Merged changes from main branch

platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -99,14 +99,14 @@ 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")
 
 FILE(GLOB serialization_files  ${CMAKE_CUURENT_SOURCE_DIR}/serialization/src/*.cpp)
 SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL")
 
 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

@@ -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

@@ -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

@@ -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/tests/CMakeLists.txt

@@ -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} ${OPENMM_AMOEBA_LIBRARY_NAME})
+    SET_TARGET_PROPERTIES(${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

@@ -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

@@ -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

@@ -87,14 +87,14 @@ 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")
 
 FILE(GLOB serialization_files  ${CMAKE_CUURENT_SOURCE_DIR}/serialization/src/*.cpp)
 SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_DRUDE_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL")
 
 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)

plugins/drude/platforms/cuda/CMakeLists.txt

@@ -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_DRUDE_TARGET} optimized ${SHARED_DRUDE_TARGET})
-SET_TARGET_PROPERTIES(${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)