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Commit 9434c6e8 authored by peastman's avatar peastman
Browse files

Created OpenCL and CUDA implementations of Continuous2DFunction

parent 4cfeb429
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Showing with 270 additions and 8 deletions
openmmapi/src/SplineFitter.cpp
View file @ 9434c6e8
......@@ -255,9 +255,9 @@ void SplineFitter::create2DNaturalSpline(const vector<double>& x, const vector<d
0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 2, -2, 0, 0, -1, 1
};
vector<double> rhs(16);
c.resize(xsize*ysize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
c.resize((xsize-1)*(ysize-1));
for (int i = 0; i < xsize-1; i++) {
for (int j = 0; j < ysize-1; j++) {
// Compute the 16 coefficients for patch (i, j).
int nexti = i+1;
......@@ -275,7 +275,7 @@ void SplineFitter::create2DNaturalSpline(const vector<double>& x, const vector<d
rhs[k+8] = e2[k]*deltay;
rhs[k+12] = e12[k]*deltax*deltay;
}
vector<double>& coeff = c[i+j*xsize];
vector<double>& coeff = c[i+j*(xsize-1)];
coeff.resize(16);
for (int k = 0; k < 16; k++) {
double sum = 0.0;
......@@ -317,7 +317,7 @@ double SplineFitter::evaluate2DSpline(const vector<double>& x, const vector<doub
double deltay = y[uppery]-y[lowery];
double da = (u-x[lowerx])/deltax;
double db = (v-y[lowery])/deltay;
const vector<double>& coeff = c[lowerx+xsize*lowery];
const vector<double>& coeff = c[lowerx+(xsize-1)*lowery];
// Evaluate the spline to determine the value and gradients.
......@@ -357,7 +357,7 @@ void SplineFitter::evaluate2DSplineDerivatives(const vector<double>& x, const ve
double deltay = y[uppery]-y[lowery];
double da = (u-x[lowerx])/deltax;
double db = (v-y[lowery])/deltay;
const vector<double>& coeff = c[lowerx+xsize*lowery];
const vector<double>& coeff = c[lowerx+(xsize-1)*lowery];
// Evaluate the spline to determine the value and gradients.
......
platforms/cuda/src/CudaExpressionUtilities.cpp
View file @ 9434c6e8
......@@ -126,6 +126,49 @@ void CudaExpressionUtilities::processExpression(stringstream& out, const Express
}
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[0] << ");\n";
out << "int coeffIndex = 4*(s+" << paramsInt[0] << "*t);\n";
out << "float4 c[4];\n";
out << "c[0] = " << functionNames[i].second << "[coeffIndex];\n";
out << "c[1] = " << functionNames[i].second << "[coeffIndex+1];\n";
out << "c[2] = " << functionNames[i].second << "[coeffIndex+2];\n";
out << "c[3] = " << functionNames[i].second << "[coeffIndex+3];\n";
out << "real da = x-s;";
out << "real db = y-t;";
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;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[2].w*db + c[2].z)*db + c[2].y)*db + c[2].x;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[1].w*db + c[1].z)*db + c[1].y)*db + c[1].x;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[0].w*db + c[0].z)*db + c[0].y)*db + c[0].x;";
}
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;";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].z*da + 2.0f*c[2].z)*da + c[1].z;";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].y*da + 2.0f*c[2].y)*da + c[1].y;";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].x*da + 2.0f*c[2].x)*da + c[1].x;";
out << nodeNames[j] << " *= " << paramsFloat[6] << ";";
}
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;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[2].w*db + 2.0f*c[2].z)*db + c[2].y;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[1].w*db + 2.0f*c[1].z)*db + c[1].y;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[0].w*db + 2.0f*c[0].z)*db + c[0].y;";
out << nodeNames[j] << " *= " << paramsFloat[7] << ";";
}
else
throw OpenMMException("Unsupported derivative order for Continuous2DFunction");
}
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();
......@@ -408,6 +451,29 @@ vector<float> CudaExpressionUtilities::computeFunctionCoefficients(const Tabulat
width = 4;
return f;
}
if (dynamic_cast<const Continuous2DFunction*>(&function) != NULL) {
// Compute the spline coefficients.
const Continuous2DFunction& fn = dynamic_cast<const Continuous2DFunction&>(function);
vector<double> values;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
fn.getFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
vector<double> x(xsize), y(ysize);
for (int i = 0; i < xsize; i++)
x[i] = xmin+i*(xmax-xmin)/(xsize-1);
for (int i = 0; i < ysize; i++)
y[i] = ymin+i*(ymax-ymin)/(ysize-1);
vector<vector<double> > c;
SplineFitter::create2DNaturalSpline(x, y, values, c);
vector<float> f(16*c.size());
for (int i = 0; i < (int) c.size(); i++) {
for (int j = 0; j < 16; j++)
f[16*i+j] = (float) c[i][j];
}
width = 4;
return f;
}
if (dynamic_cast<const Discrete1DFunction*>(&function) != NULL) {
// Record the tabulated values.
