Merged changes from main branch

platforms/reference/tests/TestReferenceCustomGBForce.cpp

@@ -281,7 +281,7 @@ void testTabulatedFunction() {
     vector<double> table;
     for (int i = 0; i < 21; i++)
         table.push_back(std::sin(0.25*i));
-    force->addFunction("fn", table, 1.0, 6.0);
+    force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
     system.addForce(force);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);

platforms/reference/tests/TestReferenceCustomHbondForce.cpp

@@ -217,7 +217,7 @@ void testCustomFunctions() {
     vector<double> function(2);
     function[0] = 0;
     function[1] = 1;
-    custom->addFunction("foo", function, 0, 10);
+    custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
     system.addForce(custom);
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);

platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp

@@ -7,7 +7,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -227,7 +227,7 @@ void testPeriodic() {
     ASSERT_EQUAL_TOL(1.9+1+0.9, state.getPotentialEnergy(), TOL);
 }
 
-void testTabulatedFunction() {
+void testContinuous1DFunction() {
     ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
@@ -238,21 +238,20 @@ void testTabulatedFunction() {
     forceField->addParticle(vector<double>());
     vector<double> table;
     for (int i = 0; i < 21; i++)
-        table.push_back(std::sin(0.25*i));
-    forceField->addFunction("fn", table, 1.0, 6.0);
+        table.push_back(sin(0.25*i));
+    forceField->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
     positions[0] = Vec3(0, 0, 0);
-    double tol = 0.01;
     for (int i = 1; i < 30; i++) {
         double x = (7.0/30.0)*i;
         positions[1] = Vec3(x, 0, 0);
         context.setPositions(positions);
         State state = context.getState(State::Forces | State::Energy);
         const vector<Vec3>& forces = state.getForces();
-        double force = (x < 1.0 || x > 6.0 ? 0.0 : -std::cos(x-1.0));
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
+        double force = (x < 1.0 || x > 6.0 ? 0.0 : -cos(x-1.0));
+        double energy = (x < 1.0 || x > 6.0 ? 0.0 : sin(x-1.0))+1.0;
         ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
         ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
         ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
@@ -262,11 +261,217 @@ void testTabulatedFunction() {
         positions[1] = Vec3(x, 0, 0);
         context.setPositions(positions);
         State state = context.getState(State::Energy);
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
+        double energy = (x < 1.0 || x > 6.0 ? 0.0 : sin(x-1.0))+1.0;
         ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
     }
 }
 
