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Commit 8e656070 authored by Lee-Ping Wang's avatar Lee-Ping Wang
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Merge branch 'master' of https://github.com/SimTk/openmm

parents 6160b726 ff6af025
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Showing with 64 additions and 125 deletions
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
View file @ 8e656070
......@@ -125,7 +125,7 @@ RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const {
void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -162,7 +162,7 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ 8e656070
......@@ -48,14 +48,12 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
const vector<pair<int, int> >& atomIndices,
const vector<RealOpenMM>& distance,
vector<RealOpenMM>& masses,
vector<AngleInfo>& angles,
RealOpenMM tolerance) {
vector<AngleInfo>& angles) {
_numberOfConstraints = numberOfConstraints;
_atomIndices = atomIndices;
_distance = distance;
_maximumNumberOfIterations = 150;
_tolerance = tolerance;
_hasInitializedMasses = false;
// work arrays
......@@ -201,28 +199,20 @@ void ReferenceCCMAAlgorithm::setMaximumNumberOfIterations(int maximumNumberOfIte
_maximumNumberOfIterations = maximumNumberOfIterations;
}
RealOpenMM ReferenceCCMAAlgorithm::getTolerance() const {
return _tolerance;
}
void ReferenceCCMAAlgorithm::setTolerance(RealOpenMM tolerance) {
_tolerance = tolerance;
}
void ReferenceCCMAAlgorithm::apply(vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses) {
applyConstraints(atomCoordinates, atomCoordinatesP, inverseMasses, false);
vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
applyConstraints(atomCoordinates, atomCoordinatesP, inverseMasses, false, tolerance);
}
void ReferenceCCMAAlgorithm::applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses) {
applyConstraints(atomCoordinates, velocities, inverseMasses, true);
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
applyConstraints(atomCoordinates, velocities, inverseMasses, true, tolerance);
}
void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses, bool constrainingVelocities) {
vector<RealOpenMM>& inverseMasses, bool constrainingVelocities, RealOpenMM tolerance) {
// temp arrays
vector<RealVec>& r_ij = _r_ij;
......@@ -242,15 +232,14 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
// setup: r_ij for each (i,j) constraint
RealOpenMM tolerance = getTolerance()*2;
for (int ii = 0; ii < _numberOfConstraints; ii++) {
int atomI = _atomIndices[ii].first;
int atomJ = _atomIndices[ii].second;
r_ij[ii] = atomCoordinates[atomI] - atomCoordinates[atomJ];
d_ij2[ii] = r_ij[ii].dot(r_ij[ii]);
}
RealOpenMM lowerTol = 1-2*getTolerance()+getTolerance()*getTolerance();
RealOpenMM upperTol = 1+2*getTolerance()+getTolerance()*getTolerance();
RealOpenMM lowerTol = 1-2*tolerance+tolerance*tolerance;
RealOpenMM upperTol = 1+2*tolerance+tolerance*tolerance;
// main loop
......@@ -267,7 +256,7 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
if (constrainingVelocities) {
RealOpenMM rrpr = rp_ij.dot(r_ij[ii]);
constraintDelta[ii] = -2*reducedMasses[ii]*rrpr/d_ij2[ii];
if (fabs(constraintDelta[ii]) <= getTolerance())
if (fabs(constraintDelta[ii]) <= tolerance)
numberConverged++;
}
else {
......
platforms/reference/src/SimTKReference/ReferenceConstraints.cpp
View file @ 8e656070
......@@ -30,6 +30,8 @@
* -------------------------------------------------------------------------- */
#include "ReferenceConstraints.h"
#include "ReferenceCCMAAlgorithm.h"
#include "ReferenceSETTLEAlgorithm.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/OpenMMException.h"
#include <map>
......@@ -39,8 +41,7 @@
using namespace OpenMM;
using namespace std;
ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tolerance) : ccma(NULL), settle(NULL) {
this->tolerance = tolerance;
ReferenceConstraints::ReferenceConstraints(const System& system) : ccma(NULL), settle(NULL) {
int numParticles = system.getNumParticles();
vector<RealOpenMM> masses(numParticles);
for (int i = 0; i < numParticles; ++i)
......@@ -141,7 +142,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tole
isSettleAtom[p2] = true;
isSettleAtom[p3] = true;
}
settle = new ReferenceSETTLEAlgorithm(atom1, atom2, atom3, distance1, distance2, masses, tolerance);
settle = new ReferenceSETTLEAlgorithm(atom1, atom2, atom3, distance1, distance2, masses);
}
// All other constraints are handled with CCMA.
......@@ -179,7 +180,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tole
// Create the CCMA object.
ccma = new ReferenceCCMAAlgorithm(numParticles, numCCMA, ccmaIndices, ccmaDistance, masses, angles, tolerance);
ccma = new ReferenceCCMAAlgorithm(numParticles, numCCMA, ccmaIndices, ccmaDistance, masses, angles);
}
}
......@@ -190,28 +191,16 @@ ReferenceConstraints::~ReferenceConstraints() {
delete settle;
}
RealOpenMM ReferenceConstraints::getTolerance() const {
return tolerance;
}
void ReferenceConstraints::setTolerance(RealOpenMM tolerance) {
this->tolerance = tolerance;
if (ccma != NULL)
ccma->setTolerance(tolerance);
if (settle != NULL)
settle->setTolerance(tolerance);
}
void ReferenceConstraints::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses) {
void ReferenceConstraints::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
if (ccma != NULL)
ccma->apply(atomCoordinates, atomCoordinatesP, inverseMasses);
ccma->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
if (settle != NULL)
settle->apply(atomCoordinates, atomCoordinatesP, inverseMasses);
settle->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
}
void ReferenceConstraints::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses) {
void ReferenceConstraints::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
if (ccma != NULL)
ccma->applyToVelocities(atomCoordinates, velocities, inverseMasses);
ccma->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
if (settle != NULL)
settle->applyToVelocities(atomCoordinates, velocities, inverseMasses);
settle->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
}
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 8e656070
......@@ -97,7 +97,7 @@ ReferenceCustomDynamics::~ReferenceCustomDynamics() {
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid){
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance){
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates;
......@@ -252,12 +252,12 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses);
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses);
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
......
platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
View file @ 8e656070
......@@ -249,11 +249,12 @@ void ReferenceDynamics::setReferenceConstraintAlgorithm( ReferenceConstraintAlgo
@param velocities velocities
@param forces forces
@param masses atom masses
@param tolerance the constraint tolerance
--------------------------------------------------------------------------------------- */
void ReferenceDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceSETTLEAlgorithm.cpp
View file @ 8e656070
......@@ -35,19 +35,23 @@ using namespace OpenMM;
using namespace std;
ReferenceSETTLEAlgorithm::ReferenceSETTLEAlgorithm(const vector<int>& atom1, const vector<int>& atom2, const vector<int>& atom3,
const vector<RealOpenMM>& distance1, const vector<RealOpenMM>& distance2, vector<RealOpenMM>& masses, RealOpenMM tolerance) :
atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses), tolerance(tolerance) {
const vector<RealOpenMM>& distance1, const vector<RealOpenMM>& distance2, vector<RealOpenMM>& masses) :
atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses) {
}
RealOpenMM ReferenceSETTLEAlgorithm::getTolerance() const {
return tolerance;
int ReferenceSETTLEAlgorithm::getNumClusters() const {
return atom1.size();
}
void ReferenceSETTLEAlgorithm::setTolerance(RealOpenMM tolerance) {
this->tolerance = tolerance;
void ReferenceSETTLEAlgorithm::getClusterParameters(int index, int& atom1, int& atom2, int& atom3, RealOpenMM& distance1, RealOpenMM& distance2) const {
atom1 = this->atom1[index];
atom2 = this->atom2[index];
atom3 = this->atom3[index];
distance1 = this->distance1[index];
distance2 = this->distance2[index];
}
void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses) {
void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
for (int index = 0; index < (int) atom1.size(); ++index) {
RealVec apos0 = atomCoordinates[atom1[index]];
RealVec xp0 = atomCoordinatesP[atom1[index]]-apos0;
......@@ -190,7 +194,7 @@ void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, v
}
}
void ReferenceSETTLEAlgorithm::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses) {
void ReferenceSETTLEAlgorithm::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
for (int index = 0; index < (int) atom1.size(); ++index) {
RealVec apos0 = atomCoordinates[atom1[index]];
RealVec apos1 = atomCoordinates[atom2[index]];
......
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp
View file @ 8e656070
......@@ -200,7 +200,7 @@ void ReferenceStochasticDynamics::updatePart2( int numberOfAtoms, vector<RealVec
--------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -235,7 +235,7 @@ void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Re
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
......
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ 8e656070
......@@ -260,7 +260,7 @@ void ReferenceVariableStochasticDynamics::updatePart2( int numberOfAtoms, vector
void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -279,7 +279,7 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
......
platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp
View file @ 8e656070
......@@ -104,7 +104,7 @@ void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) {
void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -155,7 +155,7 @@ void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vecto
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
......
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp
View file @ 8e656070
......@@ -95,7 +95,7 @@ ReferenceVerletDynamics::~ReferenceVerletDynamics( ){
void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -131,7 +131,7 @@ void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVe
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
......
platforms/reference/tests/CMakeLists.txt
View file @ 8e656070
......@@ -12,6 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
# All tests use shared libraries
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
SET_TARGET_PROPERTIES(${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/CMakeLists.txt
View file @ 8e656070
......@@ -111,7 +111,7 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
ADD_LIBRARY(${SHARED_AMOEBA_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
ADD_LIBRARY(${SHARED_AMOEBA_SERIALIZABLE_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
......@@ -121,7 +121,7 @@ ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_AMOEBA_TARGET} STATIC ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
ENDIF(OPENMM_BUILD_STATIC_LIB)
IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
......
plugins/amoeba/platforms/cuda/CMakeLists.txt
View file @ 8e656070
......@@ -109,9 +109,11 @@ ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB} ${CUDA_LIBRARIES} ${PTHREADS_LIB})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}CUDA_d optimized ${OPENMM_LIBRARY_NAME}CUDA)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_AMOEBA_TARGET} optimized ${SHARED_AMOEBA_TARGET})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
IF (APPLE)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
ELSE (APPLE)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
ENDIF (APPLE)
INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
......
plugins/amoeba/platforms/cuda/tests/CMakeLists.txt
View file @ 8e656070
......@@ -15,7 +15,9 @@ FOREACH(TEST_PROG ${TEST_PROGS})
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET})
IF (APPLE)
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA")
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ELSE (APPLE)
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ENDIF (APPLE)
ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
IF (OPENMM_BUILD_CUDA_DOUBLE_PRECISION_TESTS)
......
plugins/amoeba/platforms/reference/tests/CMakeLists.txt
View file @ 8e656070
......@@ -2,33 +2,16 @@
# Testing
#
ENABLE_TESTING()
#INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/include)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/openmmapi/include/openmm)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/src/kernels)
#SET(SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET "AmoebaTinkerParameterFile" )
#SET(AMOEBA_TINKER_PARAMETER_FILE_SOURCE_FILES "AmoebaTinkerParameterFile.cpp" )
#SET(AMOEBA_TINKER_PARAMETER_FILE_INCLUDE_FILES "AmoebaTinkerParameterFile.h" )
Set( SHARED_OPENMM__AMOEBA_TARGET OpenMMAmoeba)
Set( STATIC_OPENMM_TARGET OpenMMAmoeba_static)
Set( SHARED_CUDA_TARGET OpenMMAmoebaCuda )
Set( STATIC_CUDA_TARGET OpenMMCuda_static OpenMMAmoebaCuda_static)
#ADD_LIBRARY(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} SHARED ${AMOEBA_TINKER_PARAMETER_FILE_SOURCE_FILES} ${AMOEBA_TINKER_PARAMETER_FILE_INCLUDE_FILES} )
#SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY")
#TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME})
#TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${SHARED_OPENMM__AMOEBA_TARGET}_d optimized ${SHARED_OPENMM__AMOEBA_TARGET})
#TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET} debug ${SHARED_CUDA_TARGET}_d optimized ${SHARED_CUDA_TARGET})
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_CUDA_TARGET ${SHARED_CUDA_TARGET}_d)
SET(SHARED_OPENMM__AMOEBA_TARGET ${SHARED_OPENMM__AMOEBA_TARGET}_d)
#SET(STATIC_CUDA_TARGET ${STATIC_CUDA_TARGET}_d)
#Set(STATIC_OPENMM_TARGET ${STATIC_OPENMM_TARGET}_d)
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
#LINK_DIRECTORIES
......@@ -41,41 +24,8 @@ FOREACH(TEST_PROG ${TEST_PROGS})
# Link with shared library
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
#TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET} ${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM__AMOEBA_TARGET} )
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
