Skip to content

GitLab

Commit 6185317a authored by peastman's avatar peastman
Browse files

Implemented serialization for Drude plugin

parent 6f98dd5f
Hide whitespace changes
Inline Side-by-side
Showing with 659 additions and 7 deletions
plugins/drude/CMakeLists.txt
View file @ 6185317a
...@@ -205,9 +205,9 @@ ELSE (EXECUTABLE_OUTPUT_PATH) ...@@ -205,9 +205,9 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
SET (TEST_PATH .) SET (TEST_PATH .)
ENDIF (EXECUTABLE_OUTPUT_PATH) ENDIF (EXECUTABLE_OUTPUT_PATH)
#IF (OPENMM_BUILD_SERIALIZATION_SUPPORT) IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
# ADD_SUBDIRECTORY(serialization) ADD_SUBDIRECTORY(serialization)
#ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT) ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
#INCLUDE(ApiDoxygen.cmake) #INCLUDE(ApiDoxygen.cmake)
......
plugins/drude/platforms/cuda/src/CudaDrudeKernelFactory.cpp
View file @ 6185317a
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMMAmoeba * * OpenMMDrude *
* -------------------------------------------------------------------------- * * -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from * * This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of * * Simbios, the NIH National Center for Physics-Based Simulation of *
......
plugins/drude/platforms/opencl/src/OpenCLDrudeKernelFactory.cpp
View file @ 6185317a
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMMAmoeba * * OpenMMDrude *
* -------------------------------------------------------------------------- * * -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from * * This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of * * Simbios, the NIH National Center for Physics-Based Simulation of *
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernelFactory.cpp
View file @ 6185317a
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMMAmoeba * * OpenMMDrude *
* -------------------------------------------------------------------------- * * -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from * * This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of * * Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2011 Stanford University and the Authors. * * Portions copyright (c) 2011-2013 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
......
plugins/drude/serialization/CMakeLists.txt 0 → 100644
View file @ 6185317a
#---------------------------------------------------
# OpenMMDrude Serialization Library
#
# Creates OpenMMDrude serializatin library, base name=OpenMMDrudeSerialization.
# Default libraries are shared & optimized. Variants
# are created for static (_static) and debug (_d).
#
# Windows:
# OpenMMDrudeSerialization[_d].dll
# OpenMMDrudeSerialization[_d].lib
# Unix:
# libOpenMMDrudeSerialization[_d].so
#----------------------------------------------------
# The source is organized into subdirectories, but we handle them all from
# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
SET(OPENMM_SOURCE_SUBDIRS . ../../../serialization)
SET(OPENMM_DRUDE_SOURCE_SUBDIRS . )
# Collect up information about the version of the OpenMM library we're building
# and make it available to the code so it can be built into the binaries.
SET(OPENMM_DRUDE_LIBRARY_NAME OpenMMDrude)
SET(OPENMM_SERIALIZATION_LIBRARY_NAME OpenMMSerialization)
SET(OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME OpenMMDrudeSerialization)
# Ensure that debug libraries have "_d" appended to their names.
# CMake gets this right on Windows automatically with this definition.
IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
# But on Unix or Cygwin we have to add the suffix manually
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(OPENMM_DRUDE_LIBRARY_NAME ${OPENMM_DRUDE_LIBRARY_NAME}_d)
SET(OPENMM_SERIALIZATION_LIBRARY_NAME ${OPENMM_SERIALIZATION_LIBRARY_NAME}_d)
SET(OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME ${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME}_d)
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
# These are all the places to search for header files which are
# to be part of the API.
SET(API_INCLUDE_DIRS) # start empty
FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
# append
SET(API_INCLUDE_DIRS ${API_INCLUDE_DIRS}
${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
ENDFOREACH(subdir)