......@@ -465,6 +531,21 @@ vector<vector<double> > CudaExpressionUtilities::computeFunctionParameters(const
params[i].push_back((values.size()-1)/(max-min));
params[i].push_back(values.size()-2);
}
else if (dynamic_cast<const Continuous2DFunction*>(functions[i]) != NULL) {
const Continuous2DFunction& fn = dynamic_cast<const Continuous2DFunction&>(*functions[i]);
vector<double> values;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
fn.getFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
params[i].push_back(xsize-1);
params[i].push_back(ysize-1);
params[i].push_back(xmin);
params[i].push_back(xmax);
params[i].push_back(ymin);
params[i].push_back(ymax);
params[i].push_back((xsize-1)/(xmax-xmin));
params[i].push_back((ysize-1)/(ymax-ymin));
}
else if (dynamic_cast<const Discrete1DFunction*>(functions[i]) != NULL) {
const Discrete1DFunction& fn = dynamic_cast<const Discrete1DFunction&>(*functions[i]);
vector<double> values;
......@@ -497,6 +578,8 @@ vector<vector<double> > CudaExpressionUtilities::computeFunctionParameters(const
Lepton::CustomFunction* CudaExpressionUtilities::getFunctionPlaceholder(const TabulatedFunction& function) {
if (dynamic_cast<const Continuous1DFunction*>(&function) != NULL)
return &fp1;
if (dynamic_cast<const Continuous2DFunction*>(&function) != NULL)
return &fp2;
if (dynamic_cast<const Discrete1DFunction*>(&function) != NULL)
return &fp1;
if (dynamic_cast<const Discrete2DFunction*>(&function) != NULL)
......
platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp
View file @ 9434c6e8
......@@ -277,7 +277,6 @@ void testContinuous1DFunction() {
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
double tol = 0.01;
for (int i = 1; i < 30; i++) {
double x = (7.0/30.0)*i;
positions[1] = Vec3(x, 0, 0);
......@@ -300,6 +299,54 @@ void testContinuous1DFunction() {
}
}
void testContinuous2DFunction() {
const int xsize = 20;
const int ysize = 21;
const double xmin = 0.4;
const double xmax = 1.5;
const double ymin = 0.0;
const double ymax = 2.1;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a)+1");
forceField->addGlobalParameter("a", 0.0);
forceField->addParticle(vector<double>());
forceField->addParticle(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->addFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
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[1] = Vec3(x, 0, 0);
context.setParameter("a", y);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
double force = 0;
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
energy = sin(0.25*x)*cos(0.33*y)+1.0;
force = -0.25*cos(0.25*x)*cos(0.33*y);
}
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);
}
}
}
void testDiscrete1DFunction() {
System system;
system.addParticle(1.0);
......@@ -821,6 +868,7 @@ int main(int argc, char* argv[]) {
testCutoff();
testPeriodic();
testContinuous1DFunction();
testContinuous2DFunction();
testDiscrete1DFunction();
testDiscrete2DFunction();
testDiscrete3DFunction();
......
platforms/opencl/src/OpenCLExpressionUtilities.cpp
View file @ 9434c6e8
......@@ -126,6 +126,49 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
}
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[0] << ");\n";
out << "int coeffIndex = 4*(s+" << paramsInt[0] << "*t);\n";
out << "float4 c[4];\n";
out << "c[0] = " << functionNames[i].second << "[coeffIndex];\n";
out << "c[1] = " << functionNames[i].second << "[coeffIndex+1];\n";
out << "c[2] = " << functionNames[i].second << "[coeffIndex+2];\n";
out << "c[3] = " << functionNames[i].second << "[coeffIndex+3];\n";
out << "real da = x-s;";
out << "real db = y-t;";
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;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[2].w*db + c[2].z)*db + c[2].y)*db + c[2].x;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[1].w*db + c[1].z)*db + c[1].y)*db + c[1].x;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + ((c[0].w*db + c[0].z)*db + c[0].y)*db + c[0].x;";
}
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;";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].z*da + 2.0f*c[2].z)*da + c[1].z;";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].y*da + 2.0f*c[2].y)*da + c[1].y;";
out << nodeNames[j] << " = db*" << nodeNames[j] << " + (3.0f*c[3].x*da + 2.0f*c[2].x)*da + c[1].x;";
out << nodeNames[j] << " *= " << paramsFloat[6] << ";";
}
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;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[2].w*db + 2.0f*c[2].z)*db + c[2].y;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[1].w*db + 2.0f*c[1].z)*db + c[1].y;";
out << nodeNames[j] << " = da*" << nodeNames[j] << " + (3.0f*c[0].w*db + 2.0f*c[0].z)*db + c[0].y;";
out << nodeNames[j] << " *= " << paramsFloat[7] << ";";
}
else
throw OpenMMException("Unsupported derivative order for Continuous2DFunction");
}
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();
......@@ -408,6 +451,29 @@ vector<float> OpenCLExpressionUtilities::computeFunctionCoefficients(const Tabul
width = 4;
return f;
}
if (dynamic_cast<const Continuous2DFunction*>(&function) != NULL) {
// Compute the spline coefficients.
