="Argument">
<xsl:if test="position() > 1 or not($static='1')">, </xsl:if>
<xsl:call-template name="wrap_type"><xsl:with-param name="type_id" select="@type"/></xsl:call-template>
<xsl:value-of select="concat(' ', @name)"/>
</xsl:for-each>
<xsl:value-of select="');'"/>
</xsl:template>
<!-- Print out the description of a type in the wrapper API -->
<xsl:template name="wrap_type">
<xsl:param name="type_id"/>
<xsl:variable name="node" select="/GCC_XML/*[@id=$type_id]"/>
<xsl:choose>
<xsl:when test="$type_id=$bool_type_id">
<xsl:value-of select="'OpenMM_Boolean'"/>
</xsl:when>
<xsl:when test="$type_id=$string_type_id">
<xsl:value-of select="'char*'"/>
</xsl:when>
<xsl:when test="$type_id=$const_ref_string_type_id">
<xsl:value-of select="'const char*'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_string_type_id">
<xsl:value-of select="'OpenMM_StringArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_vec3_type_id">
<xsl:value-of select="'OpenMM_Vec3Array'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_tortor_type_id">
<xsl:value-of select="'OpenMM_3D_DoubleArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_bond_type_id">
<xsl:value-of select="'OpenMM_BondArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_2d_int_type_id">
<xsl:value-of select="'OpenMM_2D_IntArray'"/>
</xsl:when>
<xsl:when test="$type_id=$map_parameter_type_id">
<xsl:value-of select="'OpenMM_ParameterArray'"/>
</xsl:when>
<xsl:when test="$type_id=$map_property_type_id">
<xsl:value-of select="'OpenMM_PropertyArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_double_type_id">
<xsl:value-of select="'OpenMM_DoubleArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_int_type_id">
<xsl:value-of select="'OpenMM_IntArray'"/>
</xsl:when>
<xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType'">
<xsl:call-template name="wrap_type">
<xsl:with-param name="type_id" select="$node/@type"/>
</xsl:call-template>
<xsl:value-of select="'*'"/>
</xsl:when>
<xsl:when test="local-name($node)='CvQualifiedType'">
<xsl:if test="$node/@const=1">
<xsl:value-of select="'const '"/>
</xsl:if>
<xsl:call-template name="wrap_type">
<xsl:with-param name="type_id" select="$node/@type"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="local-name($node)='Enumeration'">
<xsl:variable name="class_name" select="/GCC_XML/Class[@id=$node/@context]/@name"/>
<xsl:value-of select="concat('OpenMM_', $class_name, '_', $node/@name)"/>
</xsl:when>
<xsl:when test="$node/@context=$openmm_namespace_id">
<xsl:value-of select="concat('OpenMM_', $node/@name)"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="$node/@name"/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<!-- Determine whether a method should be hidden -->
<xsl:template name="should_hide">
<xsl:variable name="class_id" select="@context"/>
<xsl:variable name="method_name" select="concat('OpenMM_', /GCC_XML/Class[@id=$class_id]/@name, '_', @name)"/>
<xsl:if test="not(empty(index-of($skip_methods, $method_name)))">1</xsl:if>
<xsl:call-template name="hide_type">
<xsl:with-param name="type_id" select="@returns"/>
</xsl:call-template>
<xsl:for-each select="Argument">
<xsl:call-template name="hide_type">
<xsl:with-param name="type_id" select="@type"/>
</xsl:call-template>
</xsl:for-each>
</xsl:template>
<!-- This is called by should_hide. It generates output if the specified type should be hidden. -->
<xsl:template name="hide_type">
<xsl:param name="type_id"/>
<xsl:variable name="node" select="/GCC_XML/*[@id=$type_id]"/>
<xsl:choose>
<xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType' or local-name($node)='CvQualifiedType'">
<xsl:call-template name="hide_type">
<xsl:with-param name="type_id" select="$node/@type"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="local-name($node)='Enumeration'">