+void testContinuous2DFunction() {
+    const int xsize = 20;
+    const int ysize = 21;
+    const double xmin = 0.4;
+    const double xmax = 1.5;
+    const double ymin = 0.0;
+    const double ymax = 2.1;
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a)+1");
+    forceField->addGlobalParameter("a", 0.0);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table(xsize*ysize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++) {
+            double x = xmin + i*(xmax-xmin)/xsize;
+            double y = ymin + j*(ymax-ymin)/ysize;
+            table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
+        }
+    }
+    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
+        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
+            positions[1] = Vec3(x, 0, 0);
+            context.setParameter("a", y);
+            context.setPositions(positions);
+            State state = context.getState(State::Forces | State::Energy);
+            const vector<Vec3>& forces = state.getForces();
+            double energy = 1;
+            double force = 0;
+            if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
+                energy = sin(0.25*x)*cos(0.33*y)+1.0;
+                force = -0.25*cos(0.25*x)*cos(0.33*y);
+            }
+            ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
+            ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
+            ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
+        }
+    }
+}
+
+void testContinuous3DFunction() {
+    const int xsize = 10;
+    const int ysize = 11;
+    const int zsize = 12;
+    const double xmin = 0.4;
+    const double xmax = 1.1;
+    const double ymin = 0.0;
+    const double ymax = 0.9;
+    const double zmin = 0.2;
+    const double zmax = 1.3;
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a,b)+1");
+    forceField->addGlobalParameter("a", 0.0);
+    forceField->addGlobalParameter("b", 0.0);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table(xsize*ysize*zsize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++) {
+            for (int k = 0; k < zsize; k++) {
+                double x = xmin + i*(xmax-xmin)/xsize;
+                double y = ymin + j*(ymax-ymin)/ysize;
+                double z = zmin + k*(zmax-zmin)/zsize;
+                table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
+            }
+        }
+    }
+    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
+        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
+            for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
+                positions[1] = Vec3(x, 0, 0);
+                context.setParameter("a", y);
+                context.setParameter("b", z);
+                context.setPositions(positions);
+                State state = context.getState(State::Forces | State::Energy);
+                const vector<Vec3>& forces = state.getForces();
+                double energy = 1;
+                double force = 0;
+                if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
+                    energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1.0;
+                    force = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
+                }
+                ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
+                ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
+                ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
+            }
+        }
+    }
+}
+
+void testDiscrete1DFunction() {
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r)+1");
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table;
+    for (int i = 0; i < 21; i++)
+        table.push_back(sin(0.25*i));
+    forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (int i = 0; i < (int) table.size(); i++) {
+        positions[1] = Vec3(i, 0, 0);
+        context.setPositions(positions);
+        State state = context.getState(State::Forces | State::Energy);
+        const vector<Vec3>& forces = state.getForces();
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
+        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
+    }
+}
+
+void testDiscrete2DFunction() {
+    const int xsize = 10;
+    const int ysize = 5;
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a)+1");
+    forceField->addGlobalParameter("a", 0.0);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table;
+    for (int i = 0; i < xsize; i++)
+        for (int j = 0; j < ysize; j++)
+            table.push_back(sin(0.25*i)+cos(0.33*j));
+    forceField->addTabulatedFunction("fn", new Discrete2DFunction(xsize, ysize, table));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (int i = 0; i < (int) table.size(); i++) {
+        positions[1] = Vec3(i%xsize, 0, 0);
+        context.setPositions(positions);
+        context.setParameter("a", i/xsize);
+        State state = context.getState(State::Forces | State::Energy);
+        const vector<Vec3>& forces = state.getForces();
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
+        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
+    }
+}
+
+void testDiscrete3DFunction() {
+    const int xsize = 8;
+    const int ysize = 5;
+    const int zsize = 6;
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a,b)+1");
+    forceField->addGlobalParameter("a", 0.0);
+    forceField->addGlobalParameter("b", 0.0);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table;
+    for (int i = 0; i < xsize; i++)
+        for (int j = 0; j < ysize; j++)
+            for (int k = 0; k < zsize; k++)
+                table.push_back(sin(0.25*i)+cos(0.33*j)+0.12345*k);
+    forceField->addTabulatedFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (int i = 0; i < (int) table.size(); i++) {
+        positions[1] = Vec3(i%xsize, 0, 0);
+        context.setPositions(positions);
+        context.setParameter("a", (i/xsize)%ysize);
+        context.setParameter("b", i/(xsize*ysize));
+        State state = context.getState(State::Forces | State::Energy);
+        const vector<Vec3>& forces = state.getForces();
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
+        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
+    }
+}
+
 void testCoulombLennardJones() {
     const int numMolecules = 300;
     const int numParticles = numMolecules*2;
@@ -658,7 +863,12 @@ int main() {
         testExclusions();
         testCutoff();
         testPeriodic();
-        testTabulatedFunction();
+        testContinuous1DFunction();
+        testContinuous2DFunction();
+        testContinuous3DFunction();
+        testDiscrete1DFunction();
+        testDiscrete2DFunction();
+        testDiscrete3DFunction();
         testCoulombLennardJones();
         testSwitchingFunction();
         testLongRangeCorrection();

platforms/reference/tests/TestReferenceEwald.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2010 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -354,6 +354,55 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
     }
 }
 