const Continuous2DFunction& fn = dynamic_cast<const Continuous2DFunction&>(function);
vector<double> values;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
fn.getFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
vector<double> x(xsize), y(ysize);
for (int i = 0; i < xsize; i++)
x[i] = xmin+i*(xmax-xmin)/(xsize-1);
for (int i = 0; i < ysize; i++)
y[i] = ymin+i*(ymax-ymin)/(ysize-1);
vector<vector<double> > c;
SplineFitter::create2DNaturalSpline(x, y, values, c);
vector<float> f(16*c.size());
for (int i = 0; i < (int) c.size(); i++) {
for (int j = 0; j < 16; j++)
f[16*i+j] = (float) c[i][j];
}
width = 4;
return f;
}
if (dynamic_cast<const Discrete1DFunction*>(&function) != NULL) {
// Record the tabulated values.
......@@ -465,6 +531,21 @@ vector<vector<double> > OpenCLExpressionUtilities::computeFunctionParameters(con
params[i].push_back((values.size()-1)/(max-min));
params[i].push_back(values.size()-2);
}
else if (dynamic_cast<const Continuous2DFunction*>(functions[i]) != NULL) {
const Continuous2DFunction& fn = dynamic_cast<const Continuous2DFunction&>(*functions[i]);
vector<double> values;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
fn.getFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
params[i].push_back(xsize-1);
params[i].push_back(ysize-1);
params[i].push_back(xmin);
params[i].push_back(xmax);
params[i].push_back(ymin);
params[i].push_back(ymax);
params[i].push_back((xsize-1)/(xmax-xmin));
params[i].push_back((ysize-1)/(ymax-ymin));
}
else if (dynamic_cast<const Discrete1DFunction*>(functions[i]) != NULL) {
const Discrete1DFunction& fn = dynamic_cast<const Discrete1DFunction&>(*functions[i]);
vector<double> values;
......@@ -497,6 +578,8 @@ vector<vector<double> > OpenCLExpressionUtilities::computeFunctionParameters(con
Lepton::CustomFunction* OpenCLExpressionUtilities::getFunctionPlaceholder(const TabulatedFunction& function) {
if (dynamic_cast<const Continuous1DFunction*>(&function) != NULL)
return &fp1;
if (dynamic_cast<const Continuous2DFunction*>(&function) != NULL)
return &fp2;
if (dynamic_cast<const Discrete1DFunction*>(&function) != NULL)
return &fp1;
if (dynamic_cast<const Discrete2DFunction*>(&function) != NULL)
......
platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp
View file @ 9434c6e8
......@@ -277,7 +277,6 @@ void testContinuous1DFunction() {
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
double tol = 0.01;
for (int i = 1; i < 30; i++) {
double x = (7.0/30.0)*i;
positions[1] = Vec3(x, 0, 0);
......@@ -300,6 +299,54 @@ void testContinuous1DFunction() {
}
}
void testContinuous2DFunction() {
const int xsize = 20;
const int ysize = 21;
const double xmin = 0.4;
const double xmax = 1.5;
const double ymin = 0.0;
const double ymax = 2.1;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a)+1");
forceField->addGlobalParameter("a", 0.0);
forceField->addParticle(vector<double>());
forceField->addParticle(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->addFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
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[1] = Vec3(x, 0, 0);
context.setParameter("a", y);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
double force = 0;
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
energy = sin(0.25*x)*cos(0.33*y)+1.0;
force = -0.25*cos(0.25*x)*cos(0.33*y);
}
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);
}
}
}
void testDiscrete1DFunction() {
System system;
system.addParticle(1.0);
......@@ -820,6 +867,7 @@ int main(int argc, char* argv[]) {
testCutoff();
testPeriodic();
testContinuous1DFunction();
testContinuous2DFunction();
testDiscrete1DFunction();
testDiscrete2DFunction();
testDiscrete3DFunction();
......
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