<xsl:call-template name="hide_type">
<xsl:with-param name="type_id" select="$node/@context"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="$node/@context=$openmm_namespace_id and not(empty(index-of($hide_classes, $node/@name)))">
<xsl:value-of select="1"/>
</xsl:when>
</xsl:choose>
</xsl:template>
</xsl:stylesheet>
plugins/amoeba/wrappers/CWrapper_Source.xslt deleted 100644 → 0
View file @ 99ef4344
<?xml version="1.0" encoding="ISO-8859-1"?>
<xsl:stylesheet version="2.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output method="text" omit-xml-declaration="yes"/>
<xsl:variable name="std_namespace_id" select="/GCC_XML/Namespace[@name='std']/@id"/>
<xsl:variable name="openmm_namespace_id" select="/GCC_XML/Namespace[@name='OpenMM']/@id"/>
<xsl:variable name="void_type_id" select="/GCC_XML/FundamentalType[@name='void']/@id"/>
<xsl:variable name="bool_type_id" select="/GCC_XML/FundamentalType[@name='bool']/@id"/>
<xsl:variable name="double_type_id" select="/GCC_XML/FundamentalType[@name='double']/@id"/>
<xsl:variable name="string_type_id" select="/GCC_XML/*[@name='string' and @context=$std_namespace_id]/@id"/>
<xsl:variable name="const_string_type_id" select="/GCC_XML/CvQualifiedType[@type=$string_type_id]/@id"/>
<xsl:variable name="const_ref_string_type_id" select="/GCC_XML/ReferenceType[@type=$const_string_type_id]/@id"/>
<xsl:variable name="vec3_type_id" select="/GCC_XML/Class[@name='Vec3' and @context=$openmm_namespace_id]/@id"/>
<xsl:variable name="vector_string_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::basic_string')]/@id"/>
<xsl:variable name="vector_vec3_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;OpenMM::Vec3')]/@id"/>
<xsl:variable name="vector_bond_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::pair&lt;int, int')]/@id"/>
<xsl:variable name="vector_2d_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::vector&lt;int')]/@id"/>
<xsl:variable name="map_parameter_type_id" select="/GCC_XML/Class[starts-with(@name, 'map&lt;std::basic_string') and contains(@name, 'double')]/@id"/>
<xsl:variable name="map_property_type_id" select="/GCC_XML/Class[starts-with(@name, 'map&lt;std::basic_string') and not(contains(@name, 'double'))]/@id"/>
<xsl:variable name="vector_double_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;double')]/@id"/>
<xsl:variable name="vector_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;int')]/@id"/>
<xsl:variable name="vector_tortor_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::vector&lt;std::vector&lt;double')]/@id"/>
<xsl:variable name="newline">
<xsl:text>
</xsl:text>
</xsl:variable>
<!-- Do not generate functions for the following classes -->
<xsl:variable name="skip_classes" select="('Vec3', 'Context', 'Kernel', 'System', 'Stream', 'KernelImpl', 'StreamImpl', 'KernelFactory', 'StreamFactory', 'ContextImpl', 'OpenMMException', 'Force', 'ForceImpl')"/>
<!-- Do not generate the following functions -->
<xsl:variable name="skip_methods" select="('OpenMM_Context_getState', 'OpenMM_Platform_loadPluginsFromDirectory')"/>
<!-- Suppress any function which references any of the following classes -->
<xsl:variable name="hide_classes" select="('Kernel', 'Stream', 'KernelImpl', 'StreamImpl', 'KernelFactory', 'StreamFactory', 'ContextImpl')"/>
<!-- Main loop over all classes in the OpenMM namespace -->
<xsl:template match="/GCC_XML">
#include "OpenMM.h"
#include "OpenMMAmoeba.h"
#include "../../../wrappers/OpenMMCWrapper.h"
#include "AmoebaOpenMMCWrapper.h"
#include &lt;cstring&gt;
#include &lt;vector&gt;
using namespace OpenMM;
using namespace std;
extern "C" {
/* OpenMM_2D_IntArray */
OPENMM_EXPORT_AMOEBA OpenMM_2D_IntArray* OpenMM_2D_IntArray_create(int size) {
return reinterpret_cast&lt;OpenMM_2D_IntArray*&gt;(new vector&lt;vector&lt;int&gt; &gt;(size));
}
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_destroy(OpenMM_2D_IntArray* array) {
delete reinterpret_cast&lt;vector&lt;vector&lt;int&gt; &gt;*&gt;(array);
}
OPENMM_EXPORT_AMOEBA int OpenMM_2D_IntArray_getSize(const OpenMM_2D_IntArray* array) {
return reinterpret_cast&lt;const vector&lt;vector&lt;int&gt; &gt;*&gt;(array)->size();
}
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_resize(OpenMM_2D_IntArray* array, int size) {
reinterpret_cast&lt;vector&lt;vector&lt;int&gt; &gt;*&gt;(array)->resize(size);
}
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_append(OpenMM_2D_IntArray* array, int index1, int value ) {
vector&lt;vector&lt;int&gt; &gt;* array2DInt = reinterpret_cast&lt;vector&lt;vector&lt;int&gt; &gt;*&gt;(array);
if( array2DInt->size() &lt;= index1 ){
array2DInt->resize( index1+1 );
}
(*array2DInt)[index1].push_back( value );
}
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_set(OpenMM_2D_IntArray* array, int index1, int index2, int value) {
vector&lt;vector&lt;int&gt; &gt;* array2DInt = reinterpret_cast&lt;vector&lt;vector&lt;int&gt; &gt;*&gt;(array);
if( array2DInt->size() &lt;= index1 ){
array2DInt->resize( index1+1 );
}
if( array2DInt[index1].size() &lt;= index2 ){
array2DInt[index1].resize( index2+1 );
}
(*array2DInt)[index1][index2] = value;
}
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_get(const OpenMM_2D_IntArray* array, int index1, int index2, int* value) {
const vector&lt;vector&lt;int&gt; &gt;* array2DInt = reinterpret_cast&lt;const vector&lt;vector&lt;int&gt; &gt;*&gt;(array);
if ( array2DInt->size() &lt;= index1 )
throw OpenMMException("OpenMM_2D_IntArray_get: first index out of range.");
if ( (*array2DInt)[index1].size() &lt;= index2 )
throw OpenMMException("OpenMM_2D_IntArray_get: second index out of range.");
*value = (*array2DInt)[index1][index2];
}
/* OpenMM_3D_DoubleArray */
OPENMM_EXPORT_AMOEBA OpenMM_3D_DoubleArray* OpenMM_3D_DoubleArray_create(int size1, int size2, int size3) {
int ii, jj;
std::vector&lt; std::vector&lt; std::vector&lt;double&gt; &gt; &gt;* v3D_Array = new std::vector&lt;std::vector&lt;std::vector&lt;double&gt; &gt; &gt;(size1);
for( ii = 0; ii &lt; size1; ii++ ){
(*v3D_Array)[ii].resize(size2);
for( jj = 0; jj &lt; size2; jj++ ){
(*v3D_Array)[ii][jj].resize(size3);
}
}
return reinterpret_cast&lt;OpenMM_3D_DoubleArray*&gt;(v3D_Array);
}
OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array, int index1, int index2, OpenMM_DoubleArray* values) {
unsigned int ii;
std::vector&lt; std::vector&lt; std::vector&lt;double&gt; &gt; &gt;* v3D_Array = reinterpret_cast&lt;std::vector&lt;std::vector&lt;std::vector&lt;double&gt; &gt; &gt;*&gt;(array);
std::vector&lt;double&gt; * value_array = reinterpret_cast&lt;std::vector&lt;double&gt; *&gt;(values);
for( ii = 0; ii &lt; (*value_array).size(); ii++ ){
(*v3D_Array)[index1][index2][ii] = (*value_array)[ii];
}
}
OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy( OpenMM_3D_DoubleArray* array) {
delete reinterpret_cast&lt;std::vector&lt;std::vector&lt;std::vector&lt;double&gt; &gt; &gt;*&gt;(array);
}
<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>
<!-- Class members -->
<xsl:for-each select="Class[@context=$openmm_namespace_id and empty(index-of($skip_classes, @name))]">
<xsl:call-template name="class"/>
</xsl:for-each>
}
</xsl:template>
<!-- Print out the definitions for a (Primitive)Array type -->
<xsl:template name="primitive_array">
<xsl:param name="element_type"/>
<xsl:param name="name"/>
/* <xsl:value-of select="$name"/> */
OPENMM_EXPORT_AMOEBA <xsl:value-of select="$name"/>* <xsl:value-of select="$name"/>_create(int size) {
