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Commit cecc774a authored by Peter Eastman's avatar Peter Eastman
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Merge branch 'master' into hardwall

parents 1dfa0e59 a20944f6
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Showing with 403 additions and 3312 deletions
platforms/opencl/include/OpenCLNonbondedUtilities.h
View file @ cecc774a
......@@ -150,8 +150,12 @@ public:
void prepareInteractions(int forceGroups);
/**
* Compute the nonbonded interactions.
*
* @param forceGroups the flags specifying which force groups to include
* @param includeForces whether to compute forces
* @param includeEnergy whether to compute the potential energy
*/
void computeInteractions(int forceGroups);
void computeInteractions(int forceGroups, bool includeForces, bool includeEnergy);
/**
* Check to see if the neighbor list arrays are large enough, and make them bigger if necessary.
*
......@@ -247,8 +251,10 @@ public:
* @param useExclusions specifies whether exclusions are applied to this interaction
* @param isSymmetric specifies whether the interaction is symmetric
* @param groups the set of force groups this kernel is for
* @param includeForces whether this kernel should compute forces
* @param includeEnergy whether this kernel should compute potential energy
*/
cl::Kernel createInteractionKernel(const std::string& source, const std::vector<ParameterInfo>& params, const std::vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups);
cl::Kernel createInteractionKernel(const std::string& source, const std::vector<ParameterInfo>& params, const std::vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups, bool includeForces, bool includeEnergy);
/**
* Create the set of kernels that will be needed for a particular combination of force groups.
*
......@@ -294,7 +300,8 @@ class OpenCLNonbondedUtilities::KernelSet {
public:
bool hasForces;
double cutoffDistance;
cl::Kernel forceKernel;
std::string source;
cl::Kernel forceKernel, energyKernel, forceEnergyKernel;
cl::Kernel findBlockBoundsKernel;
cl::Kernel sortBoxDataKernel;
cl::Kernel findInteractingBlocksKernel;
......
platforms/opencl/src/OpenCLBondedUtilities.cpp
View file @ cecc774a
......@@ -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 @ cecc774a
......@@ -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++) {
......@@ -103,175 +98,222 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
temps.push_back(make_pair(*nodes[j], name2));
}
out << "{\n";
vector<string> paramsFloat, paramsInt;
for (int j = 0; j < (int) functionParams[i].size(); j++) {
paramsFloat.push_back(context.doubleToString(functionParams[i][j]));
paramsInt.push_back(context.intToString((int) functionParams[i][j]));
}
if (dynamic_cast<const Continuous1DFunction*>(functions[i]) != NULL) {
out << "real x = " << getTempName(node.getChildren()[0], temps) << ";\n";
out << "if (x >= " << paramsFloat[0] << " && x <= " << paramsFloat[1] << ") {\n";
out << "x = (x - " << paramsFloat[0] << ")*" << paramsFloat[2] << ";\n";
out << "int index = (int) (floor(x));\n";
out << "index = min(index, " << paramsInt[3] << ");\n";
out << "float4 coeff = " << functionNames[i].second << "[index];\n";
out << "real b = x-index;\n";
out << "real a = 1.0f-b;\n";
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0)
out << nodeNames[j] << " = a*coeff.x+b*coeff.y+((a*a*a-a)*coeff.z+(b*b*b-b)*coeff.w)/(" << paramsFloat[2] << "*" << paramsFloat[2] << ");\n";
else
out << nodeNames[j] << " = (coeff.y-coeff.x)*" << paramsFloat[2] << "+((1.0f-3.0f*a*a)*coeff.z+(3.0f*b*b-1.0f)*coeff.w)/" << paramsFloat[2] << ";\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";
}
else if (dynamic_cast<const Continuous2DFunction*>(functions[i]) != NULL) {
out << "real x = " << getTempName(node.getChildren()[0], temps) << ";\n";
out << "real y = " << getTempName(node.getChildren()[1], temps) << ";\n";
out << "if (x >= " << paramsFloat[2] << " && x <= " << paramsFloat[3] << " && y >= " << paramsFloat[4] << " && y <= " << paramsFloat[5] << ") {\n";
out << "x = (x - " << paramsFloat[2] << ")*" << paramsFloat[6] << ";\n";
out << "y = (y - " << paramsFloat[4] << ")*" << paramsFloat[7] << ";\n";
out << "int s = min((int) floor(x), " << paramsInt[0] << ");\n";
out << "int t = min((int) floor(y), " << paramsInt[1] << ");\n";
out << "int coeffIndex = 4*(s+" << paramsInt[0] << "*t);\n";
out << "float4 c[4];\n";
for (int j = 0; j < 4; j++)
out << "c[" << j << "] = " << functionNames[i].second << "[coeffIndex+" << j << "];\n";
out << "real da = x-s;\n";
out << "real db = y-t;\n";
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();
if (derivOrder[0] == 0 && derivOrder[1] == 0) {
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[3].w*db + c[3].z)*db + c[3].y)*db + c[3].x;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[2].w*db + c[2].z)*db + c[2].y)*db + c[2].x;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[1].w*db + c[1].z)*db + c[1].y)*db + c[1].x;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[0].w*db + c[0].z)*db + c[0].y)*db + c[0].x;\n";
}
else if (derivOrder[0] == 1 && derivOrder[1] == 0) {
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].w*da + 2.0f*c[2].w)*da + c[1].w;\n";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].z*da + 2.0f*c[2].z)*da + c[1].z;\n";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].y*da + 2.0f*c[2].y)*da + c[1].y;\n";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].x*da + 2.0f*c[2].x)*da + c[1].x;\n";
out << nodeNames[j] << " *= " << paramsFloat[6] << ";\n";
}
else if (derivOrder[0] == 0 && derivOrder[1] == 1) {
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[3].w*db + 2.0f*c[3].z)*db + c[3].y;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[2].w*db + 2.0f*c[2].z)*db + c[2].y;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[1].w*db + 2.0f*c[1].z)*db + c[1].y;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[0].w*db + 2.0f*c[0].z)*db + c[0].y;\n";
out << nodeNames[j] << " *= " << paramsFloat[7] << ";\n";
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;
}
}
else
throw OpenMMException("Unsupported derivative order for Continuous2DFunction");
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";
}
out << "}\n";
}
else if (dynamic_cast<const Continuous3DFunction*>(functions[i]) != NULL) {
out << "real x = " << getTempName(node.getChildren()[0], temps) << ";\n";
out << "real y = " << getTempName(node.getChildren()[1], temps) << ";\n";
out << "real z = " << getTempName(node.getChildren()[2], temps) << ";\n";
out << "if (x >= " << paramsFloat[3] << " && x <= " << paramsFloat[4] << " && y >= " << paramsFloat[5] << " && y <= " << paramsFloat[6] << " && z >= " << paramsFloat[7] << " && z <= " << paramsFloat[8] << ") {\n";
out << "x = (x - " << paramsFloat[3] << ")*" << paramsFloat[9] << ";\n";
out << "y = (y - " << paramsFloat[5] << ")*" << paramsFloat[10] << ";\n";
out << "z = (z - " << paramsFloat[7] << ")*" << paramsFloat[11] << ";\n";
out << "int s = min((int) floor(x), " << paramsInt[0] << ");\n";
out << "int t = min((int) floor(y), " << paramsInt[1] << ");\n";
out << "int u = min((int) floor(z), " << paramsInt[2] << ");\n";
out << "int coeffIndex = 16*(s+" << paramsInt[0] << "*(t+" << paramsInt[1] << "*u));\n";
out << "float4 c[16];\n";
for (int j = 0; j < 16; j++)
out << "c[" << j << "] = " << functionNames[i].second << "[coeffIndex+" << j << "];\n";
out << "real da = x-s;\n";
out << "real db = y-t;\n";
out << "real dc = z-u;\n";
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0 && derivOrder[1] == 0 && derivOrder[2] == 0) {
out << "real value[4] = {0, 0, 0, 0};\n";
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = k + 4*m;
out << "value[" << m << "] = db*value[" << m << "] + ((c[" << base << "].w*da + c[" << base << "].z)*da + c[" << base << "].y)*da + c[" << base << "].x;\n";
}
out << nodeNames[j] << " = value[0] + dc*(value[1] + dc*(value[2] + dc*value[3]));\n";
}
else if (derivOrder[0] == 1 && derivOrder[1] == 0 && derivOrder[2] == 0) {
out << "real derivx[4] = {0, 0, 0, 0};\n";
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = k + 4*m;
out << "derivx[" << m << "] = db*derivx[" << m << "] + (3*c[" << base << "].w*da + 2*c[" << base << "].z)*da + c[" << base << "].y;\n";
}
out << nodeNames[j] << " = derivx[0] + dc*(derivx[1] + dc*(derivx[2] + dc*derivx[3]));\n";
out << nodeNames[j] << " *= " << paramsFloat[9] << ";\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]));
paramsInt.push_back(context.intToString((int) functionParams[i][j]));
}
if (dynamic_cast<const Continuous1DFunction*>(functions[i]) != NULL) {
out << "real x = " << getTempName(node.getChildren()[0], temps) << ";\n";
out << "if (x >= " << paramsFloat[0] << " && x <= " << paramsFloat[1] << ") {\n";
out << "x = (x - " << paramsFloat[0] << ")*" << paramsFloat[2] << ";\n";
out << "int index = (int) (floor(x));\n";
out << "index = min(index, " << paramsInt[3] << ");\n";
out << "float4 coeff = " << functionNames[i].second << "[index];\n";
out << "real b = x-index;\n";
out << "real a = 1.0f-b;\n";
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0)
out << nodeNames[j] << " = a*coeff.x+b*coeff.y+((a*a*a-a)*coeff.z+(b*b*b-b)*coeff.w)/(" << paramsFloat[2] << "*" << paramsFloat[2] << ");\n";
else
out << nodeNames[j] << " = (coeff.y-coeff.x)*" << paramsFloat[2] << "+((1.0f-3.0f*a*a)*coeff.z+(3.0f*b*b-1.0f)*coeff.w)/" << paramsFloat[2] << ";\n";
}
else if (derivOrder[0] == 0 && derivOrder[1] == 1 && derivOrder[2] == 0) {
const string suffixes[] = {".x", ".y", ".z", ".w"};
out << "real derivy[4] = {0, 0, 0, 0};\n";
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = 4*m;
string suffix = suffixes[m];
out << "derivy[" << m << "] = da*derivy[" << m << "] + (3*c[" << (base+3) << "]" << suffix << "*db + 2*c[" << (base+2) << "]" << suffix << ")*db + c[" << (base+1) << "]" << suffix << ";\n";
}
out << nodeNames[j] << " = derivy[0] + dc*(derivy[1] + dc*(derivy[2] + dc*derivy[3]));\n";
out << nodeNames[j] << " *= " << paramsFloat[10] << ";\n";
out << "}\n";
}
