Python 2/3 compatibility in single code base, plus python 3 testing on travis.

plugins/amoeba/platforms/cuda/src/kernels/sphericalMultipoles.cu

+__device__ void buildQIRotationMatrix(real3 deltaR, real rInv, real (&rotationMatrix)[3][3]) {
+    real3 vectorZ = deltaR*rInv;
+    real3 vectorX = vectorZ;
+    if (deltaR.y != 0 || deltaR.z != 0)
+        vectorX.x += 1;
+    else
+        vectorX.y += 1;
+
+    vectorX -= vectorZ*dot(vectorX, vectorZ);
+    vectorX = normalize(vectorX);
+    real3 vectorY = cross(vectorZ, vectorX);
+
+    // Reorder the Cartesian {x,y,z} dipole rotation matrix, to account
+    // for spherical harmonic ordering {z,x,y}.
+    rotationMatrix[0][0] = vectorZ.z;
+    rotationMatrix[0][1] = vectorZ.x;
+    rotationMatrix[0][2] = vectorZ.y;
+    rotationMatrix[1][0] = vectorX.z;
+    rotationMatrix[1][1] = vectorX.x;
+    rotationMatrix[1][2] = vectorX.y;
+    rotationMatrix[2][0] = vectorY.z;
+    rotationMatrix[2][1] = vectorY.x;
+    rotationMatrix[2][2] = vectorY.y;
+}
+
+__device__ real3 rotateDipole(real3& dipole, const real (&rotationMatrix)[3][3]) {
+    return make_real3(rotationMatrix[0][0]*dipole.x + rotationMatrix[0][1]*dipole.y + rotationMatrix[0][2]*dipole.z,
+                      rotationMatrix[1][0]*dipole.x + rotationMatrix[1][1]*dipole.y + rotationMatrix[1][2]*dipole.z,
+                      rotationMatrix[2][0]*dipole.x + rotationMatrix[2][1]*dipole.y + rotationMatrix[2][2]*dipole.z);
+}
+
+
+__device__ void rotateQuadupoles(const real (&rotationMatrix)[3][3], const real* quad1, const real* quad2, real* rotated1, real* rotated2) {
+    real sqrtThree = SQRT((real) 3);
+    real element;
+    element = 0.5f*(3.0f*rotationMatrix[0][0]*rotationMatrix[0][0] - 1.0f);
+    rotated1[0] += quad1[0]*element;
+    rotated2[0] += quad2[0]*element;
+    element = sqrtThree*rotationMatrix[0][0]*rotationMatrix[0][1];
+    rotated1[0] += quad1[1]*element;
+    rotated2[0] += quad2[1]*element;
+    element = sqrtThree*rotationMatrix[0][0]*rotationMatrix[0][2];
+    rotated1[0] += quad1[2]*element;
+    rotated2[0] += quad2[2]*element;
+    element = 0.5f*sqrtThree*(rotationMatrix[0][1]*rotationMatrix[0][1] - rotationMatrix[0][2]*rotationMatrix[0][2]);
+    rotated1[0] += quad1[3]*element;
+    rotated2[0] += quad2[3]*element;
+    element = sqrtThree*rotationMatrix[0][1]*rotationMatrix[0][2];
+    rotated1[0] += quad1[4]*element;
+    rotated2[0] += quad2[4]*element;
+    element = sqrtThree*rotationMatrix[0][0]*rotationMatrix[1][0];
+    rotated1[1] += quad1[0]*element;
+    rotated2[1] += quad2[0]*element;
+    element = rotationMatrix[1][0]*rotationMatrix[0][1] + rotationMatrix[0][0]*rotationMatrix[1][1];
+    rotated1[1] += quad1[1]*element;
+    rotated2[1] += quad2[1]*element;
+    element = rotationMatrix[1][0]*rotationMatrix[0][2] + rotationMatrix[0][0]*rotationMatrix[1][2];
+    rotated1[1] += quad1[2]*element;
+    rotated2[1] += quad2[2]*element;
+    element = rotationMatrix[0][1]*rotationMatrix[1][1] - rotationMatrix[0][2]*rotationMatrix[1][2];
+    rotated1[1] += quad1[3]*element;
+    rotated2[1] += quad2[3]*element;
+    element = rotationMatrix[1][1]*rotationMatrix[0][2] + rotationMatrix[0][1]*rotationMatrix[1][2];
+    rotated1[1] += quad1[4]*element;
+    rotated2[1] += quad2[4]*element;
+    element = sqrtThree*rotationMatrix[0][0]*rotationMatrix[2][0];
+    rotated1[2] += quad1[0]*element;
+    rotated2[2] += quad2[0]*element;
+    element = rotationMatrix[2][0]*rotationMatrix[0][1] + rotationMatrix[0][0]*rotationMatrix[2][1];
+    rotated1[2] += quad1[1]*element;
+    rotated2[2] += quad2[1]*element;
+    element = rotationMatrix[2][0]*rotationMatrix[0][2] + rotationMatrix[0][0]*rotationMatrix[2][2];
+    rotated1[2] += quad1[2]*element;
+    rotated2[2] += quad2[2]*element;
+    element = rotationMatrix[0][1]*rotationMatrix[2][1] - rotationMatrix[0][2]*rotationMatrix[2][2];
+    rotated1[2] += quad1[3]*element;
+    rotated2[2] += quad2[3]*element;
+    element = rotationMatrix[2][1]*rotationMatrix[0][2] + rotationMatrix[0][1]*rotationMatrix[2][2];
+    rotated1[2] += quad1[4]*element;
+    rotated2[2] += quad2[4]*element;
+    element = 0.5f*sqrtThree*(rotationMatrix[1][0]*rotationMatrix[1][0] - rotationMatrix[2][0]*rotationMatrix[2][0]);
+    rotated1[3] += quad1[0]*element;
+    rotated2[3] += quad2[0]*element;
+    element = rotationMatrix[1][0]*rotationMatrix[1][1] - rotationMatrix[2][0]*rotationMatrix[2][1];
+    rotated1[3] += quad1[1]*element;
+    rotated2[3] += quad2[1]*element;
+    element = rotationMatrix[1][0]*rotationMatrix[1][2] - rotationMatrix[2][0]*rotationMatrix[2][2];
+    rotated1[3] += quad1[2]*element;
+    rotated2[3] += quad2[2]*element;
+    element = 0.5f*(rotationMatrix[1][1]*rotationMatrix[1][1] - rotationMatrix[2][1]*rotationMatrix[2][1] - rotationMatrix[1][2]*rotationMatrix[1][2] + rotationMatrix[2][2]*rotationMatrix[2][2]);
+    rotated1[3] += quad1[3]*element;
+    rotated2[3] += quad2[3]*element;
+    element = rotationMatrix[1][1]*rotationMatrix[1][2] - rotationMatrix[2][1]*rotationMatrix[2][2];
+    rotated1[3] += quad1[4]*element;
+    rotated2[3] += quad2[4]*element;
+    element = sqrtThree*rotationMatrix[1][0]*rotationMatrix[2][0];
+    rotated1[4] += quad1[0]*element;
+    rotated2[4] += quad2[0]*element;
+    element = rotationMatrix[2][0]*rotationMatrix[1][1] + rotationMatrix[1][0]*rotationMatrix[2][1];
+    rotated1[4] += quad1[1]*element;
+    rotated2[4] += quad2[1]*element;
+    element = rotationMatrix[2][0]*rotationMatrix[1][2] + rotationMatrix[1][0]*rotationMatrix[2][2];
+    rotated1[4] += quad1[2]*element;
+    rotated2[4] += quad2[2]*element;
+    element = rotationMatrix[1][1]*rotationMatrix[2][1] - rotationMatrix[1][2]*rotationMatrix[2][2];
+    rotated1[4] += quad1[3]*element;
+    rotated2[4] += quad2[3]*element;
+    element = rotationMatrix[2][1]*rotationMatrix[1][2] + rotationMatrix[1][1]*rotationMatrix[2][2];
+    rotated1[4] += quad1[4]*element;
+    rotated2[4] += quad2[4]*element;
+}