return reinterpret_cast&lt;<xsl:value-of select="$name"/>*&gt;(new vector&lt;<xsl:value-of select="$element_type"/>&gt;(size));
}
OPENMM_EXPORT_AMOEBA void <xsl:value-of select="$name"/>_destroy(<xsl:value-of select="$name"/>* array) {
delete reinterpret_cast&lt;vector&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(array);
}
OPENMM_EXPORT_AMOEBA int <xsl:value-of select="$name"/>_getSize(const <xsl:value-of select="$name"/>* array) {
return reinterpret_cast&lt;const vector&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(array)->size();
}
OPENMM_EXPORT_AMOEBA void <xsl:value-of select="$name"/>_resize(<xsl:value-of select="$name"/>* array, int size) {
reinterpret_cast&lt;vector&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(array)->resize(size);
}
OPENMM_EXPORT_AMOEBA void <xsl:value-of select="$name"/>_append(<xsl:value-of select="$name"/>* array, <xsl:value-of select="$element_type"/> value) {
reinterpret_cast&lt;vector&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(array)->push_back(value);
}
OPENMM_EXPORT_AMOEBA void <xsl:value-of select="$name"/>_set(<xsl:value-of select="$name"/>* array, int index, <xsl:value-of select="$element_type"/> value) {
(*reinterpret_cast&lt;vector&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(array))[index] = value;
}
OPENMM_EXPORT_AMOEBA <info xml:space="preserve"> <xsl:value-of select="$element_type"/> <xsl:value-of select="$name"/>_get(const <xsl:value-of select="$name"/>* array, int index) {
return (*reinterpret_cast&lt;const vector&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(array))[index];
}
</info>
</xsl:template>
<!-- Print out information for a class -->
<xsl:template name="class">
<xsl:variable name="class_name" select="@name"/>
<xsl:variable name="class_id" select="@id"/>
/* OpenMM::<xsl:value-of select="concat(@name, '*/')"/>
<!-- Constructors and destructor -->
<xsl:if test="not(@abstract=1)">
<xsl:variable name="constructors" select="/GCC_XML/Constructor[@context=$class_id and @access='public' and not(@artificial='1')]"/>
<xsl:for-each select="$constructors">
<xsl:call-template name="constructor">
<xsl:with-param name="suffix" select="if (position() > 1) then concat('_', position()) else ''"/>
</xsl:call-template>
</xsl:for-each>
</xsl:if>
OPENMM_EXPORT_AMOEBA void OpenMM_<xsl:value-of select="concat(@name, '_destroy(OpenMM_', @name, '* target) {')"/>
delete reinterpret_cast&lt;<xsl:value-of select="@name"/>*&gt;(target);
}
<!-- Methods -->
<xsl:variable name="methods" select="/GCC_XML/Method[@context=$class_id and @access='public']"/>
<xsl:for-each select="$methods">
<xsl:variable name="node" select="."/>
<!-- The next line is to deal with overloaded methods that have a const and a non-const version. -->
<xsl:if test="not(@const=1) or empty($methods[@name=$node/@name and not(@const=1)])">
<xsl:variable name="hide">
<xsl:call-template name="should_hide"/>
</xsl:variable>
<xsl:if test="string-length($hide)=0">
<xsl:call-template name="method">
<xsl:with-param name="class_name" select="$class_name"/>
<xsl:with-param name="class_id" select="$class_id"/>
</xsl:call-template>
</xsl:if>
</xsl:if>
</xsl:for-each>
</xsl:template>
<!-- Print out the definition of a constructor -->
<xsl:template name="constructor">
<xsl:param name="suffix"/>
OPENMM_EXPORT_AMOEBA OpenMM_<xsl:value-of select="concat(@name, '* OpenMM_', @name, '_create', $suffix, '(')"/>
<xsl:for-each select="Argument">
<xsl:if test="position() > 1">, </xsl:if>
<xsl:call-template name="wrap_type"><xsl:with-param name="type_id" select="@type"/></xsl:call-template>
<xsl:value-of select="concat(' ', @name)"/>
</xsl:for-each>
<xsl:value-of select="') {'"/>
return reinterpret_cast&lt;OpenMM_<xsl:value-of select="@name"/>*&gt;(new <xsl:value-of select="concat(@name, '(')"/>
<xsl:for-each select="Argument">
<xsl:if test="position() > 1">, </xsl:if>
<xsl:call-template name="unwrap_value">
<xsl:with-param name="value" select="@name"/>
<xsl:with-param name="type_id" select="@type"/>
</xsl:call-template>
</xsl:for-each>
<xsl:value-of select="'));'"/>
}
</xsl:template>
<!-- Print out the definition of a method -->
<xsl:template name="method">
<xsl:param name="class_name"/>
<xsl:param name="class_id"/>
<!-- First the method signature -->
<xsl:value-of select="$newline"/>
OPENMM_EXPORT_AMOEBA <xsl:call-template name="wrap_type"><xsl:with-param name="type_id" select="@returns"/></xsl:call-template><xsl:value-of select="concat(' OpenMM_', $class_name, '_', @name, '(')"/>
<xsl:if test="not(@static='1')">
<xsl:if test="@const='1'">
<xsl:value-of select="'const '"/>
</xsl:if>
<xsl:value-of select="concat('OpenMM_', $class_name, '* target')"/>
</xsl:if>
<!-- Generate the list of arguments -->
<xsl:variable name="method" select="."/>
<xsl:for-each select="Argument">
<xsl:if test="position() > 1 or not($method/@static='1')">, </xsl:if>
<xsl:call-template name="wrap_type"><xsl:with-param name="type_id" select="@type"/></xsl:call-template>
<xsl:value-of select="concat(' ', @name)"/>
</xsl:for-each>
<xsl:value-of select="concat(') {', $newline, ' ')"/>
<!-- Now the method body -->
<xsl:if test="not(@returns=$void_type_id)">
<xsl:call-template name="unwrap_type"><xsl:with-param name="type_id" select="@returns"/></xsl:call-template>
<xsl:value-of select="' result = '"/>
</xsl:if>
<xsl:variable name="return_type" select="/GCC_XML/*[@id=$method/@returns]"/>
<xsl:if test="local-name($return_type)='ReferenceType'">
<xsl:value-of select="'&amp;'"/>
</xsl:if>
<xsl:choose>
<xsl:when test="@static='1'">
<!-- Invoke the method on the class -->
<xsl:value-of select="concat($class_name, '::')"/>
</xsl:when>
<xsl:otherwise>
<!-- Invoke the method on the target object -->
<xsl:value-of select="'reinterpret_cast&lt;'"/>
<xsl:if test="@const='1'">
<xsl:value-of select="'const '"/>
</xsl:if>
<xsl:value-of select="concat($class_name, '*&gt;(target)->')"/>
</xsl:otherwise>
</xsl:choose>
<xsl:value-of select="concat(@name, '(')"/>
<xsl:for-each select="Argument">
<xsl:if test="position() > 1">, </xsl:if>
<xsl:call-template name="unwrap_value">
<xsl:with-param name="value" select="@name"/>
<xsl:with-param name="type_id" select="@type"/>
</xsl:call-template>
</xsl:for-each>
<xsl:value-of select="');'"/>
<xsl:if test="not(@returns=$void_type_id)">
<xsl:value-of select="concat($newline, ' return ')"/>
<xsl:call-template name="wrap_value"><xsl:with-param name="value" select="'result'"/><xsl:with-param name="type_id" select="@returns"/></xsl:call-template>
<xsl:value-of select="';'"/>
</xsl:if>
};
</xsl:template>
<!-- Print out the description of a type in the wrapper API -->
<xsl:template name="wrap_type">
<xsl:param name="type_id"/>
<xsl:variable name="node" select="/GCC_XML/*[@id=$type_id]"/>
<xsl:choose>
<xsl:when test="$type_id=$bool_type_id">
<xsl:value-of select="'OpenMM_Boolean'"/>
</xsl:when>
<xsl:when test="$type_id=$string_type_id">
<xsl:value-of select="'char*'"/>
</xsl:when>
<xsl:when test="$type_id=$const_ref_string_type_id">
<xsl:value-of select="'const char*'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_string_type_id">
<xsl:value-of select="'OpenMM_StringArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_vec3_type_id">
<xsl:value-of select="'OpenMM_Vec3Array'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_bond_type_id">
<xsl:value-of select="'OpenMM_BondArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_tortor_type_id">
<xsl:value-of select="'OpenMM_3D_DoubleArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_2d_int_type_id">
