Fixes to dispersion PME

openmmapi/include/openmm/NonbondedForce.h

@@ -101,18 +101,18 @@ public:
          */
         CutoffPeriodic = 2,
         /**
-         * Periodic boundary conditions are used, and Ewald summation is used to compute the interaction of each particle
+         * Periodic boundary conditions are used, and Ewald summation is used to compute the Coulomb interaction of each particle
          * with all periodic copies of every other particle.
          */
         Ewald = 3,
         /**
-         * Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
+         * Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the Coulomb interaction of each particle
          * with all periodic copies of every other particle.
          */
         PME = 4,
         /**
          * Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
-         * with all periodic copies of every other particle for both electrostatics and dispersion.  No switching is used for either interaction.
+         * with all periodic copies of every other particle for both Coulomb and Lennard-Jones.  No switching is used for either interaction.
          */
         LJPME = 5
     };

openmmapi/src/NonbondedForce.cpp

@@ -48,7 +48,8 @@ using std::stringstream;
 using std::vector;
 
 NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), switchingDistance(-1.0), rfDielectric(78.3),
-        ewaldErrorTol(5e-4), alpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1), nx(0), ny(0), nz(0) {
+        ewaldErrorTol(5e-4), alpha(0.0), dalpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1),
+        nx(0), ny(0), nz(0), dnx(0), dny(0), dnz(0) {
 }
 
 NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {

openmmapi/src/NonbondedForceImpl.cpp

@@ -90,9 +90,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
         exceptions[particle1].insert(particle2);
         exceptions[particle2].insert(particle1);
     }
-    if (owner.getNonbondedMethod() == NonbondedForce::CutoffPeriodic ||
-            owner.getNonbondedMethod() == NonbondedForce::Ewald ||
-            owner.getNonbondedMethod() == NonbondedForce::PME) {
+    if (owner.getNonbondedMethod() != NonbondedForce::NoCutoff) {
         Vec3 boxVectors[3];
         system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double cutoff = owner.getCutoffDistance();
@@ -161,12 +159,19 @@ void NonbondedForceImpl::calcPMEParameters(const System& system, const Nonbonded
         system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double tol = force.getEwaldErrorTolerance();
         alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
+        if (lj) {
+            xsize = (int) ceil(alpha*boxVectors[0][0]/(3*pow(tol, 0.05)));
+            ysize = (int) ceil(alpha*boxVectors[1][1]/(3*pow(tol, 0.05)));
+            zsize = (int) ceil(alpha*boxVectors[2][2]/(3*pow(tol, 0.05)));
+        }
+        else {
             xsize = (int) ceil(2*alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
             ysize = (int) ceil(2*alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
             zsize = (int) ceil(2*alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
-        xsize = max(xsize, 5);
-        ysize = max(ysize, 5);
-        zsize = max(zsize, 5);
+        }
+        xsize = max(xsize, 6);
+        ysize = max(ysize, 6);
+        zsize = max(zsize, 6);
     }
 }
 

platforms/cpu/tests/TestCpuDispersionPME.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) 2017 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 "CpuTests.h"
+#include "TestDispersionPME.h"
+
+void runPlatformTests() {
+}
+

platforms/cuda/src/kernels/coulombLennardJones.cu

@@ -30,7 +30,7 @@
             const real dar6 = dar4*dar2;
             const real invR2 = invR*invR;
             const real expDar2 = EXP(-dar2);
-            const real2 sigExpProd = sigmaEpsilon1*sigmaEpsilon2;
+            const float2 sigExpProd = sigmaEpsilon1*sigmaEpsilon2;
             const real c6 = 64*sigExpProd.x*sigExpProd.x*sigExpProd.x*sigExpProd.y;
             const real coef = invR2*invR2*invR2*c6;
             const real eprefac = 1.0f + dar2 + 0.5f*dar4;

platforms/cuda/src/kernels/pme.cu

@@ -23,7 +23,7 @@ extern "C" __global__ void gridSpreadCharge(const real4* __restrict__ posq, real
         real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
         real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, const int2* __restrict__ pmeAtomGridIndex
 #ifdef USE_LJPME
-        , const real2* __restrict__ sigmaEpsilon
+        , const float2* __restrict__ sigmaEpsilon
 #endif
         ) {
     real3 data[PME_ORDER];
@@ -68,7 +68,7 @@ extern "C" __global__ void gridSpreadCharge(const real4* __restrict__ posq, real
         // Spread the charge from this atom onto each grid point.
         
 #ifdef USE_LJPME
-        const real2 sigEps = sigmaEpsilon[atom];
+        const float2 sigEps = sigmaEpsilon[atom];
         const real charge = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y;
 #else
         const real charge = pos.w;
@@ -250,7 +250,7 @@ void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __
         real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
         real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, const int2* __restrict__ pmeAtomGridIndex
 #ifdef USE_LJPME
-        , const real2* __restrict__ sigmaEpsilon
+        , const float2* __restrict__ sigmaEpsilon
 #endif
         ) {
     real3 data[PME_ORDER];
@@ -325,7 +325,7 @@ void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __
             }
         }
 #ifdef USE_LJPME
-        const real2 sigEps = sigmaEpsilon[atom];
+        const float2 sigEps = sigmaEpsilon[atom];
         real q = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y;
 #else
         real q = pos.w*EPSILON_FACTOR;

platforms/cuda/tests/TestCudaDispersionPME.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) 2017 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 "CudaTests.h"
+#include "TestDispersionPME.h"
+
+void runPlatformTests() {
+}

platforms/opencl/tests/TestOpenCLDispersionPME.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) 2017 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 "OpenCLTests.h"
+#include "TestDispersionPME.h"
+
+void runPlatformTests() {
+}

platforms/reference/tests/TestReferenceDispersionPME.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) 2017 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 "ReferenceTests.h"
+#include "TestDispersionPME.h"
+
+void runPlatformTests() {
+}