plugins/amoeba/platforms/cuda/tests/CMakeLists.txt

@@ -17,7 +17,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     IF (APPLE)
         SET_TARGET_PROPERTIES(${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 "${EXTRA_COMPILE_FLAGS}")
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${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/cuda/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp

@@ -6980,7 +6980,7 @@ static void compareForcesEnergy(std::string& testName, double expectedEnergy, do
                                 const std::vector<Vec3>& expectedForces,
                                 const std::vector<Vec3>& forces, double tolerance) {
     for (unsigned int ii = 0; ii < forces.size(); ii++) {
-        ASSERT_EQUAL_VEC_MOD(expectedForces[ii], forces[ii], tolerance, testName);
+        ASSERT_EQUAL_VEC(expectedForces[ii], forces[ii], tolerance);
     }
     ASSERT_EQUAL_TOL_MOD(expectedEnergy, energy, tolerance, testName);
 }

plugins/amoeba/platforms/reference/CMakeLists.txt

@@ -71,7 +71,7 @@ ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_AMOEBA_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 

plugins/amoeba/platforms/reference/tests/CMakeLists.txt

@@ -12,7 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # Link with shared library
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp

@@ -6983,7 +6983,7 @@ static void compareForcesEnergy(std::string& testName, double expectedEnergy, do
                                 const std::vector<Vec3>& forces, double tolerance) {
     for (unsigned int ii = 0; ii < forces.size(); ii++) {
-        ASSERT_EQUAL_VEC_MOD(expectedForces[ii], forces[ii], tolerance, testName);
+        ASSERT_EQUAL_VEC(expectedForces[ii], forces[ii], tolerance);
     }
     ASSERT_EQUAL_TOL_MOD(expectedEnergy, energy, tolerance, testName);
 }

plugins/amoeba/serialization/tests/CMakeLists.txt

@@ -12,7 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # All tests use shared libraries
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/cpupme/CMakeLists.txt

@@ -75,7 +75,7 @@ IF (OPENMM_BUILD_SHARED_LIB)
     IF (FFTW_THREADS_LIBRARY)
         TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${FFTW_THREADS_LIBRARY})
     ENDIF (FFTW_THREADS_LIBRARY)
-    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_SHARED_LIBRARY")
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_SHARED_LIBRARY")
 
     INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
 ENDIF (OPENMM_BUILD_SHARED_LIB)
@@ -88,7 +88,7 @@ IF(OPENMM_BUILD_STATIC_LIB)
     IF (FFTW_THREADS_LIBRARY)
         TARGET_LINK_LIBRARIES(${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")
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_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)