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Commit 4cfeb429 authored by peastman's avatar peastman
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Created reference implementation of Continuous2DFunction

parent 5b0e8f29
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openmmapi/include/openmm/TabulatedFunction.h
View file @ 4cfeb429
......@@ -70,7 +70,7 @@ public:
* Create a Continuous1DFunction f(x) based on a set of tabulated values.
*
* @param values the tabulated values of the function f(x) at uniformly spaced values of x between min
* and max. A natural cubic spline is used to interpolated between the tabulated values.
* and max. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero for x < min or x > max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
......@@ -80,7 +80,7 @@ public:
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x) at uniformly spaced values of x between min
* and max. A natural cubic spline is used to interpolated between the tabulated values.
* and max. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero for x < min or x > max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
......@@ -90,7 +90,7 @@ public:
* Set the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x) at uniformly spaced values of x between min
* and max. A natural cubic spline is used to interpolated between the tabulated values.
* and max. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero for x < min or x > max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
......@@ -101,6 +101,62 @@ private:
double min, max;
};
/**
* This is a TabulatedFunction that computes a continuous two dimensional function.
*/
class OPENMM_EXPORT Continuous2DFunction : public TabulatedFunction {
public:
/**
* Create a Continuous2DFunction f(x,y) based on a set of tabulated values.
*
* @param values the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
* and xmax, and ysize values of y between ymin and ymax. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero when x or y is outside its specified range. The values should be ordered so that
* values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
*/
Continuous2DFunction(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax);
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
* and xmax, and ysize values of y between ymin and ymax. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero when x or y is outside its specified range. The values should be ordered so that
* values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
*/
void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const;
/**
* Set the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
* and xmax, and ysize values of y between ymin and ymax. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero when x or y is outside its specified range. The values should be ordered so that
* values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
*/
void setFunctionParameters(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax);
private:
std::vector<double> values;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
};
/**
* This is a TabulatedFunction that computes a discrete one dimensional function f(x).
* To evaluate it, x is rounded to the nearest integer and the table element with that
......
openmmapi/src/SplineFitter.cpp
View file @ 4cfeb429
......@@ -219,7 +219,7 @@ void SplineFitter::create2DNaturalSpline(const vector<double>& x, const vector<d
t[j] = values[i+xsize*j];
SplineFitter::createNaturalSpline(y, t, deriv);
for (int j = 0; j < ysize; j++)
d2[i+xsize*j] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
d2[i+xsize*j] = SplineFitter::evaluateSplineDerivative(y, t, deriv, y[j]);
}
// Compute cross derivatives.
......
openmmapi/src/TabulatedFunction.cpp
View file @ 4cfeb429
......@@ -35,7 +35,7 @@
using namespace OpenMM;
using namespace std;
Continuous1DFunction::Continuous1DFunction(const std::vector<double>& values, double min, double max) {
Continuous1DFunction::Continuous1DFunction(const vector<double>& values, double min, double max) {
if (max <= min)
throw OpenMMException("Continuous1DFunction: max <= min for a tabulated function.");
if (values.size() < 2)
......@@ -45,13 +45,13 @@ Continuous1DFunction::Continuous1DFunction(const std::vector<double>& values, do
this->max = max;
}
void Continuous1DFunction::getFunctionParameters(std::vector<double>& values, double& min, double& max) const {
void Continuous1DFunction::getFunctionParameters(vector<double>& values, double& min, double& max) const {
values = this->values;
min = this->min;
max = this->max;
}
void Continuous1DFunction::setFunctionParameters(const std::vector<double>& values, double min, double max) {
void Continuous1DFunction::setFunctionParameters(const vector<double>& values, double min, double max) {