# We'll need both *relative* path names, starting with their API_INCLUDE_DIRS,
# and absolute pathnames.
SET(API_REL_INCLUDE_FILES) # start these out empty
SET(API_ABS_INCLUDE_FILES)
FOREACH(dir ${API_INCLUDE_DIRS})
FILE(GLOB fullpaths ${dir}/*.h) # returns full pathnames
SET(API_ABS_INCLUDE_FILES ${API_ABS_INCLUDE_FILES} ${fullpaths})
FOREACH(pathname ${fullpaths})
GET_FILENAME_COMPONENT(filename ${pathname} NAME)
SET(API_REL_INCLUDE_FILES ${API_REL_INCLUDE_FILES} ${dir}/${filename})
ENDFOREACH(pathname)
ENDFOREACH(dir)
# collect up source files
SET(SOURCE_FILES) # empty
SET(SOURCE_INCLUDE_FILES)
FOREACH(subdir ${OPENMM_DRUDE_SOURCE_SUBDIRS})
FILE(GLOB_RECURSE src_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.c)
FILE(GLOB incl_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.hpp)
SET(SOURCE_FILES ${SOURCE_FILES} ${src_files}) #append
SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../../serialization/${subdir}/include)
ENDFOREACH(subdir)
#Message( "API_REL_INCLUDE_FILES=${API_REL_INCLUDE_FILES}\n" )
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src )
# Create the library
ADD_LIBRARY(${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME} ${OPENMM_DRUDE_LIBRARY_NAME} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${SHARED_TARGET})
SET_TARGET_PROPERTIES(${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME} PROPERTIES COMPILE_FLAGS "-DOPENMM_DRUDE_SERIALIZATION_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME})
ADD_SUBDIRECTORY(tests)
plugins/drude/serialization/include/openmm/serialization/DrudeForceProxy.h 0 → 100644
View file @ 6185317a
#ifndef OPENMM_DRUDE_FORCE_PROXY_H_
#define OPENMM_DRUDE_FORCE_PROXY_H_
/* -------------------------------------------------------------------------- *
* OpenMMDrude *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportDrudeSerialization.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
/**
* This is a proxy for serializing DrudeForce objects.
*/
class OPENMM_EXPORT_DRUDE_SERIALIZATION DrudeForceProxy : public SerializationProxy {
public:
DrudeForceProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
} // namespace OpenMM
#endif /*OPENMM_DRUDE_FORCE_PROXY_H_*/
plugins/drude/serialization/include/openmm/serialization/DrudeLangevinIntegratorProxy.h 0 → 100644
View file @ 6185317a
#ifndef OPENMM_DRUDE_LANGEVIN_INTEGRATOR_PROXY_H_
#define OPENMM_DRUDE_LANGEVIN_INTEGRATOR_PROXY_H_
/* -------------------------------------------------------------------------- *
* OpenMMDrude *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/internal/windowsExportDrudeSerialization.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
/**
* This is a proxy for serializing DrudeLangevinIntegrator objects.
*/
class OPENMM_EXPORT_DRUDE_SERIALIZATION DrudeLangevinIntegratorProxy : public SerializationProxy {
public:
DrudeLangevinIntegratorProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
} // namespace OpenMM
#endif /*OPENMM_DRUDE_LANGEVIN_INTEGRATOR_PROXY_H_*/
plugins/drude/serialization/include/openmm/serialization/internal/windowsExportDrudeSerialization.h 0 → 100644
View file @ 6185317a
#ifndef OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_H_
#define OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_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_DRUDE_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_DRUDE_SERIALIZATION_BUILDING_SHARED_LIBRARY)
#define OPENMM_EXPORT_DRUDE_SERIALIZATION __declspec(dllexport)
#elif defined(OPENMM_DRUDE_SERIALIZATION_BUILDING_STATIC_LIBRARY) || defined(OPENMM_DRUDE_SERIALIZATION_USE_STATIC_LIBRARIES)
#define OPENMM_EXPORT_DRUDE_SERIALIZATION
#else
#define OPENMM_EXPORT_DRUDE_SERIALIZATION __declspec(dllimport) // i.e., a client of a shared library
#endif
#else
#define OPENMM_EXPORT_DRUDE_SERIALIZATION // Linux, Mac
#endif
#endif // OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_H_
plugins/drude/serialization/src/DrudeForceProxy.cpp 0 → 100644
View file @ 6185317a
/* -------------------------------------------------------------------------- *
* OpenMMDrude *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/DrudeForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/DrudeForce.h"
#include <sstream>
using namespace OpenMM;
using namespace std;
DrudeForceProxy::DrudeForceProxy() : SerializationProxy("DrudeForce") {
}
void DrudeForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const DrudeForce& force = *reinterpret_cast<const DrudeForce*>(object);
SerializationNode& particles = node.createChildNode("Particles");
for (int i = 0; i < force.getNumParticles(); i++) {
int p, p1, p2, p3, p4;
double charge, polarizability, aniso12, aniso34;
force.getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
particles.createChildNode("Particle").setIntProperty("p", p).setIntProperty("p1", p1).setIntProperty("p2", p2).setIntProperty("p3", p3).setIntProperty("p4", p4)
.setDoubleProperty("charge", charge).setDoubleProperty("polarizability", polarizability).setDoubleProperty("a12", aniso12).setDoubleProperty("a34", aniso34);
}