# Link with static library
# SET(TEST_STATIC ${TEST_ROOT}Static)
# CUDA_ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
# SET_TARGET_PROPERTIES(${TEST_STATIC}
# PROPERTIES
# COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
# )
# TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_OPENMM_TARGET} ${STATIC_CUDA_TARGET})
# ADD_TEST(${TEST_STATIC} ${EXECUTABLE_OUTPUT_PATH}/${TEST_STATIC})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
# TestCudaUsingParameterFile customized w/ command-line argument (input file name used in test)
#ADD_EXECUTABLE(TestAmoebaCudaUsingParameterFile TstAmoebaCudaUsingParameterFile.cpp)
#TARGET_LINK_LIBRARIES(TestAmoebaCudaUsingParameterFile ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET})
#ADD_TEST(TestCudaUsingParameterFile "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFile" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/lambdaSdObcParameters.txt")
#ADD_TEST(TestCudaUsingParameterFile "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFile" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfNoPbcParameters.txt")
#
#SET(TEST_ROOT TestCudaUsingParameterFile)
#SET(TEST_PROG TstCudaUsingParameterFile.cpp)
#SET(TEST_STATIC ${TEST_ROOT}Static)
#SET(INCLUDE_CUDA_STATIC 1)
#IF(INCLUDE_CUDA_STATIC)
# ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
# SET_TARGET_PROPERTIES(${TEST_STATIC}
# PROPERTIES
# COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
# )
# TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_BROOK_TARGET})
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/lambdaSdObcParameters.txt")
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfNoPbcParameters.txt")
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfPbcParameters.txt" " +checkEnergyForceConsistent -checkForces" )
#ENDIF(INCLUDE_CUDA_STATIC)
plugins/amoeba/serialization/CMakeLists.txt
View file @ 8e656070
......@@ -81,7 +81,7 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src )
# Create the library
ADD_LIBRARY(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} ${OPENMM_AMOEBA_LIBRARY_NAME} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${SHARED_TARGET})
SET_TARGET_PROPERTIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_SERIALIZATION_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
SET_TARGET_PROPERTIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_SERIALIZATION_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME})
ADD_SUBDIRECTORY(tests)
plugins/amoeba/serialization/tests/CMakeLists.txt
View file @ 8e656070
......@@ -12,6 +12,7 @@ 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} ${OPENMM_AMOEBA_LIBRARY_NAME})
SET_TARGET_PROPERTIES(${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 ${TEST_PROGS})
plugins/cpupme/CMakeLists.txt
View file @ 8e656070
......@@ -85,7 +85,7 @@ TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB} ${PTHREADS_LIB} ${FFTW
IF (FFTW_THREADS_LIBRARY)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${FFTW_THREADS_LIBRARY})
ENDIF (FFTW_THREADS_LIBRARY)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_PME_BUILDING_SHARED_LIBRARY")
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_SHARED_LIBRARY")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
......
plugins/cpupme/tests/CMakeLists.txt
View file @ 8e656070
......@@ -6,7 +6,6 @@ ENABLE_TESTING()
SET(SHARED_OPENMM_PME_TARGET OpenMMPME)
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_CUDA_TARGET ${SHARED_CUDA_TARGET}_d)
SET(SHARED_OPENMM_PME_TARGET ${SHARED_OPENMM_PME_TARGET}_d)
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
......@@ -21,5 +20,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM_PME_TARGET})
SET_TARGET_PROPERTIES(${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/drude/CMakeLists.txt
View file @ 8e656070
......@@ -97,7 +97,7 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/S
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
ADD_LIBRARY(${SHARED_DRUDE_TARGET} SHARED ${SOURCE_DRUDE_FILES} ${SOURCE_DRUDE_INCLUDE_FILES} ${API_DRUDE_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${SHARED_DRUDE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_DRUDE_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
SET_TARGET_PROPERTIES(${SHARED_DRUDE_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_DRUDE_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
#IF( CREATE_SERIALIZABLE_OPENMM_DRUDE )
# ADD_LIBRARY(${SHARED_DRUDE_SERIALIZABLE_TARGET} SHARED ${SOURCE_DRUDE_FILES} ${SOURCE_DRUDE_INCLUDE_FILES} ${API_DRUDE_ABS_INCLUDE_FILES})
......@@ -107,7 +107,7 @@ SET_TARGET_PROPERTIES(${SHARED_DRUDE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_
IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_DRUDE_TARGET} STATIC ${SOURCE_DRUDE_FILES} ${SOURCE_DRUDE_INCLUDE_FILES} ${API_DRUDE_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${STATIC_DRUDE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
SET_TARGET_PROPERTIES(${STATIC_DRUDE_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
ENDIF(OPENMM_BUILD_STATIC_LIB)
#IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
......
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