+void testPMEParameters() {
+    // Create a cloud of random point charges.
+
+    const int numParticles = 51;
+    const double boxWidth = 4.7;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
+    NonbondedForce* force = new NonbondedForce();
+    system.addForce(force);
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
+        positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
+    }
+    force->setNonbondedMethod(NonbondedForce::PME);
+    ReferencePlatform platform;
+    
+    // Compute the energy with an error tolerance of 1e-3.
+
+    force->setEwaldErrorTolerance(1e-3);
+    VerletIntegrator integrator1(0.01);
+    Context context1(system, integrator1, platform);
+    context1.setPositions(positions);
+    double energy1 = context1.getState(State::Energy).getPotentialEnergy();
+    
+    // Try again with an error tolerance of 1e-4.
+
+    force->setEwaldErrorTolerance(1e-4);
+    VerletIntegrator integrator2(0.01);
+    Context context2(system, integrator2, platform);
+    context2.setPositions(positions);
+    double energy2 = context2.getState(State::Energy).getPotentialEnergy();
+    
+    // Now explicitly set the parameters.  These should match the values that were
+    // used for tolerance 1e-3.
+
+    force->setPMEParameters(2.49291157051793, 32, 32, 32);
+    VerletIntegrator integrator3(0.01);
+    Context context3(system, integrator3, platform);
+    context3.setPositions(positions);
+    double energy3 = context3.getState(State::Energy).getPotentialEnergy();
+    ASSERT_EQUAL_TOL(energy1, energy3, 1e-6);
+    ASSERT(fabs((energy1-energy2)/energy1) > 1e-5);
+}
+
 int main() {
     try {
      testEwaldExact();
@@ -362,6 +411,7 @@ int main() {
 //     testWaterSystem();
      testErrorTolerance(NonbondedForce::Ewald);
      testErrorTolerance(NonbondedForce::PME);
+     testPMEParameters();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

plugins/amoeba/CMakeLists.txt

@@ -101,7 +101,7 @@ SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DO
 
 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 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")
+  SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_STATIC_LIBRARY -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

@@ -27,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMAMOEBACUDA_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp

@@ -893,8 +893,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
 
     numMultipoles = force.getNumMultipoles();
     CudaArray& posq = cu.getPosq();
-    float4* posqf = (float4*) cu.getPinnedBuffer();
-    double4* posqd = (double4*) cu.getPinnedBuffer();
+    vector<double4> temp(posq.getSize());
+    float4* posqf = (float4*) &temp[0];
+    double4* posqd = (double4*) &temp[0];
     vector<float2> dampingAndTholeVec;
     vector<float> polarizabilityVec;
     vector<float> molecularDipolesVec;
@@ -941,7 +942,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
     multipoleParticles->upload(multipoleParticlesVec);
     molecularDipoles->upload(molecularDipolesVec);
     molecularQuadrupoles->upload(molecularQuadrupolesVec);
-    posq.upload(cu.getPinnedBuffer());
+    posq.upload(&temp[0]);
     
     // Create workspace arrays.
     

plugins/amoeba/platforms/reference/CMakeLists.txt

-#---------------------------------------------------
-# OpenMM Reference Amoeba Implementation
-#
-# Creates OpenMM library, base name=OpenMMAmoebaReference.
-# Default libraries are shared & optimized. Variants
-# are created for debug (_d).
-#
-# Windows:
-#   OpenMMAmoebaReference[_d].dll
-#   OpenMMAmoebaReference[_d].lib
-# Unix:
-#   libOpenMMAmoebaReference[_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 .)
-
-# 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(OPENMMAMOEBAREFERENCE_LIBRARY_NAME OpenMMAmoebaReference)
-
-SET(SHARED_TARGET ${OPENMMAMOEBAREFERENCE_LIBRARY_NAME})
-
-# Ensure that debug libraries have "_d" appended to their names.
-# CMake gets this right on Windows automatically with this definition.
-IF (${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(SHARED_TARGET ${SHARED_TARGET}_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_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)
-    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)
-ENDFOREACH(subdir)
-
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src/SimTKReference)
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/include)
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/src)
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/src/SimTKReference)
-
-# Create the library
-
-ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-
-IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-    SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME}_d)
-ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-    SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
-ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB})
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_AMOEBA_TARGET} optimized ${SHARED_AMOEBA_TARGET})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
-
-INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
-SUBDIRS (tests)
+#---------------------------------------------------
+# OpenMM Reference Amoeba Implementation
+#
+# Creates OpenMM library, base name=OpenMMAmoebaReference.
+# Default libraries are shared & optimized. Variants
+# are created for debug (_d).
+#
+# Windows:
+#   OpenMMAmoebaReference[_d].dll
+#   OpenMMAmoebaReference[_d].lib
+# Unix:
+#   libOpenMMAmoebaReference[_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 .)
+
+# 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(OPENMMAMOEBAREFERENCE_LIBRARY_NAME OpenMMAmoebaReference)
+
+SET(SHARED_TARGET ${OPENMMAMOEBAREFERENCE_LIBRARY_NAME})
+
+# Ensure that debug libraries have "_d" appended to their names.
+# CMake gets this right on Windows automatically with this definition.
+IF (MSVC)
+    SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
+ENDIF (MSVC)
+
+# But on Unix or Cygwin we have to add the suffix manually
+IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(SHARED_TARGET ${SHARED_TARGET}_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_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)
+    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)
+ENDFOREACH(subdir)
+
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src/SimTKReference)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/include)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/reference/src/SimTKReference)
+
+# Create the library
+
+ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+
+IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME}_d)
+ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
+ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_AMOEBA_TARGET} optimized ${SHARED_AMOEBA_TARGET})
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+
+INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
+SUBDIRS (tests)

plugins/amoeba/wrappers/generateAmoebaWrappers.py

@@ -75,9 +75,10 @@ class WrapperGenerator:
         # Read all the XML files and merge them into a single document.
         self.doc = etree.ElementTree(etree.Element('root'))
         for file in os.listdir(inputDirname):
-            root = etree.parse(os.path.join(inputDirname, file)).getroot()
-            for node in root:
-                self.doc.getroot().append(node)
+            if file.lower().endswith('xml'):
+                root = etree.parse(os.path.join(inputDirname, file)).getroot()
+                for node in root:
+                    self.doc.getroot().append(node)
 
         self.out = output
 
@@ -549,6 +550,8 @@ class CSourceGenerator(WrapperGenerator):
             unwrappedType = type[:-1].strip()
             if unwrappedType in self.classesByShortName:
                 unwrappedType  = self.classesByShortName[unwrappedType]
+            if unwrappedType == 'const std::string':
+                return 'std::string(%s)' % value
             return '*'+self.unwrapValue(unwrappedType+'*', value)
         if type in self.classesByShortName:
             return 'static_cast<%s>(%s)' % (self.classesByShortName[type], value)
@@ -1133,14 +1136,14 @@ class FortranSourceGenerator(WrapperGenerator):
         return type
     
     def isHandleType(self, type):
-        if type.startswith('OpenMM_'):
-            return True;
-        if type == 'Vec3':
-            return True
+        if type == 'OpenMM_Vec3':
+            return False
         if type.endswith('*') or type.endswith('&'):
             return self.isHandleType(type[:-1].strip())
         if type.startswith('const '):
             return self.isHandleType(type[6:].strip())
+        if type.startswith('OpenMM_'):
+            return True;
         return False
 
     def writeOutput(self):

plugins/cpupme/CMakeLists.txt

@@ -22,13 +22,13 @@ SET(OPENMM_SOURCE_SUBDIRS .)
 SET(OPENMMPME_LIBRARY_NAME OpenMMPME)
 
 SET(SHARED_TARGET ${OPENMMPME_LIBRARY_NAME})
-
+SET(STATIC_TARGET ${OPENMMPME_LIBRARY_NAME}_static)
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
@@ -74,7 +74,7 @@ ENDIF (NOT MSVC)
 # Include FFTW related files.
 INCLUDE_DIRECTORIES(${FFTW_INCLUDES})
 
-# Build the plugin library.
+# Build the shared plugin library.
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
 
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
@@ -90,4 +90,22 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FL
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
 
+# Build the static plugin library.
+IF(OPENMM_BUILD_STATIC_LIB)
+    ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
+
+    IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+        SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME}_d)
+    ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+        SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
+    ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${MAIN_OPENMM_LIB} ${PTHREADS_LIB} ${FFTW_LIBRARY})
+    IF (FFTW_THREADS_LIBRARY)
+        TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${FFTW_THREADS_LIBRARY})
+    ENDIF (FFTW_THREADS_LIBRARY)
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_STATIC_LIBRARY")
+
+    INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})
+ENDIF(OPENMM_BUILD_STATIC_LIB)
+
 SUBDIRS(tests)

plugins/cpupme/src/CpuPmeKernelFactory.cpp

@@ -32,9 +32,6 @@
 
 using namespace OpenMM;
 
-extern "C" OPENMM_EXPORT_PME void registerPlatforms() {
-}
-
 extern "C" OPENMM_EXPORT_PME void registerKernelFactories() {
     if (CpuCalcPmeReciprocalForceKernel::isProcessorSupported()) {
         CpuPmeKernelFactory* factory = new CpuPmeKernelFactory();
@@ -43,9 +40,17 @@ extern "C" OPENMM_EXPORT_PME void registerKernelFactories() {
     }
 }
 
