Merge branch 'upstream' into fork

plugins/cpupme/tests/CMakeLists.txt

+#
+# Testing
+#
+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)
+
+#LINK_DIRECTORIES
+
+# Automatically create tests using files named "Test*.cpp"
+FILE(GLOB TEST_PROGS "*Test*.cpp")
+FOREACH(TEST_PROG ${TEST_PROGS})
+    GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
+
+    # Link with shared library
+
+    ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
+    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM_PME_TARGET})
+    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
+ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/cpupme/tests/TestCpuPme.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2013 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the CPU implementation of PME.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/internal/NonbondedForceImpl.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "openmm/internal/ContextImpl.h"
+#include "../src/CpuPmeKernels.h"
+#include "SimTKOpenMMRealType.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+class IO : public CalcPmeReciprocalForceKernel::IO {
+public:
+    vector<float> posq;
+    float* force;
+    float* getPosq() {
+        return &posq[0];
+    }
+    void setForce(float* force) {
+        this->force = force;
+    }
+};
+
+void testPME() {
+    // Create a cloud of random point charges.
+
+    const int numParticles = 51;
+    const double boxWidth = 5.0;
+    const double cutoff = 1.0;
+    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);
+    force->setCutoffDistance(cutoff);
+    force->setReciprocalSpaceForceGroup(1);
+    force->setEwaldErrorTolerance(1e-4);
+    
+    // Compute the reciprocal space forces with the reference platform.
+    
+    Platform& platform = Platform::getPlatformByName("Reference");
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    State refState = context.getState(State::Forces | State::Energy, false, 1<<1);
+    
+    // Now compute them with the optimized kernel.
+    
+    double alpha;
+    int gridx, gridy, gridz;
+    NonbondedForceImpl::calcPMEParameters(system, *force, alpha, gridx, gridy, gridz);
+    CpuCalcPmeReciprocalForceKernel pme(CalcPmeReciprocalForceKernel::Name(), platform);
+    IO io;
+    double sumSquaredCharges = 0;
+    for (int i = 0; i < numParticles; i++) {
+        io.posq.push_back(positions[i][0]);
+        io.posq.push_back(positions[i][1]);
+        io.posq.push_back(positions[i][2]);
+        double charge, sigma, epsilon;
+        force->getParticleParameters(i, charge, sigma, epsilon);
+        io.posq.push_back(charge);
+        sumSquaredCharges += charge*charge;
+    }
+    double ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
+    pme.initialize(gridx, gridy, gridz, numParticles, alpha);
+    pme.beginComputation(io, Vec3(boxWidth, boxWidth, boxWidth), true);
+    double energy = pme.finishComputation(io);
+    
+    // See if they match.
+    
+    ASSERT_EQUAL_TOL(refState.getPotentialEnergy(), energy+ewaldSelfEnergy, 1e-3);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(refState.getForces()[i], Vec3(io.force[4*i], io.force[4*i+1], io.force[4*i+2]), 1e-3);
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        testPME();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp

@@ -36,7 +36,7 @@
 #include "CudaForceInfo.h"
 #include "CudaIntegrationUtilities.h"
 #include "CudaKernelSources.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include <set>
 
 using namespace OpenMM;

plugins/drude/platforms/cuda/tests/TestCudaDrudeForce.cpp

@@ -40,7 +40,7 @@
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
 #include "openmm/DrudeForce.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/cuda/tests/TestCudaDrudeSCFIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp

@@ -36,7 +36,7 @@
 #include "OpenCLForceInfo.h"
 #include "OpenCLIntegrationUtilities.h"
 #include "OpenCLKernelSources.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include <set>
 
 using namespace OpenMM;

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeForce.cpp

@@ -40,7 +40,7 @@
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
 #include "openmm/DrudeForce.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp

@@ -33,9 +33,9 @@
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
-#include "SimTKReference/ReferenceCCMAAlgorithm.h"
-#include "SimTKReference/ReferenceVirtualSites.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceCCMAAlgorithm.h"
+#include "ReferenceVirtualSites.h"
 #include <set>
 
 using namespace OpenMM;

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.h

@@ -34,7 +34,7 @@
 
 #include "ReferencePlatform.h"
 #include "openmm/DrudeKernels.h"
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include "lbfgs.h"
 #include <utility>
 #include <vector>

plugins/drude/platforms/reference/tests/TestReferenceDrudeForce.cpp

@@ -40,7 +40,7 @@
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
 #include "openmm/DrudeForce.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/reference/tests/TestReferenceDrudeSCFIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp

@@ -36,7 +36,7 @@
 #include "CudaExpressionUtilities.h"
 #include "CudaKernelSources.h"
 #include "CudaNonbondedUtilities.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 
 using namespace OpenMM;
 using namespace std;

plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp

@@ -43,7 +43,7 @@
 #include "openmm/System.h"
 #include "openmm/RPMDIntegrator.h"
 #include "openmm/VirtualSite.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp

@@ -36,7 +36,7 @@
 #include "OpenCLExpressionUtilities.h"
 #include "OpenCLFFT3D.h"
 #include "OpenCLNonbondedUtilities.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 
 using namespace OpenMM;
 using namespace std;

plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp

@@ -43,7 +43,7 @@
 #include "openmm/System.h"
 #include "openmm/RPMDIntegrator.h"
 #include "openmm/VirtualSite.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp

@@ -32,7 +32,7 @@
 #include "ReferenceRpmdKernels.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 
 using namespace OpenMM;
 using namespace std;