SerializationNode& pairs = node.createChildNode("ScreenedPairs");
for (int i = 0; i < force.getNumScreenedPairs(); i++) {
int p1, p2;
double thole;
force.getScreenedPairParameters(i, p1, p2, thole);
pairs.createChildNode("Pair").setIntProperty("p1", p1).setIntProperty("p2", p2).setDoubleProperty("thole", thole);
}
}
void* DrudeForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
DrudeForce* force = new DrudeForce();
try {
const SerializationNode& particles = node.getChildNode("Particles");
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
force->addParticle(particle.getIntProperty("p"), particle.getIntProperty("p1"), particle.getIntProperty("p2"), particle.getIntProperty("p3"), particle.getIntProperty("p4"),
particle.getDoubleProperty("charge"), particle.getDoubleProperty("polarizability"), particle.getDoubleProperty("a12"), particle.getDoubleProperty("a34"));
}
const SerializationNode& pairs = node.getChildNode("ScreenedPairs");
for (int i = 0; i < (int) pairs.getChildren().size(); i++) {
const SerializationNode& pair = pairs.getChildren()[i];
force->addScreenedPair(pair.getIntProperty("p1"), pair.getIntProperty("p2"), pair.getDoubleProperty("thole"));
}
}
catch (...) {
delete force;
throw;
}
return force;
}
plugins/drude/serialization/src/DrudeLangevinIntegratorProxy.cpp 0 → 100644
View file @ 6185317a
/* -------------------------------------------------------------------------- *
* OpenMMDrude *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/DrudeLangevinIntegratorProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/DrudeLangevinIntegrator.h"
#include <sstream>
using namespace OpenMM;
using namespace std;
DrudeLangevinIntegratorProxy::DrudeLangevinIntegratorProxy() : SerializationProxy("DrudeLangevinIntegrator") {
}
void DrudeLangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const DrudeLangevinIntegrator& integrator = *reinterpret_cast<const DrudeLangevinIntegrator*>(object);
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setDoubleProperty("temperature", integrator.getTemperature());
node.setDoubleProperty("friction", integrator.getFriction());
node.setDoubleProperty("drudeTemperature", integrator.getDrudeTemperature());
node.setDoubleProperty("drudeFriction", integrator.getDrudeFriction());
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
}
void* DrudeLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
DrudeLangevinIntegrator *integrator = new DrudeLangevinIntegrator(node.getDoubleProperty("temperature"),
node.getDoubleProperty("friction"), node.getDoubleProperty("drudeTemperature"),
node.getDoubleProperty("drudeFriction"), node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
return integrator;
}
\ No newline at end of file
plugins/drude/serialization/src/DrudeSerializationProxyRegistration.cpp 0 → 100644
View file @ 6185317a
/* -------------------------------------------------------------------------- *
* OpenMMDrude *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#ifdef WIN32
#include <windows.h>
#include <sstream>
#else
#include <dlfcn.h>
#include <dirent.h>
#include <cstdlib>
#endif
#include "openmm/OpenMMException.h"
#include "openmm/DrudeForce.h"
#include "openmm/DrudeLangevinIntegrator.h"
#include "openmm/serialization/SerializationProxy.h"
#include "openmm/serialization/DrudeForceProxy.h"
#include "openmm/serialization/DrudeLangevinIntegratorProxy.h"
#include "openmm/serialization/internal/windowsExportDrudeSerialization.h"
#if defined(WIN32)
#include <windows.h>
extern "C" OPENMM_EXPORT_DRUDE_SERIALIZATION void registerDrudeSerializationProxies();
BOOL WINAPI DllMain(HANDLE hModule, DWORD ul_reason_for_call, LPVOID lpReserved) {
if (ul_reason_for_call == DLL_PROCESS_ATTACH)
registerDrudeSerializationProxies();
return TRUE;
}
#else
extern "C" void __attribute__((constructor)) registerDrudeSerializationProxies();
#endif
using namespace OpenMM;
extern "C" OPENMM_EXPORT_DRUDE_SERIALIZATION void registerDrudeSerializationProxies() {
SerializationProxy::registerProxy(typeid(DrudeForce), new DrudeForceProxy());
SerializationProxy::registerProxy(typeid(DrudeLangevinIntegrator), new DrudeLangevinIntegratorProxy());
}
plugins/drude/serialization/tests/CMakeLists.txt 0 → 100644
View file @ 6185317a
#
# Testing
#
ENABLE_TESTING()
# Automatically create tests using files named "Test*.cpp"
FILE(GLOB TEST_PROGS "*Test*.cpp")
FOREACH(TEST_PROG ${TEST_PROGS})
GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
# All tests use shared libraries
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME} ${OPENMM_DRUDE_LIBRARY_NAME})
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
plugins/drude/serialization/tests/TestSerializeDrudeForce.cpp 0 → 100644
View file @ 6185317a
/* -------------------------------------------------------------------------- *
* OpenMMDrude *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Platform.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/DrudeForce.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
extern "C" void registerDrudeSerializationProxies();
void testSerialization() {
// Create a Force.