if (max <= min)
throw OpenMMException("Continuous1DFunction: max <= min for a tabulated function.");
if (values.size() < 2)
......@@ -61,19 +61,65 @@ void Continuous1DFunction::setFunctionParameters(const std::vector<double>& valu
this->max = max;
}
Discrete1DFunction::Discrete1DFunction(const std::vector<double>& values) {
Continuous2DFunction::Continuous2DFunction(int xsize, int ysize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax) {
if (xsize < 2 || ysize < 2)
throw OpenMMException("Continuous2DFunction: must have at least two points along each axis");
if (values.size() != xsize*ysize)
throw OpenMMException("Continuous2DFunction: incorrect number of values");
if (xmax <= xmin)
throw OpenMMException("Continuous2DFunction: xmax <= xmin for a tabulated function.");
if (ymax <= ymin)
throw OpenMMException("Continuous2DFunction: ymax <= ymin for a tabulated function.");
this->values = values;
this->xsize = xsize;
this->ysize = ysize;
this->xmin = xmin;
this->xmax = xmax;
this->ymin = ymin;
this->ymax = ymax;
}
void Continuous2DFunction::getFunctionParameters(int& xsize, int& ysize, vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const {
values = this->values;
xsize = this->xsize;
ysize = this->ysize;
xmin = this->xmin;
xmax = this->xmax;
ymin = this->ymin;
ymax = this->ymax;
}
void Continuous2DFunction::setFunctionParameters(int xsize, int ysize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax) {
if (xsize < 2 || ysize < 2)
throw OpenMMException("Continuous2DFunction: must have at least two points along each axis");
if (values.size() != xsize*ysize)
throw OpenMMException("Continuous2DFunction: incorrect number of values");
if (xmax <= xmin)
throw OpenMMException("Continuous2DFunction: xmax <= xmin for a tabulated function.");
if (ymax <= ymin)
throw OpenMMException("Continuous2DFunction: ymax <= ymin for a tabulated function.");
this->values = values;
this->xsize = xsize;
this->ysize = ysize;
this->xmin = xmin;
this->xmax = xmax;
this->ymin = ymin;
this->ymax = ymax;
}
Discrete1DFunction::Discrete1DFunction(const vector<double>& values) {
this->values = values;
}
void Discrete1DFunction::getFunctionParameters(std::vector<double>& values) const {
void Discrete1DFunction::getFunctionParameters(vector<double>& values) const {
values = this->values;
}
void Discrete1DFunction::setFunctionParameters(const std::vector<double>& values) {
void Discrete1DFunction::setFunctionParameters(const vector<double>& values) {
this->values = values;
}
Discrete2DFunction::Discrete2DFunction(int xsize, int ysize, const std::vector<double>& values) {
Discrete2DFunction::Discrete2DFunction(int xsize, int ysize, const vector<double>& values) {
if (values.size() != xsize*ysize)
throw OpenMMException("Discrete2DFunction: incorrect number of values");
this->xsize = xsize;
......@@ -81,13 +127,13 @@ Discrete2DFunction::Discrete2DFunction(int xsize, int ysize, const std::vector<d
this->values = values;
}
void Discrete2DFunction::getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values) const {
void Discrete2DFunction::getFunctionParameters(int& xsize, int& ysize, vector<double>& values) const {
xsize = this->xsize;
ysize = this->ysize;
values = this->values;
}
void Discrete2DFunction::setFunctionParameters(int xsize, int ysize, const std::vector<double>& values) {
void Discrete2DFunction::setFunctionParameters(int xsize, int ysize, const vector<double>& values) {
if (values.size() != xsize*ysize)
throw OpenMMException("Discrete2DFunction: incorrect number of values");
this->xsize = xsize;
......@@ -95,7 +141,7 @@ void Discrete2DFunction::setFunctionParameters(int xsize, int ysize, const std::
this->values = values;
}
Discrete3DFunction::Discrete3DFunction(int xsize, int ysize, int zsize, const std::vector<double>& values) {
Discrete3DFunction::Discrete3DFunction(int xsize, int ysize, int zsize, const vector<double>& values) {
if (values.size() != xsize*ysize*zsize)
throw OpenMMException("Discrete3DFunction: incorrect number of values");
this->xsize = xsize;
......@@ -104,14 +150,14 @@ Discrete3DFunction::Discrete3DFunction(int xsize, int ysize, int zsize, const st
this->values = values;
}
void Discrete3DFunction::getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values) const {
void Discrete3DFunction::getFunctionParameters(int& xsize, int& ysize, int& zsize, vector<double>& values) const {
xsize = this->xsize;
ysize = this->ysize;
zsize = this->zsize;
values = this->values;
}
void Discrete3DFunction::setFunctionParameters(int xsize, int ysize, int zsize, const std::vector<double>& values) {
void Discrete3DFunction::setFunctionParameters(int xsize, int ysize, int zsize, const vector<double>& values) {
if (values.size() != xsize*ysize*zsize)
throw OpenMMException("Discrete3DFunction: incorrect number of values");
this->xsize = xsize;
......
