Created OpenCL implementation of periodicdistance()

platforms/opencl/include/OpenCLExpressionUtilities.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -89,6 +89,10 @@ public:
      * @param function   the function for which to get a placeholder
      */
     Lepton::CustomFunction* getFunctionPlaceholder(const TabulatedFunction& function);
+    /**
+     * Get a Lepton::CustomFunction that can be used to represent the periodicdistance() function when parsing expressions.
+     */
+    Lepton::CustomFunction* getPeriodicDistancePlaceholder();
 private:
     class FunctionPlaceholder : public Lepton::CustomFunction {
         public:
@@ -114,13 +118,13 @@ private:
             const std::vector<const TabulatedFunction*>& functions, const std::vector<std::pair<std::string, std::string> >& functionNames,
             const std::string& prefix, const std::vector<std::vector<double> >& functionParams, const std::vector<Lepton::ParsedExpression>& allExpressions, const std::string& tempType);
     std::string getTempName(const Lepton::ExpressionTreeNode& node, const std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& temps);
-    void findRelatedTabulatedFunctions(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
+    void findRelatedCustomFunctions(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
             std::vector<const Lepton::ExpressionTreeNode*>& nodes);
     void findRelatedPowers(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
             std::map<int, const Lepton::ExpressionTreeNode*>& powers);
     std::vector<std::vector<double> > computeFunctionParameters(const std::vector<const TabulatedFunction*>& functions);
     OpenCLContext& context;
-    FunctionPlaceholder fp1, fp2, fp3;
+    FunctionPlaceholder fp1, fp2, fp3, periodicDistance;
 };
 
 } // namespace OpenMM

platforms/opencl/src/OpenCLBondedUtilities.cpp

@@ -181,7 +181,7 @@ void OpenCLBondedUtilities::initialize(const System& system) {
         for (int i = 0; i < (int) prefixCode.size(); i++)
             s<<prefixCode[i];
         string bufferType = (context.getSupports64BitGlobalAtomics() ? "long" : "real4");
-        s<<"__kernel void computeBondedForces(__global "<<bufferType<<"* restrict forceBuffers, __global real* restrict energyBuffer, __global const real4* restrict posq, int groups";
+        s<<"__kernel void computeBondedForces(__global "<<bufferType<<"* restrict forceBuffers, __global real* restrict energyBuffer, __global const real4* restrict posq, int groups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ";
         for (int i = 0; i < setSize; i++) {
             int force = set[i];
             string indexType = "uint"+(indexWidth[force] == 1 ? "" : context.intToString(indexWidth[force]));
@@ -267,7 +267,7 @@ void OpenCLBondedUtilities::computeInteractions(int groups) {
                 kernel.setArg<cl::Buffer>(index++, context.getForceBuffers().getDeviceBuffer());
             kernel.setArg<cl::Buffer>(index++, context.getEnergyBuffer().getDeviceBuffer());
             kernel.setArg<cl::Buffer>(index++, context.getPosq().getDeviceBuffer());
-            index++;
+            index += 6;
             for (int j = 0; j < (int) forceSets[i].size(); j++) {
                 kernel.setArg<cl::Buffer>(index++, atomIndices[forceSets[i][j]]->getDeviceBuffer());
                 kernel.setArg<cl::Buffer>(index++, bufferIndices[forceSets[i][j]]->getDeviceBuffer());
@@ -277,7 +277,22 @@ void OpenCLBondedUtilities::computeInteractions(int groups) {
         }
     }
     for (int i = 0; i < (int) kernels.size(); i++) {
-        kernels[i].setArg<cl_int>(3, groups);
+        cl::Kernel& kernel = kernels[i];
+        kernel.setArg<cl_int>(3, groups);
+        if (context.getUseDoublePrecision()) {
+            kernel.setArg<mm_double4>(4, context.getPeriodicBoxSizeDouble());
+            kernel.setArg<mm_double4>(5, context.getInvPeriodicBoxSizeDouble());
+            kernel.setArg<mm_double4>(6, context.getPeriodicBoxVecXDouble());
+            kernel.setArg<mm_double4>(7, context.getPeriodicBoxVecYDouble());
+            kernel.setArg<mm_double4>(8, context.getPeriodicBoxVecZDouble());
+        }
+        else {
+            kernel.setArg<mm_float4>(4, context.getPeriodicBoxSize());
+            kernel.setArg<mm_float4>(5, context.getInvPeriodicBoxSize());
+            kernel.setArg<mm_float4>(6, context.getPeriodicBoxVecX());
+            kernel.setArg<mm_float4>(7, context.getPeriodicBoxVecY());
+            kernel.setArg<mm_float4>(8, context.getPeriodicBoxVecZ());
+        }
         context.executeKernel(kernels[i], maxBonds);
     }
 }

platforms/opencl/src/OpenCLExpressionUtilities.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) 2009-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,7 +33,7 @@ using namespace OpenMM;
 using namespace Lepton;
 using namespace std;
 