DrudeForce force1;
force1.addParticle(0, 1, 2, 3, 4, 0.5, 1.0, 1.5, 2.0);
force1.addParticle(2, 3, 7, 8, 9, 0.1, 1e-4, 1.0, 0.9);
force1.addParticle(5, 6, -1, -1, -1, 0.2, 0.1, 1.0, 1.0);
force1.addScreenedPair(0, 1, 2.6);
force1.addScreenedPair(1, 2, 2.2);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<DrudeForce>(&force1, "Force", buffer);
DrudeForce* copy = XmlSerializer::deserialize<DrudeForce>(buffer);
// Compare the two forces to see if they are identical.
DrudeForce& force2 = *copy;
ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
for (int i = 0; i < (int) force1.getNumParticles(); i++) {
int a1, a2, a3, a4, a5, b1, b2, b3, b4, b5;
double charge1, charge2;
double polar1, polar2;
double aa12, ba12, aa34, ba34;
force1.getParticleParameters(i, a1, a2, a3, a4, a5, charge1, polar1, aa12, aa34);
force2.getParticleParameters(i, b1, b2, b3, b4, b5, charge2, polar2, ba12, ba34);
ASSERT_EQUAL(a1, b1);
ASSERT_EQUAL(a2, b2);
ASSERT_EQUAL(a3, b3);
ASSERT_EQUAL(a4, b4);
ASSERT_EQUAL(a5, b5);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(polar1, polar2);
ASSERT_EQUAL(aa12, ba12);
ASSERT_EQUAL(aa34, ba34);
}
ASSERT_EQUAL(force1.getNumScreenedPairs(), force2.getNumScreenedPairs());
for (int i = 0; i < (int) force1.getNumScreenedPairs(); i++) {
int a1, a2, b1, b2;
double thole1, thole2;
force1.getScreenedPairParameters(i, a1, a2, thole1);
force1.getScreenedPairParameters(i, b1, b2, thole2);
ASSERT_EQUAL(a1, b1);
ASSERT_EQUAL(a2, b2);
ASSERT_EQUAL(thole1, thole2);
}
}
int main() {
try {
registerDrudeSerializationProxies();
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
plugins/drude/serialization/tests/TestSerializeDrudeLangevinIntegrator.cpp 0 → 100644
View file @ 6185317a
/* -------------------------------------------------------------------------- *
* OpenMMDrude *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Platform.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/DrudeLangevinIntegrator.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
extern "C" void registerDrudeSerializationProxies();
void testSerialization() {
// Create an Integrator.
DrudeLangevinIntegrator integ1(301.1, 0.95, 10.5, 1.2, 0.001);
integ1.setRandomNumberSeed(18);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<DrudeLangevinIntegrator>(&integ1, "Integrator", buffer);
DrudeLangevinIntegrator* copy = XmlSerializer::deserialize<DrudeLangevinIntegrator>(buffer);
// Compare the two integrators to see if they are identical.
DrudeLangevinIntegrator& integ2 = *copy;
ASSERT_EQUAL(integ1.getTemperature(), integ2.getTemperature());
ASSERT_EQUAL(integ1.getFriction(), integ2.getFriction());
ASSERT_EQUAL(integ1.getDrudeTemperature(), integ2.getDrudeTemperature());
ASSERT_EQUAL(integ1.getDrudeFriction(), integ2.getDrudeFriction());
ASSERT_EQUAL(integ1.getRandomNumberSeed(), integ2.getRandomNumberSeed());
}
int main() {
try {
registerDrudeSerializationProxies();
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment