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Commit 4c696473 authored by peastman's avatar peastman
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Merge pull request #1137 from peastman/periodic 

Created periodicdistance() function for CustomExternalForce
parents 69fd88d7 eaef52d9
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Showing with 661 additions and 346 deletions
openmmapi/include/openmm/CustomExternalForce.h
View file @ 4c696473
......@@ -67,6 +67,14 @@ namespace OpenMM {
* force->addPerParticleParameter("z0");
* </pre></tt>
*
* Special care is needed in systems that use periodic boundary conditions. In that case, each particle really represents
* an infinite set of particles repeating through space. The variables x, y, and z contain the coordinates of one of those
* periodic copies, but there is no guarantee about which. It might even change from one time step to the next. You can handle
* this situation by using the function periodicdistance(x1, y1, z1, x2, y2, z2), which returns the minimum distance between
* periodic copies of the points (x1, y1, z1) and (x2, y2, z2). For example, the force given above would be rewritten as
*
* <tt>CustomExternalForce* force = new CustomExternalForce("k*periodicdistance(x, y, z, x0, y0, z0)^2");</tt>
*
* Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
* functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select. All trigonometric functions
* are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise.
......
platforms/cuda/include/CudaExpressionUtilities.h
View file @ 4c696473
......@@ -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);
CudaContext& context;
FunctionPlaceholder fp1, fp2, fp3;
FunctionPlaceholder fp1, fp2, fp3, periodicDistance;
};
} // namespace OpenMM
......
platforms/cuda/src/CudaBondedUtilities.cpp
View file @ 4c696473
......@@ -99,7 +99,7 @@ void CudaBondedUtilities::initialize(const System& system) {
s<<CudaKernelSources::vectorOps;
for (int i = 0; i < (int) prefixCode.size(); i++)
s<<prefixCode[i];
s<<"extern \"C\" __global__ void computeBondedForces(unsigned long long* __restrict__ forceBuffer, real* __restrict__ energyBuffer, const real4* __restrict__ posq, int groups";
s<<"extern \"C\" __global__ void computeBondedForces(unsigned long long* __restrict__ forceBuffer, real* __restrict__ energyBuffer, const real4* __restrict__ posq, int groups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ";
for (int force = 0; force < numForces; force++) {
for (int i = 0; i < (int) atomIndices[force].size(); i++) {
int indexWidth = atomIndices[force][i]->getElementSize()/4;
......@@ -161,6 +161,11 @@ void CudaBondedUtilities::computeInteractions(int groups) {
kernelArgs.push_back(&context.getEnergyBuffer().getDevicePointer());
kernelArgs.push_back(&context.getPosq().getDevicePointer());
kernelArgs.push_back(NULL);
kernelArgs.push_back(context.getPeriodicBoxSizePointer());
kernelArgs.push_back(context.getInvPeriodicBoxSizePointer());
kernelArgs.push_back(context.getPeriodicBoxVecXPointer());
kernelArgs.push_back(context.getPeriodicBoxVecYPointer());
kernelArgs.push_back(context.getPeriodicBoxVecZPointer());
for (int i = 0; i < (int) atomIndices.size(); i++)
for (int j = 0; j < (int) atomIndices[i].size(); j++)
kernelArgs.push_back(&atomIndices[i][j]->getDevicePointer());
......
platforms/cuda/src/CudaExpressionUtilities.cpp
View file @ 4c696473
......@@ -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;
CudaExpressionUtilities::CudaExpressionUtilities(CudaContext& context) : context(context), fp1(1), fp2(2), fp3(3) {
CudaExpressionUtilities::CudaExpressionUtilities(CudaContext& context) : context(context), fp1(1), fp2(2), fp3(3), periodicDistance(6) {
}
string CudaExpressionUtilities::createExpressions(const map<string, ParsedExpression>& expressions, const map<string, string>& variables,
......@@ -79,11 +79,6 @@ void CudaExpressionUtilities::processExpression(stringstream& out, const Express
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 CudaExpressionUtilities::processExpression(stringstream& out, const Express
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 CudaExpressionUtilities::processExpression(stringstream& out, const Express
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 = make_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 CudaExpressionUtilities::processExpression(stringstream& out, const Express
}
}
}
}
out << "}";
break;
}
......@@ -483,7 +525,7 @@ string CudaExpressionUtilities::getTempName(const ExpressionTreeNode& node, cons
throw OpenMMException(out.str());
}
void CudaExpressionUtilities::findRelatedTabulatedFunctions(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode,
void CudaExpressionUtilities::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.
......@@ -504,7 +546,7 @@ void CudaExpressionUtilities::findRelatedTabulatedFunctions(const ExpressionTree
}
else
for (int i = 0; i < (int) searchNode.getChildren().size(); i++)
findRelatedTabulatedFunctions(node, searchNode.getChildren()[i], nodes);
findRelatedCustomFunctions(node, searchNode.getChildren()[i], nodes);
}
void CudaExpressionUtilities::findRelatedPowers(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode, map<int, const ExpressionTreeNode*>& powers) {
......@@ -730,3 +772,7 @@ Lepton::CustomFunction* CudaExpressionUtilities::getFunctionPlaceholder(const Ta
return &fp3;
throw OpenMMException("getFunctionPlaceholder: Unknown function type");
}
Lepton::CustomFunction* CudaExpressionUtilities::getPeriodicDistancePlaceholder() {
return &periodicDistance;
}
platforms/cuda/src/CudaKernels.cpp
View file @ 4c696473
......@@ -3652,7 +3652,9 @@ void CudaCalcCustomExternalForceKernel::initialize(const System& system, const C
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = (float) force.getGlobalParameterDefaultValue(i);
}
Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
map<string, Lepton::CustomFunction*> customFunctions;
customFunctions["periodicdistance"] = cu.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/cuda/tests/TestCudaCustomExternalForce.cpp
View file @ 4c696473
......@@ -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) 2008-2012 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;
......
platforms/opencl/include/OpenCLExpressionUtilities.h
View file @ 4c696473
......@@ -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
View file @ 4c696473
......@@ -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
View file @ 4c696473
......@@ -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
View file @ 4c696473
......@@ -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
View file @ 4c696473
......@@ -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;
......
platforms/reference/include/ReferenceKernels.h
View file @ 4c696473
......@@ -37,6 +37,7 @@
#include "SimTKOpenMMRealType.h"
#include "ReferenceNeighborList.h"
#include "lepton/CompiledExpression.h"
#include "lepton/CustomFunction.h"
#include "lepton/ExpressionProgram.h"
namespace OpenMM {
......@@ -795,11 +796,23 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
private:
class PeriodicDistanceFunction;
int numParticles;
std::vector<int> particles;
RealOpenMM **particleParamArray;
Lepton::CompiledExpression energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
std::vector<std::string> parameterNames, globalParameterNames;
RealVec* boxVectors;
};
class ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction : public Lepton::CustomFunction {
public:
RealVec** boxVectorHandle;
PeriodicDistanceFunction(RealVec** boxVectorHandle);
int getNumArguments() const;
double evaluate(const double* arguments) const;
double evaluateDerivative(const double* arguments, const int* derivOrder) const;
Lepton::CustomFunction* clone() const;
};
/**
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 4c696473
......@@ -1402,6 +1402,46 @@ void ReferenceCalcCustomGBForceKernel::copyParametersToContext(ContextImpl& cont
}
}
ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction::PeriodicDistanceFunction(RealVec** boxVectorHandle) : boxVectorHandle(boxVectorHandle) {
}
int ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction::getNumArguments() const {
return 6;
}
double ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction::evaluate(const double* arguments) const {
RealVec* boxVectors = *boxVectorHandle;
RealVec delta = RealVec(arguments[0], arguments[1], arguments[2])-RealVec(arguments[3], arguments[4], arguments[5]);
delta -= boxVectors[2]*floor(delta[2]/boxVectors[2][2]+0.5);
delta -= boxVectors[1]*floor(delta[1]/boxVectors[1][1]+0.5);
delta -= boxVectors[0]*floor(delta[0]/boxVectors[0][0]+0.5);
return sqrt(delta.dot(delta));
}
double ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
int argIndex = -1;
for (int i = 0; i < 6; i++) {
if (derivOrder[i] > 0) {
if (derivOrder[i] > 1 || argIndex != -1)
throw OpenMMException("Unsupported derivative of periodicdistance"); // Should be impossible for this to happen.
argIndex = i;
}
}
RealVec* boxVectors = *boxVectorHandle;
RealVec delta = RealVec(arguments[0], arguments[1], arguments[2])-RealVec(arguments[3], arguments[4], arguments[5]);
delta -= boxVectors[2]*floor(delta[2]/boxVectors[2][2]+0.5);
delta -= boxVectors[1]*floor(delta[1]/boxVectors[1][1]+0.5);
delta -= boxVectors[0]*floor(delta[0]/boxVectors[0][0]+0.5);
double r = sqrt(delta.dot(delta));
if (argIndex < 3)
return delta[argIndex]/r;
return -delta[argIndex-3]/r;
}
Lepton::CustomFunction* ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction::clone() const {
return new PeriodicDistanceFunction(boxVectorHandle);
}
ReferenceCalcCustomExternalForceKernel::~ReferenceCalcCustomExternalForceKernel() {
disposeRealArray(particleParamArray, numParticles);
}
......@@ -1423,7 +1463,10 @@ void ReferenceCalcCustomExternalForceKernel::initialize(const System& system, co
// Parse the expression used to calculate the force.
Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
map<string, Lepton::CustomFunction*> functions;
PeriodicDistanceFunction periodicDistance(&boxVectors);
functions["periodicdistance"] = &periodicDistance;
Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions).optimize();
energyExpression = expression.createCompiledExpression();
forceExpressionX = expression.differentiate("x").createCompiledExpression();
forceExpressionY = expression.differentiate("y").createCompiledExpression();
......@@ -1437,6 +1480,7 @@ void ReferenceCalcCustomExternalForceKernel::initialize(const System& system, co
double ReferenceCalcCustomExternalForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
boxVectors = extractBoxVectors(context);
RealOpenMM energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
......
platforms/reference/tests/TestReferenceCustomExternalForce.cpp
View file @ 4c696473
......@@ -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: *
* *
......@@ -101,9 +101,51 @@ void testForce() {
}
}
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-6);
ASSERT_EQUAL_TOL(delta.dot(delta), state.getPotentialEnergy(), 1e-6);
integrator.step(1);
}
}
int main() {
try {
testForce();
testPeriodic();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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