+#ifdef OPENMM_PME_BUILDING_STATIC_LIBRARY
+extern "C" void registerCpuPmeKernelFactories() {
+    registerKernelFactories();
+}
+#else
 extern "C" OPENMM_EXPORT_PME void registerCpuPmeKernelFactories() {
     registerKernelFactories();
 }
+extern "C" OPENMM_EXPORT_PME void registerPlatforms() {
+}
+#endif
 
 KernelImpl* CpuPmeKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
     if (name == CalcPmeReciprocalForceKernel::Name())

plugins/drude/CMakeLists.txt

@@ -82,7 +82,7 @@ SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DO
 
 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 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")
+  SET_TARGET_PROPERTIES(${STATIC_DRUDE_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_DRUDE_BUILDING_STATIC_LIBRARY -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
 ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 # ----------------------------------------------------------------------------

plugins/drude/platforms/cuda/CMakeLists.txt

@@ -27,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMDRUDECUDA_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)

plugins/drude/platforms/opencl/CMakeLists.txt

@@ -27,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMDRUDEOPENCL_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)

plugins/drude/platforms/reference/CMakeLists.txt

@@ -27,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMDRUDEREFERENCE_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)

plugins/rpmd/platforms/cuda/CMakeLists.txt

@@ -27,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMRPMDCUDA_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)

plugins/rpmd/platforms/opencl/CMakeLists.txt

@@ -27,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMRPMDOPENCL_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)

plugins/rpmd/platforms/reference/CMakeLists.txt

@@ -27,9 +27,9 @@ SET(SHARED_TARGET ${OPENMMRPMDREFERENCE_LIBRARY_NAME})
 
 # Ensure that debug libraries have "_d" appended to their names.
 # CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+IF (MSVC)
     SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+ENDIF (MSVC)
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)

serialization/include/openmm/serialization/TabulatedFunctionProxies.h

+#ifndef OPENMM_TABULATEDFUNCTION_PROXIES_H_
+#define OPENMM_TABULATEDFUNCTION_PROXIES_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * 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) 2014 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/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing Continuous1DFunction objects.
+ */
+    
+class OPENMM_EXPORT Continuous1DFunctionProxy : public SerializationProxy {
+public:
+    Continuous1DFunctionProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+/**
+ * This is a proxy for serializing Continuous2DFunction objects.
+ */
+    
+class OPENMM_EXPORT Continuous2DFunctionProxy : public SerializationProxy {
+public:
+    Continuous2DFunctionProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+/**
+ * This is a proxy for serializing Continuous3DFunction objects.
+ */
+    
+class OPENMM_EXPORT Continuous3DFunctionProxy : public SerializationProxy {
+public:
+    Continuous3DFunctionProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+/**
+ * This is a proxy for serializing Discrete1DFunction objects.
+ */
+    
+class OPENMM_EXPORT Discrete1DFunctionProxy : public SerializationProxy {
+public:
+    Discrete1DFunctionProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+/**
+ * This is a proxy for serializing Discrete2DFunction objects.
+ */
+    
+class OPENMM_EXPORT Discrete2DFunctionProxy : public SerializationProxy {
+public:
+    Discrete2DFunctionProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+/**
+ * This is a proxy for serializing Discrete3DFunction objects.
+ */
+    
+class OPENMM_EXPORT Discrete3DFunctionProxy : public SerializationProxy {
+public:
+    Discrete3DFunctionProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_TABULATEDFUNCTION_PROXIES_H_*/

serialization/src/CustomCompoundBondForceProxy.cpp

@@ -73,6 +73,9 @@ void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNo
             node.setDoubleProperty(key.str(), params[j]);
         }
     }
+    SerializationNode& functions = node.createChildNode("Functions");
+    for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
+        functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
 }
 
 void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) const {
@@ -110,6 +113,22 @@ void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) c
             }
             force->addBond(particles, params);
         }
+        const SerializationNode& functions = node.getChildNode("Functions");
+        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
+            const SerializationNode& function = functions.getChildren()[i];
+            if (function.hasProperty("type")) {
+                force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
+            }
+            else {
+                // This is an old file created before TabulatedFunction existed.
+                
+                const SerializationNode& valuesNode = function.getChildNode("Values");
+                vector<double> values;
+                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
+                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
+            }
+        }
         return force;
     }
     catch (...) {