else if (dynamic_cast<const Continuous2DFunction*>(functions[i]) != NULL) {
out << "real x = " << getTempName(node.getChildren()[0], temps) << ";\n";
out << "real y = " << getTempName(node.getChildren()[1], temps) << ";\n";
out << "if (x >= " << paramsFloat[2] << " && x <= " << paramsFloat[3] << " && y >= " << paramsFloat[4] << " && y <= " << paramsFloat[5] << ") {\n";
out << "x = (x - " << paramsFloat[2] << ")*" << paramsFloat[6] << ";\n";
out << "y = (y - " << paramsFloat[4] << ")*" << paramsFloat[7] << ";\n";
out << "int s = min((int) floor(x), " << paramsInt[0] << ");\n";
out << "int t = min((int) floor(y), " << paramsInt[1] << ");\n";
out << "int coeffIndex = 4*(s+" << paramsInt[0] << "*t);\n";
out << "float4 c[4];\n";
for (int j = 0; j < 4; j++)
out << "c[" << j << "] = " << functionNames[i].second << "[coeffIndex+" << j << "];\n";
out << "real da = x-s;\n";
out << "real db = y-t;\n";
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0 && derivOrder[1] == 0) {
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[3].w*db + c[3].z)*db + c[3].y)*db + c[3].x;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[2].w*db + c[2].z)*db + c[2].y)*db + c[2].x;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[1].w*db + c[1].z)*db + c[1].y)*db + c[1].x;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[0].w*db + c[0].z)*db + c[0].y)*db + c[0].x;\n";
}
else if (derivOrder[0] == 1 && derivOrder[1] == 0) {
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].w*da + 2.0f*c[2].w)*da + c[1].w;\n";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].z*da + 2.0f*c[2].z)*da + c[1].z;\n";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].y*da + 2.0f*c[2].y)*da + c[1].y;\n";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].x*da + 2.0f*c[2].x)*da + c[1].x;\n";
out << nodeNames[j] << " *= " << paramsFloat[6] << ";\n";
}
else if (derivOrder[0] == 0 && derivOrder[1] == 1) {
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[3].w*db + 2.0f*c[3].z)*db + c[3].y;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[2].w*db + 2.0f*c[2].z)*db + c[2].y;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[1].w*db + 2.0f*c[1].z)*db + c[1].y;\n";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[0].w*db + 2.0f*c[0].z)*db + c[0].y;\n";
out << nodeNames[j] << " *= " << paramsFloat[7] << ";\n";
}
else
throw OpenMMException("Unsupported derivative order for Continuous2DFunction");
}
else if (derivOrder[0] == 0 && derivOrder[1] == 0 && derivOrder[2] == 1) {
out << "real derivz[4] = {0, 0, 0, 0};\n";
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = k + 4*m;
out << "derivz[" << m << "] = db*derivz[" << m << "] + ((c[" << base << "].w*da + c[" << base << "].z)*da + c[" << base << "].y)*da + c[" << base << "].x;\n";
}
out << nodeNames[j] << " = derivz[1] + dc*(2*derivz[2] + dc*3*derivz[3]);\n";
out << nodeNames[j] << " *= " << paramsFloat[11] << ";\n";
out << "}\n";
}
else if (dynamic_cast<const Continuous3DFunction*>(functions[i]) != NULL) {
out << "real x = " << getTempName(node.getChildren()[0], temps) << ";\n";
out << "real y = " << getTempName(node.getChildren()[1], temps) << ";\n";
out << "real z = " << getTempName(node.getChildren()[2], temps) << ";\n";
out << "if (x >= " << paramsFloat[3] << " && x <= " << paramsFloat[4] << " && y >= " << paramsFloat[5] << " && y <= " << paramsFloat[6] << " && z >= " << paramsFloat[7] << " && z <= " << paramsFloat[8] << ") {\n";
out << "x = (x - " << paramsFloat[3] << ")*" << paramsFloat[9] << ";\n";
out << "y = (y - " << paramsFloat[5] << ")*" << paramsFloat[10] << ";\n";
out << "z = (z - " << paramsFloat[7] << ")*" << paramsFloat[11] << ";\n";
out << "int s = min((int) floor(x), " << paramsInt[0] << ");\n";
out << "int t = min((int) floor(y), " << paramsInt[1] << ");\n";
out << "int u = min((int) floor(z), " << paramsInt[2] << ");\n";
out << "int coeffIndex = 16*(s+" << paramsInt[0] << "*(t+" << paramsInt[1] << "*u));\n";
out << "float4 c[16];\n";
for (int j = 0; j < 16; j++)
out << "c[" << j << "] = " << functionNames[i].second << "[coeffIndex+" << j << "];\n";
out << "real da = x-s;\n";
out << "real db = y-t;\n";
out << "real dc = z-u;\n";
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0 && derivOrder[1] == 0 && derivOrder[2] == 0) {
out << "real value[4] = {0, 0, 0, 0};\n";
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = k + 4*m;
out << "value[" << m << "] = db*value[" << m << "] + ((c[" << base << "].w*da + c[" << base << "].z)*da + c[" << base << "].y)*da + c[" << base << "].x;\n";
}
out << nodeNames[j] << " = value[0] + dc*(value[1] + dc*(value[2] + dc*value[3]));\n";
}
else if (derivOrder[0] == 1 && derivOrder[1] == 0 && derivOrder[2] == 0) {
out << "real derivx[4] = {0, 0, 0, 0};\n";
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = k + 4*m;
out << "derivx[" << m << "] = db*derivx[" << m << "] + (3*c[" << base << "].w*da + 2*c[" << base << "].z)*da + c[" << base << "].y;\n";
}
out << nodeNames[j] << " = derivx[0] + dc*(derivx[1] + dc*(derivx[2] + dc*derivx[3]));\n";
out << nodeNames[j] << " *= " << paramsFloat[9] << ";\n";
}
else if (derivOrder[0] == 0 && derivOrder[1] == 1 && derivOrder[2] == 0) {
const string suffixes[] = {".x", ".y", ".z", ".w"};
out << "real derivy[4] = {0, 0, 0, 0};\n";
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = 4*m;
string suffix = suffixes[m];
out << "derivy[" << m << "] = da*derivy[" << m << "] + (3*c[" << (base+3) << "]" << suffix << "*db + 2*c[" << (base+2) << "]" << suffix << ")*db + c[" << (base+1) << "]" << suffix << ";\n";
}
out << nodeNames[j] << " = derivy[0] + dc*(derivy[1] + dc*(derivy[2] + dc*derivy[3]));\n";
out << nodeNames[j] << " *= " << paramsFloat[10] << ";\n";
}
else if (derivOrder[0] == 0 && derivOrder[1] == 0 && derivOrder[2] == 1) {
out << "real derivz[4] = {0, 0, 0, 0};\n";
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = k + 4*m;
out << "derivz[" << m << "] = db*derivz[" << m << "] + ((c[" << base << "].w*da + c[" << base << "].z)*da + c[" << base << "].y)*da + c[" << base << "].x;\n";
}
out << nodeNames[j] << " = derivz[1] + dc*(2*derivz[2] + dc*3*derivz[3]);\n";
out << nodeNames[j] << " *= " << paramsFloat[11] << ";\n";
}
else
throw OpenMMException("Unsupported derivative order for Continuous2DFunction");
}
else
throw OpenMMException("Unsupported derivative order for Continuous2DFunction");
out << "}\n";
}
out << "}\n";
}
else if (dynamic_cast<const Discrete1DFunction*>(functions[i]) != NULL) {
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0) {
out << "real x = " << getTempName(node.getChildren()[0], temps) << ";\n";
out << "if (x >= 0 && x < " << paramsInt[0] << ") {\n";
out << "int index = (int) floor(x+0.5f);\n";
out << nodeNames[j] << " = " << functionNames[i].second << "[index];\n";
out << "}\n";
else if (dynamic_cast<const Discrete1DFunction*>(functions[i]) != NULL) {
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0) {
out << "real x = " << getTempName(node.getChildren()[0], temps) << ";\n";
out << "if (x >= 0 && x < " << paramsInt[0] << ") {\n";
out << "int index = (int) floor(x+0.5f);\n";
out << nodeNames[j] << " = " << functionNames[i].second << "[index];\n";
out << "}\n";
}
}
}
}
else if (dynamic_cast<const Discrete2DFunction*>(functions[i]) != NULL) {
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0 && derivOrder[1] == 0) {
out << "int x = (int) floor(" << getTempName(node.getChildren()[0], temps) << "+0.5f);\n";
out << "int y = (int) floor(" << getTempName(node.getChildren()[1], temps) << "+0.5f);\n";
out << "int xsize = " << paramsInt[0] << ";\n";
out << "int ysize = " << paramsInt[1] << ";\n";
out << "int index = x+y*xsize;\n";
out << "if (index >= 0 && index < xsize*ysize)\n";
out << nodeNames[j] << " = " << functionNames[i].second << "[index];\n";
else if (dynamic_cast<const Discrete2DFunction*>(functions[i]) != NULL) {
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0 && derivOrder[1] == 0) {
out << "int x = (int) floor(" << getTempName(node.getChildren()[0], temps) << "+0.5f);\n";
out << "int y = (int) floor(" << getTempName(node.getChildren()[1], temps) << "+0.5f);\n";
out << "int xsize = " << paramsInt[0] << ";\n";
out << "int ysize = " << paramsInt[1] << ";\n";
out << "int index = x+y*xsize;\n";
out << "if (index >= 0 && index < xsize*ysize)\n";
out << nodeNames[j] << " = " << functionNames[i].second << "[index];\n";
}
}
}
}
else if (dynamic_cast<const Discrete3DFunction*>(functions[i]) != NULL) {
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0 && derivOrder[1] == 0 && derivOrder[2] == 0) {
out << "int x = (int) floor(" << getTempName(node.getChildren()[0], temps) << "+0.5f);\n";
out << "int y = (int) floor(" << getTempName(node.getChildren()[1], temps) << "+0.5f);\n";
out << "int z = (int) floor(" << getTempName(node.getChildren()[2], temps) << "+0.5f);\n";
out << "int xsize = " << paramsInt[0] << ";\n";
out << "int ysize = " << paramsInt[1] << ";\n";
out << "int zsize = " << paramsInt[2] << ";\n";
out << "int index = x+(y+z*ysize)*xsize;\n";
out << "if (index >= 0 && index < xsize*ysize*zsize)\n";
out << nodeNames[j] << " = " << functionNames[i].second << "[index];\n";
else if (dynamic_cast<const Discrete3DFunction*>(functions[i]) != NULL) {
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
if (derivOrder[0] == 0 && derivOrder[1] == 0 && derivOrder[2] == 0) {
out << "int x = (int) floor(" << getTempName(node.getChildren()[0], temps) << "+0.5f);\n";
out << "int y = (int) floor(" << getTempName(node.getChildren()[1], temps) << "+0.5f);\n";
out << "int z = (int) floor(" << getTempName(node.getChildren()[2], temps) << "+0.5f);\n";
out << "int xsize = " << paramsInt[0] << ";\n";
out << "int ysize = " << paramsInt[1] << ";\n";
out << "int zsize = " << paramsInt[2] << ";\n";
out << "int index = x+(y+z*ysize)*xsize;\n";
out << "if (index >= 0 && index < xsize*ysize*zsize)\n";
out << nodeNames[j] << " = " << functionNames[i].second << "[index];\n";
}
}
}
}
......@@ -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 @ cecc774a
......@@ -128,7 +128,7 @@ void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, boo
double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
cl.getBondedUtilities().computeInteractions(groups);
cl.getNonbondedUtilities().computeInteractions(groups);
cl.getNonbondedUtilities().computeInteractions(groups, includeForces, includeEnergy);
double sum = 0.0;
for (vector<OpenCLContext::ForcePostComputation*>::iterator iter = cl.getPostComputations().begin(); iter != cl.getPostComputations().end(); ++iter)
sum += (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
......@@ -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/src/OpenCLNonbondedUtilities.cpp
View file @ cecc774a
......@@ -373,14 +373,17 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
lastCutoff = kernels.cutoffDistance;
}
void OpenCLNonbondedUtilities::computeInteractions(int forceGroups) {
void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) {
if ((forceGroups&groupFlags) == 0)
return;
KernelSet& kernels = groupKernels[forceGroups];
if (kernels.hasForces) {
cl::Kernel& kernel = (includeForces ? (includeEnergy ? kernels.forceEnergyKernel : kernels.forceKernel) : kernels.energyKernel);
if (*reinterpret_cast<cl_kernel*>(&kernel) == NULL)
kernel = createInteractionKernel(kernels.source, parameters, arguments, true, true, forceGroups, includeForces, includeEnergy);
if (useCutoff)
setPeriodicBoxArgs(context, kernels.forceKernel, 9);
context.executeKernel(kernels.forceKernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
setPeriodicBoxArgs(context, kernel, 9);
context.executeKernel(kernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
}
}
......@@ -406,12 +409,25 @@ bool OpenCLNonbondedUtilities::updateNeighborListSize() {
interactingTiles = OpenCLArray::create<cl_int>(context, maxTiles, "interactingTiles");
interactingAtoms = OpenCLArray::create<cl_int>(context, OpenCLContext::TileSize*maxTiles, "interactingAtoms");
for (map<int, KernelSet>::iterator iter = groupKernels.begin(); iter != groupKernels.end(); ++iter) {
iter->second.forceKernel.setArg<cl::Buffer>(7, interactingTiles->getDeviceBuffer());
iter->second.forceKernel.setArg<cl_uint>(14, maxTiles);
iter->second.forceKernel.setArg<cl::Buffer>(17, interactingAtoms->getDeviceBuffer());
iter->second.findInteractingBlocksKernel.setArg<cl::Buffer>(6, interactingTiles->getDeviceBuffer());
iter->second.findInteractingBlocksKernel.setArg<cl::Buffer>(7, interactingAtoms->getDeviceBuffer());
iter->second.findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
KernelSet& kernels = iter->second;
if (*reinterpret_cast<cl_kernel*>(&kernels.forceKernel) != NULL) {
kernels.forceKernel.setArg<cl::Buffer>(7, interactingTiles->getDeviceBuffer());
kernels.forceKernel.setArg<cl_uint>(14, maxTiles);
kernels.forceKernel.setArg<cl::Buffer>(17, interactingAtoms->getDeviceBuffer());
}
if (*reinterpret_cast<cl_kernel*>(&kernels.energyKernel) != NULL) {
kernels.energyKernel.setArg<cl::Buffer>(7, interactingTiles->getDeviceBuffer());
kernels.energyKernel.setArg<cl_uint>(14, maxTiles);
kernels.energyKernel.setArg<cl::Buffer>(17, interactingAtoms->getDeviceBuffer());
}
if (*reinterpret_cast<cl_kernel*>(&kernels.forceEnergyKernel) != NULL) {
kernels.forceEnergyKernel.setArg<cl::Buffer>(7, interactingTiles->getDeviceBuffer());
kernels.forceEnergyKernel.setArg<cl_uint>(14, maxTiles);
kernels.forceEnergyKernel.setArg<cl::Buffer>(17, interactingAtoms->getDeviceBuffer());
}
kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(6, interactingTiles->getDeviceBuffer());
kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(7, interactingAtoms->getDeviceBuffer());
kernels.findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
}
forceRebuildNeighborList = true;
return true;
......@@ -432,10 +448,21 @@ void OpenCLNonbondedUtilities::setAtomBlockRange(double startFraction, double en
// We are using a cutoff, and the kernels have already been created.
for (map<int, KernelSet>::iterator iter = groupKernels.begin(); iter != groupKernels.end(); ++iter) {
iter->second.forceKernel.setArg<cl_uint>(5, startTileIndex);
iter->second.forceKernel.setArg<cl_uint>(6, numTiles);
iter->second.findInteractingBlocksKernel.setArg<cl_uint>(10, startBlockIndex);
iter->second.findInteractingBlocksKernel.setArg<cl_uint>(11, numBlocks);
KernelSet& kernels = iter->second;
if (*reinterpret_cast<cl_kernel*>(&kernels.forceKernel) != NULL) {
kernels.forceKernel.setArg<cl_uint>(5, startTileIndex);
kernels.forceKernel.setArg<cl_uint>(6, numTiles);
}
if (*reinterpret_cast<cl_kernel*>(&kernels.energyKernel) != NULL) {
kernels.energyKernel.setArg<cl_uint>(5, startTileIndex);
kernels.energyKernel.setArg<cl_uint>(6, numTiles);
}
if (*reinterpret_cast<cl_kernel*>(&kernels.forceEnergyKernel) != NULL) {
kernels.forceEnergyKernel.setArg<cl_uint>(5, startTileIndex);
kernels.forceEnergyKernel.setArg<cl_uint>(6, numTiles);
}
kernels.findInteractingBlocksKernel.setArg<cl_uint>(10, startBlockIndex);
kernels.findInteractingBlocksKernel.setArg<cl_uint>(11, numBlocks);
}
forceRebuildNeighborList = true;
}
......@@ -453,8 +480,7 @@ void OpenCLNonbondedUtilities::createKernelsForGroups(int groups) {
}
kernels.hasForces = (source.size() > 0);
kernels.cutoffDistance = cutoff;
if (kernels.hasForces)
kernels.forceKernel = createInteractionKernel(source, parameters, arguments, true, true, groups);
kernels.source = source;
if (useCutoff) {
double padding = (usePadding ? 0.1*cutoff : 0.0);
double paddedCutoff = cutoff+padding;
......@@ -524,7 +550,7 @@ void OpenCLNonbondedUtilities::createKernelsForGroups(int groups) {
groupKernels[groups] = kernels;
}
cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& source, const vector<ParameterInfo>& params, const vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups) {
cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& source, const vector<ParameterInfo>& params, const vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups, bool includeForces, bool includeEnergy) {
map<string, string> replacements;
replacements["COMPUTE_INTERACTION"] = source;
const string suffixes[] = {"x", "y", "z", "w"};
......@@ -623,6 +649,10 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc
defines["USE_SYMMETRIC"] = "1";
if (useCutoff && context.getSIMDWidth() < 32)
defines["PRUNE_BY_CUTOFF"] = "1";
if (includeForces)
defines["INCLUDE_FORCES"] = "1";
if (includeEnergy)
defines["INCLUDE_ENERGY"] = "1";
defines["FORCE_WORK_GROUP_SIZE"] = context.intToString(forceThreadBlockSize);
double maxCutoff = 0.0;
for (int i = 0; i < 32; i++) {
......
platforms/opencl/src/kernels/nonbonded.cl
View file @ cecc774a
......@@ -34,7 +34,7 @@ __kernel void computeNonbonded(
const unsigned int warp = get_global_id(0)/TILE_SIZE;
const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1);
const unsigned int tbx = get_local_id(0) - tgx;
real energy = 0;
mixed energy = 0;
__local AtomData localData[FORCE_WORK_GROUP_SIZE];
// First loop: process tiles that contain exclusions.
......@@ -87,11 +87,13 @@ __kernel void computeNonbonded(
real tempEnergy = 0;
COMPUTE_INTERACTION
energy += 0.5f*tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
force.xyz -= delta.xyz*dEdR;
#else
force.xyz -= dEdR1.xyz;
#endif
#endif
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
......@@ -144,6 +146,7 @@ __kernel void computeNonbonded(
real tempEnergy = 0;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
......@@ -156,6 +159,7 @@ __kernel void computeNonbonded(
localData[tbx+tj].fy += dEdR2.y;
localData[tbx+tj].fz += dEdR2.z;
#endif
#endif
#ifdef PRUNE_BY_CUTOFF
}
#endif
......@@ -169,6 +173,7 @@ __kernel void computeNonbonded(
// Write results.
#ifdef INCLUDE_FORCES
#ifdef SUPPORTS_64_BIT_ATOMICS
unsigned int offset = x*TILE_SIZE + tgx;
atom_add(&forceBuffers[offset], (long) (force.x*0x100000000));
......@@ -186,6 +191,7 @@ __kernel void computeNonbonded(
forceBuffers[offset1].xyz += force.xyz;
if (x != y)
forceBuffers[offset2] += (real4) (localData[get_local_id(0)].fx, localData[get_local_id(0)].fy, localData[get_local_id(0)].fz, 0.0f);
#endif
#endif
}
......@@ -318,6 +324,7 @@ __kernel void computeNonbonded(
real tempEnergy = 0;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
......@@ -330,6 +337,7 @@ __kernel void computeNonbonded(
localData[tbx+tj].fy += dEdR2.y;
localData[tbx+tj].fz += dEdR2.z;
#endif
#endif
#ifdef PRUNE_BY_CUTOFF
}
#endif
......@@ -370,6 +378,7 @@ __kernel void computeNonbonded(
real tempEnergy = 0;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
......@@ -382,6 +391,7 @@ __kernel void computeNonbonded(
localData[tbx+tj].fy += dEdR2.y;
localData[tbx+tj].fz += dEdR2.z;
#endif
#endif
#ifdef PRUNE_BY_CUTOFF
}
#endif
......@@ -392,6 +402,7 @@ __kernel void computeNonbonded(
// Write results.
#ifdef INCLUDE_FORCES
#ifdef USE_CUTOFF
unsigned int atom2 = atomIndices[get_local_id(0)];
#else
......@@ -412,9 +423,12 @@ __kernel void computeNonbonded(
forceBuffers[offset1].xyz += force.xyz;
if (atom2 < PADDED_NUM_ATOMS)
forceBuffers[offset2] += (real4) (localData[get_local_id(0)].fx, localData[get_local_id(0)].fy, localData[get_local_id(0)].fz, 0.0f);
#endif
#endif
}
pos++;
}
energyBuffer[get_global_id(0)] += energy;
#ifdef INCLUDE_ENERGY
energyBuffer[get_global_id(0)] += (real) energy;
#endif
}
platforms/opencl/tests/OpenCLTests.h 0 → 100644
View file @ cecc774a
/* -------------------------------------------------------------------------- *
* 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) 2015 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. *
* -------------------------------------------------------------------------- */
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "OpenCLPlatform.h"
#include <string>
OpenMM::OpenCLPlatform platform;
void initializeTests(int argc, char* argv[]) {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", std::string(argv[1]));
}
platforms/opencl/tests/TestOpenCLAndersenThermostat.cpp
View file @ cecc774a
......@@ -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) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,192 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of AndersenThermostat.
*/
#include "OpenCLTests.h"
#include "TestAndersenThermostat.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
void testTemperature() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
const int numSteps = 5000;
System system;
VerletIntegrator integrator(0.003);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermstat);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
context.setPositions(positions);
context.setVelocitiesToTemperature(temp);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < numSteps; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(10);
}
ke /= numSteps;
double expected = 0.5*numParticles*3*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
}
void testConstraints() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
const int numSteps = 15000;
System system;
VerletIntegrator integrator(0.004);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
system.addConstraint(0, 1, 1);
system.addConstraint(1, 2, 1);
system.addConstraint(2, 3, 1);
system.addConstraint(3, 0, 1);
system.addConstraint(4, 5, 1);
system.addConstraint(5, 6, 1);
system.addConstraint(6, 7, 1);
system.addConstraint(7, 4, 1);
AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermstat);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
positions[2] = Vec3(1, 1, 0);
positions[3] = Vec3(0, 1, 0);
positions[4] = Vec3(1, 0, 1);
positions[5] = Vec3(1, 1, 1);
positions[6] = Vec3(0, 1, 1);
positions[7] = Vec3(0, 0, 1);
context.setPositions(positions);
context.setVelocitiesToTemperature(temp);
// Let it equilibrate.
integrator.step(5000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < numSteps; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(1);
}
ke /= numSteps;
double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermostat);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(0, 0, 0);
}
// Try twice with the same random seed.
thermostat->setRandomNumberSeed(5);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state1 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state2 = context.getState(State::Positions);
// Try twice with a different random seed.
thermostat->setRandomNumberSeed(10);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state3 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state4 = context.getState(State::Positions);
// Compare the results.
for (int i = 0; i < numParticles; i++) {
for (int j = 0; j < 3; j++) {
ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
}
}
void runPlatformTests() {
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testTemperature();
testConstraints();
testRandomSeed();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/opencl/tests/TestOpenCLBrownianIntegrator.cpp
View file @ cecc774a
......@@ -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) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,253 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/System.h"
#include "OpenCLTests.h"
#include "TestBrownianIntegrator.h"
/**
* This tests the OpenCL implementation of BrownianIntegrator.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/BrownianIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
void testSingleBond() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
double dt = 0.01;
BrownianIntegrator integrator(0, 0.1, dt);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply an overdamped harmonic oscillator, so compare it to the analytical solution.
double rate = 2*1.0/(0.1*2.0);
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::exp(-rate*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
if (i > 0) {
double expectedSpeed = -0.5*rate*std::exp(-rate*(time-0.5*dt));
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.11);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.11);
}
integrator.step(1);
}
}
void testTemperature() {
const int numParticles = 8;
const int numBonds = numParticles-1;
const double temp = 10.0;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.01);
HarmonicBondForce* forceField = new HarmonicBondForce();
for (int i = 0; i < numParticles; ++i)
system.addParticle(2.0);
for (int i = 0; i < numBonds; ++i)
forceField->addBond(i, i+1, 1.0, 5.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(i, 0, 0);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double pe = 0.0;
const int steps = 50000;
for (int i = 0; i < steps; ++i) {
State state = context.getState(State::Energy);
pe += state.getPotentialEnergy();
integrator.step(1);
}
pe /= steps;
double expected = 0.5*numBonds*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, pe, 0.1*expected);
}
void testConstraints() {
const int numParticles = 8;
const int numConstraints = 5;
const double temp = 20.0;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.001);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
system.addConstraint(0, 1, 1.0);
system.addConstraint(1, 2, 1.0);
system.addConstraint(2, 3, 1.0);
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i, 0, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions);
for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4);
}
integrator.step(1);
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
BrownianIntegrator integrator(300.0, 2.0, 0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.001);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(0, 0, 0);
}
// Try twice with the same random seed.
integrator.setRandomNumberSeed(5);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state1 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state2 = context.getState(State::Positions);
// Try twice with a different random seed.
integrator.setRandomNumberSeed(10);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state3 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state4 = context.getState(State::Positions);
// Compare the results.
for (int i = 0; i < numParticles; i++) {
for (int j = 0; j < 3; j++) {
ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
}
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testSingleBond();
testTemperature();
testConstraints();
testConstrainedMasslessParticles();
testRandomSeed();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/opencl/tests/TestOpenCLCMAPTorsionForce.cpp
View file @ cecc774a
......@@ -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) 2010-2015 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,150 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of CMAPTorsionForce.
*/
#include "OpenCLTests.h"
#include "TestCMAPTorsionForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CMAPTorsionForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
void testCMAPTorsions() {
const int mapSize = 36;
// Create two systems: one with a pair of periodic torsions, and one with a CMAP torsion
// that approximates the same force.
System system1;
for (int i = 0; i < 5; i++)
system1.addParticle(1.0);
PeriodicTorsionForce* periodic = new PeriodicTorsionForce();
periodic->addTorsion(0, 1, 2, 3, 2, M_PI/4, 1.5);
periodic->addTorsion(1, 2, 3, 4, 3, M_PI/3, 2.0);
system1.addForce(periodic);
System system2;
for (int i = 0; i < 5; i++)
system2.addParticle(1.0);
CMAPTorsionForce* cmap = new CMAPTorsionForce();
vector<double> mapEnergy(mapSize*mapSize);
for (int i = 0; i < mapSize; i++) {
double angle1 = i*2*M_PI/mapSize;
double energy1 = 1.5*(1+cos(2*angle1-M_PI/4));
for (int j = 0; j < mapSize; j++) {
double angle2 = j*2*M_PI/mapSize;
double energy2 = 2.0*(1+cos(3*angle2-M_PI/3));
mapEnergy[i+j*mapSize] = energy1+energy2;
}
}
cmap->addMap(mapSize, mapEnergy);
cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
system2.addForce(cmap);
// Set the atoms in various positions, and verify that both systems give equal forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(system1, integrator1, platform);
Context c2(system2, integrator2, platform);
for (int i = 0; i < 50; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < system1.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 0.05);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-3);
}
}
void testChangingParameters() {
// Create a system with two maps and one torsion.
const int mapSize = 8;
System system;
for (int i = 0; i < 5; i++)
system.addParticle(1.0);
CMAPTorsionForce* cmap = new CMAPTorsionForce();
vector<double> mapEnergy1(mapSize*mapSize);
vector<double> mapEnergy2(mapSize*mapSize);
for (int i = 0; i < mapSize; i++) {
double angle1 = i*2*M_PI/mapSize;
double energy1 = cos(angle1);
for (int j = 0; j < mapSize; j++) {
double angle2 = j*2*M_PI/mapSize;
double energy2 = 10*sin(angle2);
mapEnergy1[i+j*mapSize] = energy1+energy2;
mapEnergy2[i+j*mapSize] = energy1-energy2;
}
}
cmap->addMap(mapSize, mapEnergy1);
cmap->addMap(mapSize, mapEnergy2);
cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
system.addForce(cmap);
// Set particle positions so angle1=0 and angle2=PI/4.
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 1);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 1);
positions[4] = Vec3(0.5, -0.5, 1);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Check that the energy is correct.
double energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(1+10*sin(M_PI/4), energy, 1e-5);
// Modify the parameters.
cmap->setTorsionParameters(0, 1, 0, 1, 2, 3, 1, 2, 3, 4);
for (int i = 0; i < mapSize*mapSize; i++)
mapEnergy2[i] *= 2.0;
cmap->setMapParameters(1, mapSize, mapEnergy2);
cmap->updateParametersInContext(context);
// See if the results are correct.
energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5);
void runPlatformTests() {
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testCMAPTorsions();
testChangingParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/opencl/tests/TestOpenCLCMMotionRemover.cpp
View file @ cecc774a
......@@ -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) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,95 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of AndersenThermostat.
*/
#include "OpenCLTests.h"
#include "TestCMMotionRemover.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
Vec3 calcCM(const vector<Vec3>& values, System& system) {
Vec3 cm;
for (int j = 0; j < system.getNumParticles(); ++j) {
cm[0] += values[j][0]*system.getParticleMass(j);
cm[1] += values[j][1]*system.getParticleMass(j);
cm[2] += values[j][2]*system.getParticleMass(j);
}
return cm;
void runPlatformTests() {
}
void testMotionRemoval(Integrator& integrator) {
const int numParticles = 8;
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(2, 3, 2.0, 0.5);
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i+1);
nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(nonbonded);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Now run it for a while and see if the center of mass remains fixed.
Vec3 cmPos = calcCM(context.getState(State::Positions).getPositions(), system);
for (int i = 0; i < 1000; ++i) {
integrator.step(1);
State state = context.getState(State::Positions | State::Velocities);
Vec3 pos = calcCM(state.getPositions(), system);
ASSERT_EQUAL_VEC(cmPos, pos, 1e-2);
Vec3 vel = calcCM(state.getVelocities(), system);
if (i > 0) {
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), vel, 1e-2);
}
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
LangevinIntegrator langevin(0.0, 1e-5, 0.01);
testMotionRemoval(langevin);
VerletIntegrator verlet(0.01);
testMotionRemoval(verlet);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/opencl/tests/TestOpenCLCheckpoints.cpp
View file @ cecc774a
......@@ -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) 2012-2013 Stanford University and the Authors. *
* Portions copyright (c) 2012-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,45 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests creating and loading checkpoints with the OpenCL platform.
*/
#include "OpenCLPlatform.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/Context.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <sstream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
void compareStates(State& s1, State& s2) {
ASSERT_EQUAL_TOL(s1.getTime(), s2.getTime(), TOL);
int numParticles = s1.getPositions().size();
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(s1.getPositions()[i], s2.getPositions()[i], TOL);
ASSERT_EQUAL_VEC(s1.getVelocities()[i], s2.getVelocities()[i], TOL);
Vec3 a1, b1, c1, a2, b2, c2;
s1.getPeriodicBoxVectors(a1, b1, c1);
s2.getPeriodicBoxVectors(a2, b2, c2);
ASSERT_EQUAL_VEC(a1, a2, TOL);
ASSERT_EQUAL_VEC(b1, b2, TOL);
ASSERT_EQUAL_VEC(c1, c2, TOL);
for (map<string, double>::const_iterator iter = s1.getParameters().begin(); iter != s1.getParameters().end(); ++iter)
ASSERT_EQUAL(iter->second, (*s2.getParameters().find(iter->first)).second);
}
}
#include "OpenCLTests.h"
#include "TestCheckpoints.h"
void testCheckpoint() {
const int numParticles = 100;
......@@ -159,71 +122,6 @@ void testCheckpoint() {
compareStates(s6, s8);
}
void testSetState() {
const int numParticles = 10;
const double boxSize = 3.0;
const double temperature = 200.0;
System system;
system.addForce(new AndersenThermostat(0.0, 100.0));
NonbondedForce* nonbonded = new NonbondedForce();
system.addForce(nonbonded);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
}
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
context.setParameter(AndersenThermostat::Temperature(), temperature);
// Run for a little while.
integrator.step(100);
// Record the current state.
State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
// Continue the simulation for a few more steps and record a partial state.
integrator.step(10);
State s2 = context.getState(State::Positions);
// Restore the original state and see if everything gets restored correctly.
context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
context.setParameter(AndersenThermostat::Temperature(), temperature+10);
context.setState(s1);
State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
compareStates(s1, s3);
// Set the partial state and see if the correct things were set.
context.setState(s2);
State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(s2.getPositions()[i], s4.getPositions()[i], TOL);
ASSERT_EQUAL_VEC(s1.getVelocities()[i], s4.getVelocities()[i], TOL);
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testCheckpoint();
testSetState();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testCheckpoint();
}
platforms/opencl/tests/TestOpenCLCustomAngleForce.cpp
View file @ cecc774a
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,109 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of CustomAngleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomAngleForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
static OpenCLPlatform platform;
void testAngles() {
// Create a system using a CustomAngleForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomAngleForce* custom = new CustomAngleForce("scale*k*(theta-theta0)^2");
custom->addPerAngleParameter("theta0");
custom->addPerAngleParameter("k");
custom->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 1.5;
parameters[1] = 0.8;
custom->addAngle(0, 1, 2, parameters);
parameters[0] = 2.0;
parameters[1] = 0.5;
custom->addAngle(1, 2, 3, parameters);
customSystem.addForce(custom);
// Create an identical system using a HarmonicAngleForce.
System harmonicSystem;
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
HarmonicAngleForce* harmonic = new HarmonicAngleForce();
harmonic->addAngle(0, 1, 2, 1.5, 0.8);
harmonic->addAngle(1, 2, 3, 2.0, 0.5);
harmonicSystem.addForce(harmonic);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(4);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(harmonicSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = s1.getForces();
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the angle parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[1] = 0.9;
custom->setAngleParameters(0, 0, 1, 2, parameters);
parameters[0] = 2.1;
parameters[1] = 0.6;
custom->setAngleParameters(1, 1, 2, 3, parameters);
custom->updateParametersInContext(c1);
harmonic->setAngleParameters(0, 0, 1, 2, 1.6, 0.9);
harmonic->setAngleParameters(1, 1, 2, 3, 2.1, 0.6);
harmonic->updateParametersInContext(c2);
{
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = s1.getForces();
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
#include "OpenCLTests.h"
#include "TestCustomAngleForce.h"
void testParallelComputation() {
System system;
......@@ -162,20 +61,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testAngles();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/opencl/tests/TestOpenCLCustomBondForce.cpp
View file @ cecc774a
......@@ -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: *
* *
......@@ -29,111 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of CustomBondForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomBondForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
void testBonds() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("scale*k*(r-r0)^2");
forceField->addPerBondParameter("r0");
forceField->addPerBondParameter("k");
forceField->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 1.5;
parameters[1] = 0.8;
forceField->addBond(0, 1, parameters);
parameters[0] = 1.2;
parameters[1] = 0.7;
forceField->addBond(1, 2, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[1] = 0.9;
forceField->setBondParameters(0, 0, 1, parameters);
parameters[0] = 1.3;
parameters[1] = 0.8;
forceField->setBondParameters(1, 1, 2, parameters);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
}
}
void testManyParameters() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("(a+b+c+d+e+f+g+h+i)*r");
forceField->addPerBondParameter("a");
forceField->addPerBondParameter("b");
forceField->addPerBondParameter("c");
forceField->addPerBondParameter("d");
forceField->addPerBondParameter("e");
forceField->addPerBondParameter("f");
forceField->addPerBondParameter("g");
forceField->addPerBondParameter("h");
forceField->addPerBondParameter("i");
vector<double> parameters(forceField->getNumPerBondParameters());
for (int i = 0; i < (int) parameters.size(); i++)
parameters[i] = i;
forceField->addBond(0, 1, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2.5, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double f = 1+2+3+4+5+6+7+8;
ASSERT_EQUAL_VEC(Vec3(0, f, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(f*2.5, state.getPotentialEnergy(), TOL);
}
#include "OpenCLTests.h"
#include "TestCustomBondForce.h"
void testParallelComputation() {
System system;
......@@ -164,19 +61,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testBonds();
testManyParameters();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/opencl/tests/TestOpenCLCustomCentroidBondForce.cpp
View file @ cecc774a
......@@ -29,247 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the reference implementation of CustomCompoundBondForce.
*/
#include "OpenCLTests.h"
#include "TestCustomCentroidBondForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomCentroidBondForce.h"
#include "openmm/CustomCompoundBondForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
OpenCLPlatform platform;
const double TOL = 1e-5;
void testHarmonicBond() {
System system;
system.addParticle(1.0);
system.addParticle(2.0);
system.addParticle(3.0);
system.addParticle(4.0);
system.addParticle(5.0);
CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "k*distance(g1,g2)^2");
force->addPerBondParameter("k");
vector<int> particles1;
particles1.push_back(0);
particles1.push_back(1);
vector<int> particles2;
particles2.push_back(2);
particles2.push_back(3);
particles2.push_back(4);
force->addGroup(particles1);
force->addGroup(particles2);
vector<int> groups;
groups.push_back(0);
groups.push_back(1);
vector<double> parameters;
parameters.push_back(1.0);
force->addBond(groups, parameters);
system.addForce(force);
ASSERT(!system.usesPeriodicBoundaryConditions());
// The center of mass of group 0 is (1.5, 0, 0).
vector<Vec3> positions(5);
positions[0] = Vec3(2.5, 0, 0);
positions[1] = Vec3(1, 0, 0);
// The center of mass of group 1 is (-1, 0, 0).
positions[2] = Vec3(-6, 0, 0);
positions[3] = Vec3(-1, 0, 0);
positions[4] = Vec3(2, 0, 0);
// Check the forces and energy.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(2.5*2.5, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(-2*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-2*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
// Update the per-bond parameter and see if the results change.
parameters[0] = 2.0;
force->setBondParameters(0, groups, parameters);
force->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(2*2.5*2.5, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(-4*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-4*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
// All the particles should be treated as a single molecule.
vector<std::vector<int> > molecules = context.getMolecules();
ASSERT_EQUAL(1, molecules.size());
ASSERT_EQUAL(5, molecules[0].size());
}
void testComplexFunction() {
int numParticles = 5;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(2.0);
vector<double> table(20);
for (int i = 0; i < 20; i++)
table[i] = sin(0.11*i);
// When every group contains only one particle, a CustomCentroidBondForce is identical to a
// CustomCompoundBondForce. Use that to test a complicated energy function with lots of terms.
CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
compound->addGlobalParameter("scale", 0.5);
centroid->addGlobalParameter("scale", 0.5);
compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
// Add two bonds to the CustomCompoundBondForce.
vector<int> particles(4);
vector<double> parameters;
particles[0] = 0;
particles[1] = 1;
particles[2] = 2;
particles[3] = 3;
compound->addBond(particles, parameters);
particles[0] = 2;
particles[1] = 4;
particles[2] = 3;
particles[3] = 1;
compound->addBond(particles, parameters);
// Add identical bonds to the CustomCentroidBondForce. As a stronger test, make sure that
// group number is different from particle number.
vector<int> groupMembers(1);
groupMembers[0] = 3;
centroid->addGroup(groupMembers);
groupMembers[0] = 0;
centroid->addGroup(groupMembers);
groupMembers[0] = 1;
centroid->addGroup(groupMembers);
groupMembers[0] = 2;
centroid->addGroup(groupMembers);
groupMembers[0] = 4;
centroid->addGroup(groupMembers);
vector<int> groups(4);
groups[0] = 1;
groups[1] = 2;
groups[2] = 3;
groups[3] = 0;
centroid->addBond(groups, parameters);
groups[0] = 3;
groups[1] = 4;
groups[2] = 0;
groups[3] = 2;
centroid->addBond(groups, parameters);
// Add both forces as different force groups, and create a context.
centroid->setForceGroup(1);
system.addForce(compound);
system.addForce(centroid);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
// Evaluate the force and energy for various positions and see if they match.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < numParticles; j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy, false, 1<<0);
State state2 = context.getState(State::Forces | State::Energy, false, 1<<1);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), TOL);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], TOL);
}
}
void testCustomWeights() {
System system;
system.addParticle(1.0);
system.addParticle(2.0);
system.addParticle(3.0);
system.addParticle(4.0);
CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "distance(g1,g2)^2");
vector<int> particles(2);
vector<double> weights(2);
particles[0] = 0;
particles[1] = 1;
weights[0] = 0.5;
weights[1] = 1.5;
force->addGroup(particles, weights);
particles[0] = 2;
particles[1] = 3;
weights[0] = 2.0;
weights[1] = 1.0;
force->addGroup(particles, weights);
vector<int> groups;
groups.push_back(0);
groups.push_back(1);
vector<double> parameters;
force->addBond(groups, parameters);
system.addForce(force);
// The center of mass of group 0 is (0, 1, 0).
vector<Vec3> positions(4);
positions[0] = Vec3(0, 4, 0);
positions[1] = Vec3(0, 0, 0);
// The center of mass of group 1 is (0, 10, 0).
positions[2] = Vec3(0, 9, 0);
positions[3] = Vec3(0, 12, 0);
// Check the forces and energy.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(9.0*9.0, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(0, 2*9*(0.5/2.0), 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 2*9*(1.5/2.0), 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -2*9*(2.0/3.0), 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -2*9*(1.0/3.0), 0), state.getForces()[3], TOL);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testHarmonicBond();
testComplexFunction();
testCustomWeights();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp
View file @ cecc774a
......@@ -29,145 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of CustomCompoundBondForce.
*/
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomCompoundBondForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
void testBond() {
// Create a system using a CustomCompoundBondForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, "0.5*kb*((distance(p1,p2)-b0)^2+(distance(p2,p3)-b0)^2)+0.5*ka*(angle(p2,p3,p4)-a0)^2+kt*(1+cos(dihedral(p1,p2,p3,p4)-t0))");
custom->addPerBondParameter("kb");
custom->addPerBondParameter("ka");
custom->addPerBondParameter("kt");
custom->addPerBondParameter("b0");
custom->addPerBondParameter("a0");
custom->addPerBondParameter("t0");
vector<int> particles(4);
particles[0] = 0;
particles[1] = 1;
particles[2] = 3;
particles[3] = 2;
vector<double> parameters(6);
parameters[0] = 1.5;
parameters[1] = 0.8;
parameters[2] = 0.6;
parameters[3] = 1.1;
parameters[4] = 2.9;
parameters[5] = 1.3;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
// Create an identical system using standard forces.
System standardSystem;
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.1, 1.5);
bonds->addBond(1, 3, 1.1, 1.5);
standardSystem.addForce(bonds);
HarmonicAngleForce* angles = new HarmonicAngleForce();
angles->addAngle(1, 3, 2, 2.9, 0.8);
standardSystem.addForce(angles);
PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
standardSystem.addForce(torsions);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
vector<Vec3> positions(4);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[3] = 1.3;
custom->setBondParameters(0, particles, parameters);
custom->updateParametersInContext(c1);
bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
bonds->updateParametersInContext(c2);
{
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = s1.getForces();
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
void testPositionDependence() {
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(2, "scale1*distance(p1,p2)+scale2*x1+2*y2");
custom->addGlobalParameter("scale1", 0.3);
custom->addGlobalParameter("scale2", 0.2);
vector<int> particles(2);
particles[0] = 1;
particles[1] = 0;
vector<double> parameters;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(2);
positions[0] = Vec3(1.5, 1, 0);
positions[1] = Vec3(0.5, 1, 0);
VerletIntegrator integrator(0.01);
Context context(customSystem, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(0.3*1.0+0.2*0.5+2*1, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.3-0.2, 0, 0), state.getForces()[1], 1e-5);
}
#include "OpenCLTests.h"
#include "TestCustomCompoundBondForce.h"
void testParallelComputation() {
System system;
......@@ -202,165 +65,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
void testContinuous2DFunction() {
const int xsize = 10;
const int ysize = 11;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1)+1");
vector<int> particles(1, 0);
forceField->addBond(particles, vector<double>());
vector<double> table(xsize*ysize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
}
}
forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
positions[0] = Vec3(x, y, 1.5);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
Vec3 force(0, 0, 0);
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
energy = sin(0.25*x)*cos(0.33*y)+1;
force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
}
ASSERT_EQUAL_VEC(force, forces[0], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
}
}
}
void testContinuous3DFunction() {
const int xsize = 10;
const int ysize = 11;
const int zsize = 12;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
const double zmin = 0.2;
const double zmax = 1.3;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1,z1)+1");
vector<int> particles(1, 0);
forceField->addBond(particles, vector<double>());
vector<double> table(xsize*ysize*zsize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
for (int k = 0; k < zsize; k++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
double z = zmin + k*(zmax-zmin)/zsize;
table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
}
}
}
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
positions[0] = Vec3(x, y, z);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
Vec3 force(0, 0, 0);
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1;
force[0] = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
force[1] = 0.3*sin(0.25*x)*sin(0.33*y)*(1.0+z);
force[2] = -sin(0.25*x)*cos(0.33*y);
}
ASSERT_EQUAL_VEC(force, forces[0], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
}
}
}
}
void testMultipleBonds() {
// Two compound bonds using Urey-Bradley example from API doc
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(3,
"0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");
custom->addPerBondParameter("kangle");
custom->addPerBondParameter("kbond");
custom->addPerBondParameter("theta0");
custom->addPerBondParameter("r0");
vector<double> parameters(4);
parameters[0] = 1.0;
parameters[1] = 1.0;
parameters[2] = 2 * M_PI / 3;
parameters[3] = sqrt(3.0) / 2;
vector<int> particles0(3);
particles0[0] = 0;
particles0[1] = 1;
particles0[2] = 2;
vector<int> particles1(3);
particles1[0] = 1;
particles1[1] = 2;
particles1[2] = 3;
custom->addBond(particles0, parameters);
custom->addBond(particles1, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 0.5, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(0.5, 0, 0);
positions[3] = Vec3(0.6, 0, 0.4);
VerletIntegrator integrator(0.01);
Context context(customSystem, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(0.199, state.getPotentialEnergy(), 1e-3);
vector<Vec3> forces(state.getForces());
ASSERT_EQUAL_VEC(Vec3(-1.160, 0.112, 0.0), forces[0], 1e-3);
ASSERT_EQUAL_VEC(Vec3(0.927, 1.047, -0.638), forces[1], 1e-3);
ASSERT_EQUAL_VEC(Vec3(-0.543, -1.160, 0.721), forces[2], 1e-3);
ASSERT_EQUAL_VEC(Vec3(0.776, 0.0, -0.084), forces[3], 1e-3);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testBond();
testPositionDependence();
testParallelComputation();
testContinuous2DFunction();
testContinuous3DFunction();
testMultipleBonds();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/opencl/tests/TestOpenCLCustomExternalForce.cpp
View file @ cecc774a
......@@ -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: *
* *
......@@ -29,106 +29,9 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of CustomExternalForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "OpenCLTests.h"
#include "TestCustomExternalForce.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
void testForce() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomExternalForce* forceField = new CustomExternalForce("scale*(x+yscale*(y-y0)^2)");
forceField->addPerParticleParameter("y0");
forceField->addPerParticleParameter("yscale");
forceField->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 0.5;
parameters[1] = 2.0;
forceField->addParticle(0, parameters);
parameters[0] = 1.5;
parameters[1] = 3.0;
forceField->addParticle(2, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 1);
positions[2] = Vec3(1, 0, 1);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters[0] = 1.4;
parameters[1] = 3.5;
forceField->setParticleParameters(1, 2, parameters);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.5*2.0*1.4, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.5*1.4*1.4), state.getPotentialEnergy(), TOL);
}
}
void testManyParameters() {
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomExternalForce* forceField = new CustomExternalForce("xscale*(x-x0)^2+yscale*(y-y0)^2+zscale*(z-z0)^2");
forceField->addPerParticleParameter("x0");
forceField->addPerParticleParameter("y0");
forceField->addPerParticleParameter("z0");
forceField->addPerParticleParameter("xscale");
forceField->addPerParticleParameter("yscale");
forceField->addPerParticleParameter("zscale");
vector<double> parameters(6);
parameters[0] = 1.0;
parameters[1] = 2.0;
parameters[2] = 3.0;
parameters[3] = 0.1;
parameters[4] = 0.2;
parameters[5] = 0.3;
forceField->addParticle(0, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, -1, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(2*0.1*1.0, 2*0.2*3.0, 2*0.3*3.0), forces[0], TOL);
ASSERT_EQUAL_TOL(0.1*1*1 + 0.2*3*3 + 0.3*3*3, state.getPotentialEnergy(), TOL);
}
void testParallelComputation() {
System system;
......@@ -161,21 +64,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testForce();
testManyParameters();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/opencl/tests/TestOpenCLCustomGBForce.cpp
View file @ cecc774a
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
......@@ -7,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -30,453 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of CustomGBForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "sfmt/SFMT.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomGBForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMethod customMethod) {
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
const double cutoff = 2.0;
// Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
GBSAOBCForce* obc = new GBSAOBCForce();
CustomGBForce* custom = new CustomGBForce();
obc->setCutoffDistance(cutoff);
custom->setCutoffDistance(cutoff);
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
string invCutoffString = "";
if (obcMethod != GBSAOBCForce::NoCutoff) {
stringstream s;
s<<(1.0/cutoff);
invCutoffString = s.str();
}
custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
obc->addParticle(1.0, 0.2, 0.5);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.5;
custom->addParticle(params);
obc->addParticle(-1.0, 0.1, 0.5);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
else {
obc->addParticle(1.0, 0.2, 0.8);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.8;
custom->addParticle(params);
obc->addParticle(-1.0, 0.1, 0.8);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
obc->setNonbondedMethod(obcMethod);
custom->setNonbondedMethod(customMethod);
standardSystem.addForce(obc);
customSystem.addForce(custom);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, platform);
context1.setPositions(positions);
context1.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
Context context2(customSystem, integrator2, platform);
context2.setPositions(positions);
context2.setVelocities(velocities);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
// Try changing the particle parameters and make sure it's still correct.
for (int i = 0; i < numMolecules/2; i++) {
obc->setParticleParameters(2*i, 1.1, 0.3, 0.6);
params[0] = 1.1;
params[1] = 0.3;
params[2] = 0.6;
custom->setParticleParameters(2*i, params);
obc->setParticleParameters(2*i+1, -1.1, 0.2, 0.4);
params[0] = -1.1;
params[1] = 0.2;
params[2] = 0.4;
custom->setParticleParameters(2*i+1, params);
}
obc->updateParametersInContext(context1);
custom->updateParametersInContext(context2);
state1 = context1.getState(State::Forces | State::Energy);
state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
}
void testMembrane() {
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
// Create a system with an implicit membrane.
System system;
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
}
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
CustomGBForce* custom = new CustomGBForce();
custom->setCutoffDistance(2.0);
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("thickness", 3);
custom->addGlobalParameter("solventDielectric", 78.3);
custom->addGlobalParameter("soluteDielectric", 1);
custom->addComputedValue("Imol", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("Imem", "(1/radius+2*log(2)/thickness)/(1+exp(7.2*(abs(z)+radius-0.5*thickness)))", CustomGBForce::SingleParticle);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=max(Imol,Imem)*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.5;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
else {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.8;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
system.addForce(custom);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-2;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
}
void testTabulatedFunction() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "0", CustomGBForce::ParticlePair);
force->addEnergyTerm("fn(r)+1", CustomGBForce::ParticlePair);
force->addParticle(vector<double>());
force->addParticle(vector<double>());
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(std::sin(0.25*i));
force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 1; i < 30; i++) {
double x = (7.0/30.0)*i;
positions[1] = Vec3(x, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double force = (x < 1.0 || x > 6.0 ? 0.0 : -std::cos(x-1.0));
double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
}
for (int i = 1; i < 20; i++) {
double x = 0.25*i+1.0;
positions[1] = Vec3(x, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
}
}
void testMultipleChainRules() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "2*r", CustomGBForce::ParticlePair);
force->addComputedValue("b", "a+1", CustomGBForce::SingleParticle);
force->addComputedValue("c", "2*b+a", CustomGBForce::SingleParticle);
force->addEnergyTerm("0.1*a+1*b+10*c", CustomGBForce::SingleParticle); // 0.1*(2*r) + 2*r+1 + 10*(3*a+2) = 0.2*r + 2*r+1 + 40*r+20+20*r = 62.2*r+21
force->addParticle(vector<double>());
force->addParticle(vector<double>());
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 1; i < 5; i++) {
positions[1] = Vec3(i, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(124.4, 0, 0), forces[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(-124.4, 0, 0), forces[1], 1e-4);
ASSERT_EQUAL_TOL(2*(62.2*i+21), state.getPotentialEnergy(), 0.02);
}
}
void testPositionDependence() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "r", CustomGBForce::ParticlePair);
force->addComputedValue("b", "a+x*y", CustomGBForce::SingleParticle);
force->addEnergyTerm("b*z", CustomGBForce::SingleParticle);
force->addEnergyTerm("b1+b2", CustomGBForce::ParticlePair); // = 2*r+x1*y1+x2*y2
force->addParticle(vector<double>());
force->addParticle(vector<double>());
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
vector<Vec3> forces(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < 5; i++) {
positions[0] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
positions[1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
Vec3 delta = positions[0]-positions[1];
double r = sqrt(delta.dot(delta));
double energy = 2*r+positions[0][0]*positions[0][1]+positions[1][0]*positions[1][1];
for (int j = 0; j < 2; j++)
energy += positions[j][2]*(r+positions[j][0]*positions[j][1]);
Vec3 force1(-(1+positions[0][2])*delta[0]/r-(1+positions[0][2])*positions[0][1]-(1+positions[1][2])*delta[0]/r,
-(1+positions[0][2])*delta[1]/r-(1+positions[0][2])*positions[0][0]-(1+positions[1][2])*delta[1]/r,
-(1+positions[0][2])*delta[2]/r-(r+positions[0][0]*positions[0][1])-(1+positions[1][2])*delta[2]/r);
Vec3 force2((1+positions[0][2])*delta[0]/r+(1+positions[1][2])*delta[0]/r-(1+positions[1][2])*positions[1][1],
(1+positions[0][2])*delta[1]/r+(1+positions[1][2])*delta[1]/r-(1+positions[1][2])*positions[1][0],
(1+positions[0][2])*delta[2]/r+(1+positions[1][2])*delta[2]/r-(r+positions[1][0]*positions[1][1]));
ASSERT_EQUAL_VEC(force1, forces[0], 1e-4);
ASSERT_EQUAL_VEC(force2, forces[1], 1e-4);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(2), positions3(2);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
}
}
void testExclusions() {
for (int i = 0; i < 4; i++) {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "r", i < 2 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
force->addEnergyTerm("a", CustomGBForce::SingleParticle);
force->addEnergyTerm("(1+a1+a2)*r", i%2 == 0 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
force->addParticle(vector<double>());
force->addParticle(vector<double>());
force->addExclusion(0, 1);
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double f, energy;
switch (i)
{
case 0: // e = 0
f = 0;
energy = 0;
break;
case 1: // e = r
f = 1;
energy = 1;
break;
case 2: // e = 2r
f = 2;
energy = 2;
break;
case 3: // e = 3r + 2r^2
f = 7;
energy = 5;
break;
default:
ASSERT(false);
}
ASSERT_EQUAL_VEC(Vec3(f, 0, 0), forces[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(-f, 0, 0), forces[1], 1e-4);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = stepSize/norm;
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-3*abs(state.getPotentialEnergy()));
}
}
#include "OpenCLTests.h"
#include "TestCustomGBForce.h"
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testOBC(GBSAOBCForce::NoCutoff, CustomGBForce::NoCutoff);
testOBC(GBSAOBCForce::CutoffNonPeriodic, CustomGBForce::CutoffNonPeriodic);
testOBC(GBSAOBCForce::CutoffPeriodic, CustomGBForce::CutoffPeriodic);
testMembrane();
testTabulatedFunction();
testMultipleChainRules();
testPositionDependence();
testExclusions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/opencl/tests/TestOpenCLCustomHbondForce.cpp
View file @ cecc774a
......@@ -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) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,221 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of CustomHbondForce.
*/
#include "OpenCLTests.h"
#include "TestCustomHbondForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomHbondForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
void testHbond() {
// Create a system using a CustomHbondForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomHbondForce* custom = new CustomHbondForce("0.5*kr*(distance(d1,a1)-r0)^2 + 0.5*ktheta*(angle(a1,d1,d2)-theta0)^2 + 0.5*kpsi*(angle(d1,a1,a2)-psi0)^2 + kchi*(1+cos(n*dihedral(a3,a2,a1,d1)-chi0))");
custom->addPerDonorParameter("r0");
custom->addPerDonorParameter("theta0");
custom->addPerDonorParameter("psi0");
custom->addPerAcceptorParameter("chi0");
custom->addPerAcceptorParameter("n");
custom->addGlobalParameter("kr", 0.4);
custom->addGlobalParameter("ktheta", 0.5);
custom->addGlobalParameter("kpsi", 0.6);
custom->addGlobalParameter("kchi", 0.7);
vector<double> parameters(3);
parameters[0] = 1.5;
parameters[1] = 1.7;
parameters[2] = 1.9;
custom->addDonor(1, 0, -1, parameters);
parameters.resize(2);
parameters[0] = 2.1;
parameters[1] = 2;
custom->addAcceptor(2, 3, 4, parameters);
custom->setCutoffDistance(10.0);
customSystem.addForce(custom);
// Create an identical system using HarmonicBondForce, HarmonicAngleForce, and PeriodicTorsionForce.
System standardSystem;
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
HarmonicBondForce* bond = new HarmonicBondForce();
bond->addBond(1, 2, 1.5, 0.4);
standardSystem.addForce(bond);
HarmonicAngleForce* angle = new HarmonicAngleForce();
angle->addAngle(0, 1, 2, 1.7, 0.5);
angle->addAngle(1, 2, 3, 1.9, 0.6);
standardSystem.addForce(angle);
PeriodicTorsionForce* torsion = new PeriodicTorsionForce();
torsion->addTorsion(1, 2, 3, 4, 2, 2.1, 0.7);
standardSystem.addForce(torsion);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters.resize(3);
parameters[0] = 1.4;
parameters[1] = 1.7;
parameters[2] = 1.9;
custom->setDonorParameters(0, 1, 0, -1, parameters);
parameters.resize(2);
parameters[0] = 2.2;
parameters[1] = 2;
custom->setAcceptorParameters(0, 2, 3, 4, parameters);
bond->setBondParameters(0, 1, 2, 1.4, 0.4);
torsion->setTorsionParameters(0, 1, 2, 3, 4, 2, 2.2, 0.7);
custom->updateParametersInContext(c1);
bond->updateParametersInContext(c2);
torsion->updateParametersInContext(c2);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
void runPlatformTests() {
}
void testExclusions() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomHbondForce* custom = new CustomHbondForce("(distance(d1,a1)-1)^2");
custom->addDonor(0, 1, -1, vector<double>());
custom->addDonor(1, 0, -1, vector<double>());
custom->addAcceptor(2, 0, -1, vector<double>());
custom->addExclusion(1, 0);
system.addForce(custom);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
positions[2] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(2, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(1.0, state.getPotentialEnergy(), TOL);
}
void testCutoff() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomHbondForce* custom = new CustomHbondForce("(distance(d1,a1)-1)^2");
custom->addDonor(0, 1, -1, vector<double>());
custom->addDonor(1, 0, -1, vector<double>());
custom->addAcceptor(2, 0, -1, vector<double>());
custom->setNonbondedMethod(CustomHbondForce::CutoffNonPeriodic);
custom->setCutoffDistance(2.5);
system.addForce(custom);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 3, 0);
positions[2] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(2, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(1.0, state.getPotentialEnergy(), TOL);
}
void testCustomFunctions() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomHbondForce* custom = new CustomHbondForce("foo(distance(d1,a1))");
custom->addDonor(1, 0, -1, vector<double>());
custom->addDonor(2, 0, -1, vector<double>());
custom->addAcceptor(0, 1, -1, vector<double>());
vector<double> function(2);
function[0] = 0;
function[1] = 1;
custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
system.addForce(custom);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
positions[2] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0.1, 0.1, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -0.1, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.1, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.1*2+0.1*2, state.getPotentialEnergy(), TOL);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testHbond();
testExclusions();
testCutoff();
testCustomFunctions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp
View file @ cecc774a
......@@ -29,666 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of CustomIntegrator.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/CustomIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
static OpenCLPlatform platform;
const double TOL = 1e-5;
/**
* Test a simple leapfrog integrator on a single bond.
*/
void testSingleBond() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.setKineticEnergyExpression("m*v1*v1/2; v1=v+0.5*dt*f/m");
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
vector<Vec3> velocities(2);
velocities[0] = Vec3(-0.5*dt*0.5*0.5, 0, 0);
velocities[1] = Vec3(0.5*dt*0.5*0.5, 0, 0);
context.setVelocities(velocities);
// This is simply a harmonic oscillator, so compare it to the analytical solution.
const double freq = 1.0;;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities | State::Energy);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 1e-4);
double expectedSpeed = -0.5*freq*std::sin(freq*(time-dt/2));
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 1e-4);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
ASSERT_EQUAL_TOL(0.5*0.5*0.5, energy, 1e-4);
integrator.step(1);
}
}
/**
* Test an integrator that enforces constraints.
*/
void testConstraints() {
const int numParticles = 8;
System system;
CustomIntegrator integrator(0.002);
integrator.addPerDofVariable("oldx", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "(x-oldx)/dt");
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i%2 == 0 ? 5.0 : 10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numParticles-1; ++i)
system.addConstraint(i, i+1, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy);
for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5);
}
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
if (i == 1)
initialEnergy = energy;
else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1);
}
}
/**
* Test an integrator that applies constraints directly to velocities.
*/
void testVelocityConstraints() {
const int numParticles = 10;
System system;
CustomIntegrator integrator(0.002);
integrator.addPerDofVariable("x1", 0);
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("x1", "x");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x-x1)/dt");
integrator.addConstrainVelocities();
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i%2 == 0 ? 5.0 : 10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
// Constrain the first three particles with SHAKE.
system.addConstraint(0, 1, 1.0);
system.addConstraint(1, 2, 1.0);
// Constrain the next three with SETTLE.
system.addConstraint(3, 4, 1.0);
system.addConstraint(5, 4, 1.0);
system.addConstraint(3, 5, sqrt(2.0));
// Constraint the rest with CCMA.
for (int i = 6; i < numParticles-1; ++i)
system.addConstraint(i, i+1, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
integrator.step(2);
State state = context.getState(State::Positions | State::Velocities | State::Energy);
for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5);
if (i > 0) {
Vec3 v1 = state.getVelocities()[particle1];
Vec3 v2 = state.getVelocities()[particle2];
double vel = (v1-v2).dot(p1-p2);
ASSERT_EQUAL_TOL(0.0, vel, 2e-5);
}
}
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
if (i == 0)
initialEnergy = energy;
else if (i > 0)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
CustomIntegrator integrator(0.002);
integrator.addPerDofVariable("oldx", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "(x-oldx)/dt");
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities | State::Positions);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
/**
* Test an integrator with an AndersenThermostat to see if updateContextState()
* is being handled correctly.
*/
void testWithThermostat() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
const int numSteps = 5000;
System system;
CustomIntegrator integrator(0.003);
integrator.addUpdateContextState();
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermostat);
integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
context.setPositions(positions);
context.setVelocitiesToTemperature(temp);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < numSteps; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(10);
}
ke /= numSteps;
double expected = 0.5*numParticles*3*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
}
/**
* Test a Monte Carlo integrator that uses global variables and depends on energy.
*/
void testMonteCarlo() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
const double kT = BOLTZ*300.0;
integrator.addGlobalVariable("kT", kT);
integrator.addGlobalVariable("oldE", 0);
integrator.addGlobalVariable("accept", 0);
integrator.addPerDofVariable("oldx", 0);
integrator.addComputeGlobal("oldE", "energy");
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*gaussian");
integrator.addComputeGlobal("accept", "step(exp((oldE-energy)/kT)-uniform)");
integrator.addComputePerDof("x", "select(accept, x, oldx)");
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 2.0, 10.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// Compute the histogram of distances and see if it satisfies a Boltzmann distribution.
const int numBins = 100;
const double maxDist = 4.0;
const int numIterations = 5000;
vector<int> counts(numBins, 0);
for (int i = 0; i < numIterations; ++i) {
integrator.step(10);
State state = context.getState(State::Positions);
Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
double dist = sqrt(delta.dot(delta));
if (dist < maxDist)
counts[(int) (numBins*dist/maxDist)]++;
}
vector<double> expected(numBins, 0);
double sum = 0;
for (int i = 0; i < numBins; i++) {
double dist = (i+0.5)*maxDist/numBins;
expected[i] = dist*dist*exp(-5.0*(dist-2)*(dist-2)/kT);
sum += expected[i];
}
for (int i = 0; i < numBins; i++)
ASSERT_USUALLY_EQUAL_TOL((double) counts[i]/numIterations, expected[i]/sum, 0.01);
}
/**
* Test the ComputeSum operation.
*/
void testSum() {
const int numParticles = 200;
const double boxSize = 10;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nb = new NonbondedForce();
system.addForce(nb);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(i%10 == 0 ? 0.0 : 1.5);
nb->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 1)
close = true;
}
}
}
CustomIntegrator integrator(0.005);
integrator.addGlobalVariable("ke", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputeSum("ke", "m*v*v/2");
Context context(system, integrator, platform);
context.setPositions(positions);
// See if the sum is being computed correctly.
for (int i = 0; i < 100; ++i) {
State state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state.getKineticEnergy(), integrator.getGlobalVariable(0), 1e-5);
integrator.step(1);
}
}
/**
* Test an integrator that both uses and modifies a context parameter.
*/
void testParameter() {
System system;
system.addParticle(1.0);
AndersenThermostat* thermostat = new AndersenThermostat(0.1, 0.1);
system.addForce(thermostat);
CustomIntegrator integrator(0.1);
integrator.addGlobalVariable("temp", 0);
integrator.addComputeGlobal("temp", "AndersenTemperature");
integrator.addComputeGlobal("AndersenTemperature", "temp*2");
integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
Context context(system, integrator, platform);
// See if the parameter is being used correctly.
for (int i = 0; i < 10; i++) {
integrator.step(1);
ASSERT_EQUAL_TOL(context.getParameter("AndersenTemperature"), 0.1*(1<<(i+1)), 1e-5);
}
}
/**
* Test random number distributions.