<xsl:value-of select="'OpenMM_2D_IntArray'"/>
</xsl:when>
<xsl:when test="$type_id=$map_parameter_type_id">
<xsl:value-of select="'OpenMM_ParameterArray'"/>
</xsl:when>
<xsl:when test="$type_id=$map_property_type_id">
<xsl:value-of select="'OpenMM_PropertyArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_double_type_id">
<xsl:value-of select="'OpenMM_DoubleArray'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_int_type_id">
<xsl:value-of select="'OpenMM_IntArray'"/>
</xsl:when>
<xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType'">
<xsl:call-template name="wrap_type">
<xsl:with-param name="type_id" select="$node/@type"/>
</xsl:call-template>
<xsl:value-of select="'*'"/>
</xsl:when>
<xsl:when test="local-name($node)='CvQualifiedType'">
<xsl:if test="$node/@const=1">
<xsl:value-of select="'const '"/>
</xsl:if>
<xsl:call-template name="wrap_type">
<xsl:with-param name="type_id" select="$node/@type"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="local-name($node)='Enumeration'">
<xsl:variable name="class_name" select="/GCC_XML/Class[@id=$node/@context]/@name"/>
<xsl:value-of select="concat('OpenMM_', $class_name, '_', $node/@name)"/>
</xsl:when>
<xsl:when test="$node/@context=$openmm_namespace_id">
<xsl:value-of select="concat('OpenMM_', $node/@name)"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="$node/@name"/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<!-- Print out the description of a type in the native API -->
<xsl:template name="unwrap_type">
<xsl:param name="type_id"/>
<xsl:variable name="node" select="/GCC_XML/*[@id=$type_id]"/>
<xsl:choose>
<xsl:when test="$type_id=$vector_string_type_id">
<xsl:value-of select="'vector&lt;string&gt;'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_vec3_type_id">
<xsl:value-of select="'vector&lt;Vec3&gt;'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_bond_type_id">
<xsl:value-of select="'vector&lt;pair&lt;int, int&gt; &gt;'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_2d_int_type_id">
<xsl:value-of select="'vector&lt;vector&lt;int&gt; &gt;'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_tortor_type_id">
<xsl:value-of select="'vector&lt;vector&lt;vector&lt;double&gt; &gt; &gt;'"/>
</xsl:when>
<xsl:when test="$type_id=$map_parameter_type_id">
<xsl:value-of select="'map&lt;string, double&gt;'"/>
</xsl:when>
<xsl:when test="$type_id=$map_property_type_id">
<xsl:value-of select="'map&lt;string, string&gt;'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_double_type_id">
<xsl:value-of select="'vector&lt;double&gt;'"/>
</xsl:when>
<xsl:when test="$type_id=$vector_int_type_id">
<xsl:value-of select="'vector&lt;int&gt;'"/>
</xsl:when>
<xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType'">
<xsl:call-template name="unwrap_type">
<xsl:with-param name="type_id" select="$node/@type"/>
</xsl:call-template>
<xsl:value-of select="'*'"/>
</xsl:when>
<xsl:when test="local-name($node)='CvQualifiedType'">
<xsl:if test="$node/@const=1">
<xsl:value-of select="'const '"/>
</xsl:if>
<xsl:call-template name="unwrap_type">
<xsl:with-param name="type_id" select="$node/@type"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="local-name($node)='Enumeration'">
<xsl:variable name="class_name" select="/GCC_XML/Class[@id=$node/@context]/@name"/>
<xsl:value-of select="concat($class_name, '::', $node/@name)"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="$node/@name"/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<!-- Print out a value, if necessary casting from a native type to a wrapped type -->
<xsl:template name="wrap_value">
<xsl:param name="value"/>
<xsl:param name="type_id"/>
<xsl:variable name="node" select="/GCC_XML/*[@id=$type_id]"/>
<xsl:choose>
<xsl:when test="$type_id=$bool_type_id">