-OpenCLExpressionUtilities::OpenCLExpressionUtilities(OpenCLContext& context) : context(context), fp1(1), fp2(2), fp3(3) {
+OpenCLExpressionUtilities::OpenCLExpressionUtilities(OpenCLContext& context) : context(context), fp1(1), fp2(2), fp3(3), periodicDistance(6) {
 }
 
 string OpenCLExpressionUtilities::createExpressions(const map<string, ParsedExpression>& expressions, const map<string, string>& variables,
@@ -79,11 +79,6 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
             throw OpenMMException("Unknown variable in expression: "+node.getOperation().getName());
         case Operation::CUSTOM:
         {
-            int i;
-            for (i = 0; i < (int) functionNames.size() && functionNames[i].first != node.getOperation().getName(); i++)
-                ;
-            if (i == functionNames.size())
-                throw OpenMMException("Unknown function in expression: "+node.getOperation().getName());
             out << "0.0f;\n";
             temps.push_back(make_pair(node, name));
             hasRecordedNode = true;
@@ -93,7 +88,7 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
 
             vector<const ExpressionTreeNode*> nodes;
             for (int j = 0; j < (int) allExpressions.size(); j++)
-                findRelatedTabulatedFunctions(node, allExpressions[j].getRootNode(), nodes);
+                findRelatedCustomFunctions(node, allExpressions[j].getRootNode(), nodes);
             vector<string> nodeNames;
             nodeNames.push_back(name);
             for (int j = 1; j < (int) nodes.size(); j++) {
@@ -103,6 +98,52 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
                 temps.push_back(make_pair(*nodes[j], name2));
             }
             out << "{\n";
+            if (node.getOperation().getName() == "periodicdistance") {
+                // This is the periodicdistance() function.
+
+                out << tempType << "3 periodicDistance_delta = (real3) (";
+                for (int i = 0; i < 3; i++) {
+                    if (i > 0)
+                        out << ", ";
+                    out << getTempName(node.getChildren()[i], temps) << "-" << getTempName(node.getChildren()[i+3], temps);
+                }
+                out << ");\n";
+                out << "APPLY_PERIODIC_TO_DELTA(periodicDistance_delta)\n";
+                out << tempType << " periodicDistance_rinv = RSQRT(periodicDistance_delta.x*periodicDistance_delta.x + periodicDistance_delta.y*periodicDistance_delta.y + periodicDistance_delta.z*periodicDistance_delta.z);\n";
+                for (int j = 0; j < nodes.size(); j++) {
+                    const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
+                    int argIndex = -1;
+                    for (int k = 0; k < 6; k++) {
+                        if (derivOrder[k] > 0) {
+                            if (derivOrder[k] > 1 || argIndex != -1)
+                                throw OpenMMException("Unsupported derivative of periodicdistance"); // Should be impossible for this to happen.
+                            argIndex = k;
+                        }
+                    }
+                    if (argIndex == -1)
+                        out << nodeNames[j] << " = RECIP(periodicDistance_rinv);\n";
+                    else if (argIndex == 0)
+                        out << nodeNames[j] << " = periodicDistance_delta.x*periodicDistance_rinv;\n";
+                    else if (argIndex == 1)
+                        out << nodeNames[j] << " = periodicDistance_delta.y*periodicDistance_rinv;\n";
+                    else if (argIndex == 2)
+                        out << nodeNames[j] << " = periodicDistance_delta.z*periodicDistance_rinv;\n";
+                    else if (argIndex == 3)
+                        out << nodeNames[j] << " = -periodicDistance_delta.x*periodicDistance_rinv;\n";
+                    else if (argIndex == 4)
+                        out << nodeNames[j] << " = -periodicDistance_delta.y*periodicDistance_rinv;\n";
+                    else if (argIndex == 5)
+                        out << nodeNames[j] << " = -periodicDistance_delta.z*periodicDistance_rinv;\n";
+                }
+            }
+            else {
+                // This is a tabulated function.
+
+                int i;
+                for (i = 0; i < (int) functionNames.size() && functionNames[i].first != node.getOperation().getName(); i++)
+                    ;
+                if (i == functionNames.size())
+                    throw OpenMMException("Unknown function in expression: "+node.getOperation().getName());
                 vector<string> paramsFloat, paramsInt;
                 for (int j = 0; j < (int) functionParams[i].size(); j++) {
                     paramsFloat.push_back(context.doubleToString(functionParams[i][j]));
@@ -275,6 +316,7 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
                         }
                     }
                 }
+            }
             out << "}";
             break;
         }
@@ -475,7 +517,7 @@ string OpenCLExpressionUtilities::getTempName(const ExpressionTreeNode& node, co
     throw OpenMMException(out.str());
 }
 