*/
void testRandomDistributions() {
const int numParticles = 100;
const int numBins = 20;
const int numSteps = 100;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
integrator.addPerDofVariable("a", 0);
integrator.addPerDofVariable("b", 0);
integrator.addComputePerDof("a", "uniform");
integrator.addComputePerDof("b", "gaussian");
Context context(system, integrator, platform);
// See if the random numbers are distributed correctly.
vector<int> bins(numBins);
double mean = 0.0;
double var = 0.0;
double skew = 0.0;
double kurtosis = 0.0;
vector<Vec3> values;
for (int i = 0; i < numSteps; i++) {
integrator.step(1);
integrator.getPerDofVariable(0, values);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
double v = values[i][j];
ASSERT(v >= 0 && v < 1);
bins[(int) (v*numBins)]++;
}
integrator.getPerDofVariable(1, values);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
double v = values[i][j];
mean += v;
var += v*v;
skew += v*v*v;
kurtosis += v*v*v*v;
}
}
// Check the distribution of uniform randoms.
int numValues = numParticles*numSteps*3;
double expected = numValues/(double) numBins;
double tol = 4*sqrt(expected);
for (int i = 0; i < numBins; i++)
ASSERT(bins[i] >= expected-tol && bins[i] <= expected+tol);
// Check the distribution of gaussian randoms.
mean /= numValues;
var /= numValues;
skew /= numValues;
kurtosis /= numValues;
double c2 = var-mean*mean;
double c3 = skew-3*var*mean+2*mean*mean*mean;
double c4 = kurtosis-4*skew*mean-3*var*var+12*var*mean*mean-6*mean*mean*mean*mean;
ASSERT_EQUAL_TOL(0.0, mean, 3.0/sqrt((double) numValues));
ASSERT_EQUAL_TOL(1.0, c2, 3.0/pow(numValues, 1.0/3.0));
ASSERT_EQUAL_TOL(0.0, c3, 3.0/pow(numValues, 1.0/4.0));
ASSERT_EQUAL_TOL(0.0, c4, 3.0/pow(numValues, 1.0/4.0));
}
/**
* Test getting and setting per-DOF variables.
*/
void testPerDofVariables() {
const int numParticles = 200;
const double boxSize = 10;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nb = new NonbondedForce();
system.addForce(nb);
nb->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.5);
nb->addParticle(i%2 == 0 ? 1 : -1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
close = true;
}
}
}
CustomIntegrator integrator(0.01);
integrator.addPerDofVariable("temp", 0);
integrator.addPerDofVariable("pos", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("pos", "x");
Context context(system, integrator, platform);
context.setPositions(positions);
vector<Vec3> initialValues(numParticles);
for (int i = 0; i < numParticles; i++)
initialValues[i] = Vec3(i+0.1, i+0.2, i+0.3);
integrator.setPerDofVariable(0, initialValues);
// Run a simulation, then query per-DOF values and see if they are correct.
vector<Vec3> values;
context.getState(State::Forces); // Cause atom reordering to happen before the first step
for (int i = 0; i < 200; ++i) {
integrator.step(1);
State state = context.getState(State::Positions);
integrator.getPerDofVariable(0, values);
for (int j = 0; j < numParticles; j++)
ASSERT_EQUAL_VEC(initialValues[j], values[j], 1e-5);
integrator.getPerDofVariable(1, values);
for (int j = 0; j < numParticles; j++)
ASSERT_EQUAL_VEC(state.getPositions()[j], values[j], 1e-5);
}
}
/**
* Test evaluating force groups separately.
*/
void testForceGroups() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
CustomIntegrator integrator(0.01);
integrator.addPerDofVariable("outf", 0);
integrator.addPerDofVariable("outf1", 0);
integrator.addPerDofVariable("outf2", 0);
integrator.addGlobalVariable("oute", 0);
integrator.addGlobalVariable("oute1", 0);
integrator.addGlobalVariable("oute2", 0);
integrator.addComputePerDof("outf", "f");
integrator.addComputePerDof("outf1", "f1");
integrator.addComputePerDof("outf2", "f2");
integrator.addComputeGlobal("oute", "energy");
integrator.addComputeGlobal("oute1", "energy1");
integrator.addComputeGlobal("oute2", "energy2");
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.5, 1.1);
bonds->setForceGroup(1);
system.addForce(bonds);
NonbondedForce* nb = new NonbondedForce();
nb->addParticle(0.2, 1, 0);
nb->addParticle(0.2, 1, 0);
nb->setForceGroup(2);
system.addForce(nb);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// See if the various forces are computed correctly.
integrator.step(1);
vector<Vec3> f, f1, f2;
double e1 = 0.5*1.1*0.5*0.5;
double e2 = 138.935456*0.2*0.2/2.0;
integrator.getPerDofVariable(0, f);
integrator.getPerDofVariable(1, f1);
integrator.getPerDofVariable(2, f2);
ASSERT_EQUAL_VEC(Vec3(1.1*0.5, 0, 0), f1[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-1.1*0.5, 0, 0), f1[1], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-138.935456*0.2*0.2/4.0, 0, 0), f2[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(138.935456*0.2*0.2/4.0, 0, 0), f2[1], 1e-5);
ASSERT_EQUAL_VEC(f1[0]+f2[0], f[0], 1e-5);
ASSERT_EQUAL_VEC(f1[1]+f2[1], f[1], 1e-5);
ASSERT_EQUAL_TOL(e1, integrator.getGlobalVariable(1), 1e-5);
ASSERT_EQUAL_TOL(e2, integrator.getGlobalVariable(2), 1e-5);
ASSERT_EQUAL_TOL(e1+e2, integrator.getGlobalVariable(0), 1e-5);
// Make sure they also match the values returned by the Context.
State s = context.getState(State::Forces | State::Energy, false);
State s1 = context.getState(State::Forces | State::Energy, false, 2);
State s2 = context.getState(State::Forces | State::Energy, false, 4);
vector<Vec3> c, c1, c2;
c = context.getState(State::Forces, false).getForces();
c1 = context.getState(State::Forces, false, 2).getForces();
c2 = context.getState(State::Forces, false, 4).getForces();
ASSERT_EQUAL_VEC(f[0], c[0], 1e-5);
ASSERT_EQUAL_VEC(f[1], c[1], 1e-5);
ASSERT_EQUAL_VEC(f1[0], c1[0], 1e-5);
ASSERT_EQUAL_VEC(f1[1], c1[1], 1e-5);
ASSERT_EQUAL_VEC(f2[0], c2[0], 1e-5);
ASSERT_EQUAL_VEC(f2[1], c2[1], 1e-5);
ASSERT_EQUAL_TOL(s.getPotentialEnergy(), integrator.getGlobalVariable(0), 1e-5);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), integrator.getGlobalVariable(1), 1e-5);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), integrator.getGlobalVariable(2), 1e-5);
}
/**
* Test a multiple time step r-RESPA integrator.
*/
void testRespa() {
const int numParticles = 8;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
CustomIntegrator integrator(0.002);
integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
for (int i = 0; i < 2; i++) {
integrator.addComputePerDof("v", "v+0.5*(dt/2)*f0/m");
integrator.addComputePerDof("x", "x+(dt/2)*v");
integrator.addComputePerDof("v", "v+0.5*(dt/2)*f0/m");
}
integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
HarmonicBondForce* bonds = new HarmonicBondForce();
for (int i = 0; i < numParticles-2; i++)
bonds->addBond(i, i+1, 1.0, 0.5);
system.addForce(bonds);
NonbondedForce* nb = new NonbondedForce();
nb->setCutoffDistance(2.0);
nb->setNonbondedMethod(NonbondedForce::Ewald);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i%2 == 0 ? 5.0 : 10.0);
nb->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
nb->setForceGroup(1);
nb->setReciprocalSpaceForceGroup(0);
system.addForce(nb);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and monitor energy conservations.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Energy);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
if (i == 1)
initialEnergy = energy;
else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05);
integrator.step(2);
}
}
#include "OpenCLTests.h"
#include "TestCustomIntegrator.h"
/**
* Make sure random numbers are computed correctly when steps get merged.
......@@ -756,117 +98,6 @@ void testMergedRandoms() {
}
}
void testIfBlock() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addGlobalVariable("a", 0);
integrator.addGlobalVariable("b", 0);
integrator.addComputeGlobal("b", "1");
integrator.beginIfBlock("a < 3.5");
integrator.addComputeGlobal("b", "a+1");
integrator.endBlock();
Context context(system, integrator, platform);
// Set "a" to 1.7 and verify that "b" gets set to a+1.
integrator.setGlobalVariable(0, 1.7);
integrator.step(1);
ASSERT_EQUAL_TOL(2.7, integrator.getGlobalVariable(1), 1e-6);
// Now set it to a value that should cause the block to be skipped.
integrator.setGlobalVariable(0, 4.1);
integrator.step(1);
ASSERT_EQUAL_TOL(1.0, integrator.getGlobalVariable(1), 1e-6);
}
void testWhileBlock() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addGlobalVariable("a", 0);
integrator.addGlobalVariable("b", 0);
integrator.addComputeGlobal("b", "1");
integrator.beginWhileBlock("b <= a");
integrator.addComputeGlobal("b", "b+1");
integrator.endBlock();
Context context(system, integrator, platform);
// Try a case where the loop should be skipped.
integrator.setGlobalVariable(0, -3.3);
integrator.step(1);
ASSERT_EQUAL_TOL(1.0, integrator.getGlobalVariable(1), 1e-6);
// In this case it should be executed exactly once.
integrator.setGlobalVariable(0, 1.2);
integrator.step(1);
ASSERT_EQUAL_TOL(2.0, integrator.getGlobalVariable(1), 1e-6);
// In this case, it should be executed several times.
integrator.setGlobalVariable(0, 5.3);
integrator.step(1);
ASSERT_EQUAL_TOL(6.0, integrator.getGlobalVariable(1), 1e-6);
}
/**
* Test modifying a global variable, then using it in a per-DOF computation.
*/
void testChangingGlobal() {
System system;
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
integrator.addGlobalVariable("g", 0);
integrator.addPerDofVariable("a", 0);
integrator.addPerDofVariable("b", 0);
integrator.addComputeGlobal("g", "g+1");
integrator.addComputePerDof("a", "0.5");
integrator.addComputePerDof("b", "a+g");
Context context(system, integrator, platform);
// See if everything is being calculated correctly..
for (int i = 0; i < 10; i++) {
integrator.step(1);
ASSERT_EQUAL_TOL(i+1.0, integrator.getGlobalVariable(0), 1e-5);
vector<Vec3> values;
integrator.getPerDofVariable(1, values);
ASSERT_EQUAL_VEC(Vec3(i+1.5, i+1.5, i+1.5), values[0], 1e-5);
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testSingleBond();
testConstraints();
testVelocityConstraints();
testConstrainedMasslessParticles();
testWithThermostat();
testMonteCarlo();
testSum();
testParameter();
testRandomDistributions();
testPerDofVariables();
testForceGroups();
testRespa();
testMergedRandoms();
testIfBlock();
testWhileBlock();
testChangingGlobal();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testMergedRandoms();
}
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