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Commit 48d93893 authored by Peter Eastman's avatar Peter Eastman
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A few optimizations. Also added a new test case.

parent 72d59cbe
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Showing with 197 additions and 5 deletions
platforms/opencl/src/OpenCLExpressionUtilities.cpp
View file @ 48d93893
......@@ -177,8 +177,34 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
out << doubleToString(dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()) << "*" << getTempName(node.getChildren()[0], temps);
break;
case Operation::POWER_CONSTANT:
out << "pow(" << getTempName(node.getChildren()[0], temps) << ", " << doubleToString(dynamic_cast<const Operation::PowerConstant*>(&node.getOperation())->getValue()) << ")";
{
double exponent = dynamic_cast<const Operation::PowerConstant*>(&node.getOperation())->getValue();
if (exponent == 0.0)
out << "1.0f";
else if (exponent == (int) exponent) {
out << "0.0f;\n";
out << "{\n";
out << "float multiplier = " << (exponent < 0.0 ? "1.0f/" : "") << getTempName(node.getChildren()[0], temps) << ";\n";
int exp = (int) fabs(exponent);
bool hasAssigned = false;
while (exp != 0) {
if (exp%2 == 1) {
if (!hasAssigned)
out << name << " = multiplier;\n";
else
out << name << " *= multiplier;\n";
hasAssigned = true;
}
exp >>= 1;
if (exp != 0)
out << "multiplier *= multiplier;\n";
}
out << "}";
}
else
out << "pow(" << getTempName(node.getChildren()[0], temps) << ", " << doubleToString(exponent) << ")";
break;
}
default:
throw OpenMMException("Internal error: Unknown operation in user-defined expression: "+node.getOperation().getName());
}
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 48d93893
......@@ -553,6 +553,8 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
vector<mm_float2> sigmaEpsilonVector(numParticles);
vector<vector<int> > exclusionList(numParticles);
double sumSquaredCharges = 0.0;
bool hasCoulomb = false;
bool hasLJ = false;
for (int i = 0; i < numParticles; i++) {
double charge, sigma, epsilon;
force.getParticleParameters(i, charge, sigma, epsilon);
......@@ -560,6 +562,10 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
sigmaEpsilonVector[i] = (mm_float2) {(float) (0.5*sigma), (float) (2.0*sqrt(epsilon))};
exclusionList[i].push_back(i);
sumSquaredCharges += charge*charge;
if (charge != 0.0)
hasCoulomb = true;
if (epsilon != 0.0)
hasLJ = true;
}
for (int i = 0; i < (int) exclusions.size(); i++) {
exclusionList[exclusions[i].first].push_back(exclusions[i].second);
......@@ -572,6 +578,8 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
map<string, string> defines;
defines["HAS_COULOMB"] = (hasCoulomb ? "1" : "0");
defines["HAS_LENNARD_JONES"] = (hasLJ ? "1" : "0");
if (useCutoff) {
// Compute the reaction field constants.
......
platforms/opencl/src/kernels/coulombLennardJones.cl
View file @ 48d93893
......@@ -13,6 +13,7 @@ if (r2 < CUTOFF_SQUARED) {
tempEnergy += -prefactor*(1.0f-erfcAlphaR);
}
else {
#if HAS_LENNARD_JONES
float sig = sigmaEpsilon1.x + sigmaEpsilon2.x;
float sig2 = invR*sig;
sig2 *= sig2;
......@@ -20,6 +21,10 @@ if (r2 < CUTOFF_SQUARED) {
float eps = sigmaEpsilon1.y*sigmaEpsilon2.y;
tempForce = eps*(12.0f*sig6 - 6.0f)*sig6 + prefactor*(erfcAlphaR+alphaR*exp(-alphaR*alphaR)*TWO_OVER_SQRT_PI);
tempEnergy += eps*(sig6 - 1.0f)*sig6 + prefactor*erfcAlphaR;
#else
tempForce = prefactor*(erfcAlphaR+alphaR*exp(-alphaR*alphaR)*TWO_OVER_SQRT_PI);
tempEnergy += prefactor*erfcAlphaR;
#endif
}
dEdR += tempForce*invR*invR;
}
......@@ -30,21 +35,26 @@ if (!isExcluded && r2 < CUTOFF_SQUARED) {
#else
if (!isExcluded) {
#endif
float tempForce = 0.0f;
#if HAS_LENNARD_JONES
float sig = sigmaEpsilon1.x + sigmaEpsilon2.x;
float sig2 = invR*sig;
sig2 *= sig2;
float sig6 = sig2*sig2*sig2;
float eps = sigmaEpsilon1.y*sigmaEpsilon2.y;
float tempForce = eps*(12.0f*sig6 - 6.0f)*sig6;
tempForce = eps*(12.0f*sig6 - 6.0f)*sig6;
tempEnergy += eps*(sig6 - 1.0f)*sig6;
#ifdef USE_CUTOFF
#endif
#if HAS_COULOMB
#ifdef USE_CUTOFF
const float prefactor = 138.935485f*posq1.w*posq2.w;
tempForce += prefactor*(invR - 2.0f*REACTION_FIELD_K*r2);
tempEnergy += prefactor*(invR + REACTION_FIELD_K*r2 - REACTION_FIELD_C);
#else
#else
const float prefactor = 138.935485f*posq1.w*posq2.w*invR;
tempForce += prefactor;
tempEnergy += prefactor;
#endif
#endif
dEdR += tempForce*invR*invR;
}
......
platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp
View file @ 48d93893
......@@ -35,9 +35,11 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "../src/sfmt/SFMT.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
......@@ -234,6 +236,77 @@ void testTabulatedFunction(bool interpolating) {
}
}
void testCoulombLennardJones() {
const int numMolecules = 300;
const int numParticles = numMolecules*2;
const double boxSize = 20.0;
OpenCLPlatform platform;
// Create two systems: one with a NonbondedForce, and one using a CustomNonbondedForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
NonbondedForce* standardNonbonded = new NonbondedForce();
CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6) + 138.935485*q/r");
customNonbonded->addParameter("q", "q1*q2");
customNonbonded->addParameter("sigma", "0.5*(sigma1+sigma2)");
customNonbonded->addParameter("eps", "sqrt(eps1*eps2)");
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
standardNonbonded->addParticle(1.0, 0.2, 0.1);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.1;
customNonbonded->addParticle(params);
standardNonbonded->addParticle(1.0, 0.1, 0.1);
params[1] = 0.1;
customNonbonded->addParticle(params);
}
else {
standardNonbonded->addParticle(1.0, 0.2, 0.2);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.2;
customNonbonded->addParticle(params);
standardNonbonded->addParticle(1.0, 0.1, 0.2);
params[1] = 0.1;
customNonbonded->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(), boxSize*genrand_real2(), boxSize*genrand_real2());
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(), genrand_real2(), genrand_real2());
velocities[2*i+1] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
standardNonbonded->addException(2*i, 2*i+1, 0.0, 1.0, 0.0);
customNonbonded->addException(2*i, 2*i+1, vector<double>());
}
standardNonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
customNonbonded->setNonbondedMethod(CustomNonbondedForce::NoCutoff);
standardSystem.addForce(standardNonbonded);
customSystem.addForce(customNonbonded);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, platform);
Context context2(customSystem, integrator2, platform);
context1.setPositions(positions);
context2.setPositions(positions);
context1.setVelocities(velocities);
context2.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
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);
}
}
int main() {
try {
testSimpleExpression();
......@@ -243,6 +316,7 @@ int main() {
testPeriodic();
testTabulatedFunction(true);
testTabulatedFunction(false);
testCoulombLennardJones();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp
View file @ 48d93893
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -35,9 +35,11 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "../src/sfmt/SFMT.h"
#include "openmm/Context.h"
#include "ReferencePlatform.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
......@@ -234,6 +236,77 @@ void testTabulatedFunction(bool interpolating) {
}
}
void testCoulombLennardJones() {
const int numMolecules = 300;
const int numParticles = numMolecules*2;
const double boxSize = 20.0;
ReferencePlatform platform;
// Create two systems: one with a NonbondedForce, and one using a CustomNonbondedForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
NonbondedForce* standardNonbonded = new NonbondedForce();
CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6) + 138.935485*q/r");
customNonbonded->addParameter("q", "q1*q2");
customNonbonded->addParameter("sigma", "0.5*(sigma1+sigma2)");
customNonbonded->addParameter("eps", "sqrt(eps1*eps2)");
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
standardNonbonded->addParticle(1.0, 0.2, 0.1);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.1;
customNonbonded->addParticle(params);
standardNonbonded->addParticle(1.0, 0.1, 0.1);
params[1] = 0.1;
customNonbonded->addParticle(params);
}
else {
standardNonbonded->addParticle(1.0, 0.2, 0.2);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.2;
customNonbonded->addParticle(params);
standardNonbonded->addParticle(1.0, 0.1, 0.2);
params[1] = 0.1;
customNonbonded->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(), boxSize*genrand_real2(), boxSize*genrand_real2());
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(), genrand_real2(), genrand_real2());
velocities[2*i+1] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
standardNonbonded->addException(2*i, 2*i+1, 0.0, 1.0, 0.0);
customNonbonded->addException(2*i, 2*i+1, vector<double>());
}
standardNonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
customNonbonded->setNonbondedMethod(CustomNonbondedForce::NoCutoff);
standardSystem.addForce(standardNonbonded);
customSystem.addForce(customNonbonded);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, platform);
Context context2(customSystem, integrator2, platform);
context1.setPositions(positions);
context2.setPositions(positions);
context1.setVelocities(velocities);
context2.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
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);
}
}
int main() {
try {
testSimpleExpression();
......@@ -243,6 +316,7 @@ int main() {
testPeriodic();
testTabulatedFunction(true);
testTabulatedFunction(false);
testCoulombLennardJones();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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