-void OpenCLExpressionUtilities::findRelatedTabulatedFunctions(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode,
+void OpenCLExpressionUtilities::findRelatedCustomFunctions(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode,
             vector<const Lepton::ExpressionTreeNode*>& nodes) {
     if (searchNode.getOperation().getId() == Operation::CUSTOM && node.getOperation().getName() == searchNode.getOperation().getName()) {
         // Make sure the arguments are identical.
@@ -496,7 +538,7 @@ void OpenCLExpressionUtilities::findRelatedTabulatedFunctions(const ExpressionTr
     }
     else
         for (int i = 0; i < (int) searchNode.getChildren().size(); i++)
-            findRelatedTabulatedFunctions(node, searchNode.getChildren()[i], nodes);
+            findRelatedCustomFunctions(node, searchNode.getChildren()[i], nodes);
 }
 
 void OpenCLExpressionUtilities::findRelatedPowers(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode, map<int, const ExpressionTreeNode*>& powers) {
@@ -722,3 +764,7 @@ Lepton::CustomFunction* OpenCLExpressionUtilities::getFunctionPlaceholder(const
         return &fp3;
     throw OpenMMException("getFunctionPlaceholder: Unknown function type");
 }
+
+Lepton::CustomFunction* OpenCLExpressionUtilities::getPeriodicDistancePlaceholder() {
+    return &periodicDistance;
+}

platforms/opencl/src/OpenCLKernels.cpp

@@ -3821,7 +3821,9 @@ void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const
         globalParamNames[i] = force.getGlobalParameterName(i);
         globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
     }
-    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
+    map<string, Lepton::CustomFunction*> customFunctions;
+    customFunctions["periodicdistance"] = cl.getExpressionUtilities().getPeriodicDistancePlaceholder();
+    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction(), customFunctions).optimize();
     Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x").optimize();
     Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y").optimize();
     Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z").optimize();

platforms/opencl/tests/TestOpenCLCustomExternalForce.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -161,6 +161,47 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
+void testPeriodic() {
+    Vec3 vx(5, 0, 0);
+    Vec3 vy(0, 6, 0);
+    Vec3 vz(1, 2, 7);
+    double x0 = 51, y0 = -17, z0 = 11.2;
+    System system;
+    system.setDefaultPeriodicBoxVectors(vx, vy, vz);
+    system.addParticle(1.0);
+    CustomExternalForce* force = new CustomExternalForce("periodicdistance(x, y, z, x0, y0, z0)^2");
+    force->addPerParticleParameter("x0");
+    force->addPerParticleParameter("y0");
+    force->addPerParticleParameter("z0");
+    vector<double> params(3);
+    params[0] = x0;
+    params[1] = y0;
+    params[2] = z0;
+    force->addParticle(0, params);
+    system.addForce(force);
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(1);
+    positions[0] = Vec3(0, 2, 0);
+    context.setPositions(positions);
+    for (int i = 0; i < 100; i++) {
+        State state = context.getState(State::Positions | State::Forces | State::Energy);
+
+        // Apply periodic boundary conditions to the difference between the two positions.
+
+        Vec3 delta = Vec3(x0, y0, z0)-state.getPositions()[0];
+        delta -= vz*floor(delta[2]/vz[2]+0.5);
+        delta -= vy*floor(delta[1]/vy[1]+0.5);
+        delta -= vx*floor(delta[0]/vx[0]+0.5);
+
+        // Verify that the force and energy are correct.
+
+        ASSERT_EQUAL_VEC(delta*2, state.getForces()[0], 1e-5);
+        ASSERT_EQUAL_TOL(delta.dot(delta), state.getPotentialEnergy(), 1e-5);
+        integrator.step(1);
+    }
+}
+
 int main(int argc, char* argv[]) {
     try {
         if (argc > 1)
@@ -168,6 +209,7 @@ int main(int argc, char* argv[]) {
         testForce();
         testManyParameters();
         testParallelComputation();
+        testPeriodic();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;