<xsl:value-of select="concat('(', $value, ' ? OpenMM_True : OpenMM_False)')"/>
</xsl:when>
<xsl:when test="$type_id=$string_type_id">
<xsl:value-of select="concat($value, '.c_str()')"/>
</xsl:when>
<xsl:when test="$type_id=$const_ref_string_type_id">
<xsl:value-of select="concat($value, '->c_str()')"/>
</xsl:when>
<xsl:when test="local-name($node)='FundamentalType'">
<xsl:value-of select="$value"/>
</xsl:when>
<xsl:otherwise>
<xsl:choose>
<xsl:when test="local-name($node)='Enumeration'">
<xsl:value-of select="'static_cast&lt;'"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="'reinterpret_cast&lt;'"/>
</xsl:otherwise>
</xsl:choose>
<xsl:call-template name="wrap_type">
<xsl:with-param name="type_id" select="$type_id"/>
</xsl:call-template>
<xsl:value-of select="concat('&gt;(', $value, ')')"/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<!-- Print out a value, if necessary casting from a wrapped type to a native type -->
<xsl:template name="unwrap_value">
<xsl:param name="value"/>
<xsl:param name="type_id"/>
<xsl:variable name="node" select="/GCC_XML/*[@id=$type_id]"/>
<xsl:choose>
<xsl:when test="$type_id=$bool_type_id">
<xsl:value-of select="concat('(', $value, ' != OpenMM_False)')"/>
</xsl:when>
<xsl:when test="$type_id=$string_type_id">
<xsl:value-of select="concat('string(', $value, ')')"/>
</xsl:when>
<xsl:when test="$type_id=$const_ref_string_type_id">
<xsl:value-of select="concat('string(', $value, ')')"/>
</xsl:when>
<xsl:when test="local-name($node)='FundamentalType'">
<xsl:value-of select="$value"/>
</xsl:when>
<xsl:when test="$type_id=$vec3_type_id">
<xsl:value-of select="concat('Vec3(', $value, '.x, ', $value, '.y, ', $value, '.z)')"/>
</xsl:when>
<xsl:otherwise>
<xsl:if test="local-name($node)='ReferenceType'"><xsl:value-of select="'*'"/></xsl:if>
<xsl:choose>
<xsl:when test="local-name($node)='Enumeration'">
<xsl:value-of select="'static_cast&lt;'"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="'reinterpret_cast&lt;'"/>
</xsl:otherwise>
</xsl:choose>
<xsl:call-template name="unwrap_type">
<xsl:with-param name="type_id" select="$type_id"/>
</xsl:call-template>
<xsl:value-of select="concat(' &gt;(', $value, ')')"/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<!-- Determine whether a method should be hidden -->
<xsl:template name="should_hide">
<xsl:variable name="class_id" select="@context"/>
<xsl:variable name="method_name" select="concat('OpenMM_', /GCC_XML/Class[@id=$class_id]/@name, '_', @name)"/>
<xsl:if test="not(empty(index-of($skip_methods, $method_name)))">1</xsl:if>
<xsl:call-template name="hide_type">
<xsl:with-param name="type_id" select="@returns"/>
</xsl:call-template>
<xsl:for-each select="Argument">
<xsl:call-template name="hide_type">
<xsl:with-param name="type_id" select="@type"/>
</xsl:call-template>
</xsl:for-each>
</xsl:template>
<!-- This is called by should_hide. It generates output if the specified type should be hidden. -->
<xsl:template name="hide_type">
<xsl:param name="type_id"/>
<xsl:variable name="node" select="/GCC_XML/*[@id=$type_id]"/>
<xsl:choose>
<xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType' or local-name($node)='CvQualifiedType'">
<xsl:call-template name="hide_type">
<xsl:with-param name="type_id" select="$node/@type"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="local-name($node)='Enumeration'">
<xsl:call-template name="hide_type">
<xsl:with-param name="type_id" select="$node/@context"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="$node/@context=$openmm_namespace_id and not(empty(index-of($hide_classes, $node/@name)))">
<xsl:value-of select="1"/>
</xsl:when>
</xsl:choose>
</xsl:template>
</xsl:stylesheet>
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