platforms/reference/include/ReferenceTabulatedFunction.h
View file @ 4cfeb429
......@@ -60,6 +60,24 @@ private:
std::vector<double> x, values, derivs;
};
/**
* This class adapts a Continuous2DFunction into a Lepton::CustomFunction.
*/
class OPENMM_EXPORT ReferenceContinuous2DFunction : public Lepton::CustomFunction {
public:
ReferenceContinuous2DFunction(const Continuous2DFunction& function);
int getNumArguments() const;
double evaluate(const double* arguments) const;
double evaluateDerivative(const double* arguments, const int* derivOrder) const;
CustomFunction* clone() const;
private:
const Continuous2DFunction& function;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
std::vector<double> x, y, values;
std::vector<std::vector<double> > c;
};
/**
* This class adapts a Discrete1DFunction into a Lepton::CustomFunction.
*/
......
platforms/reference/src/ReferenceTabulatedFunction.cpp
View file @ 4cfeb429
......@@ -41,6 +41,8 @@ using Lepton::CustomFunction;
extern "C" CustomFunction* createReferenceTabulatedFunction(const TabulatedFunction& function) {
if (dynamic_cast<const Continuous1DFunction*>(&function) != NULL)
return new ReferenceContinuous1DFunction(dynamic_cast<const Continuous1DFunction&>(function));
if (dynamic_cast<const Continuous2DFunction*>(&function) != NULL)
return new ReferenceContinuous2DFunction(dynamic_cast<const Continuous2DFunction&>(function));
if (dynamic_cast<const Discrete1DFunction*>(&function) != NULL)
return new ReferenceDiscrete1DFunction(dynamic_cast<const Discrete1DFunction&>(function));
if (dynamic_cast<const Discrete2DFunction*>(&function) != NULL)
......@@ -81,6 +83,51 @@ CustomFunction* ReferenceContinuous1DFunction::clone() const {
return new ReferenceContinuous1DFunction(function);
}
ReferenceContinuous2DFunction::ReferenceContinuous2DFunction(const Continuous2DFunction& function) : function(function) {
function.getFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
x.resize(xsize);
y.resize(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);
SplineFitter::create2DNaturalSpline(x, y, values, c);
}
int ReferenceContinuous2DFunction::getNumArguments() const {
return 2;
}
double ReferenceContinuous2DFunction::evaluate(const double* arguments) const {
double u = arguments[0];
if (u < xmin || u > xmax)
return 0.0;
double v = arguments[1];
if (v < ymin || v > ymax)
return 0.0;
return SplineFitter::evaluate2DSpline(x, y, values, c, u, v);
}
double ReferenceContinuous2DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
double u = arguments[0];
if (u < xmin || u > xmax)
return 0.0;
double v = arguments[1];
if (v < ymin || v > ymax)
return 0.0;
double dx, dy;
SplineFitter::evaluate2DSplineDerivatives(x, y, values, c, u, v, dx, dy);
if (derivOrder[0] == 1 && derivOrder[1] == 0)
return dx;
if (derivOrder[0] == 0 && derivOrder[1] == 1)
return dy;
throw OpenMMException("ReferenceContinuous2DFunction: Unsupported derivative order");
}
CustomFunction* ReferenceContinuous2DFunction::clone() const {
return new ReferenceContinuous2DFunction(function);
}
ReferenceDiscrete1DFunction::ReferenceDiscrete1DFunction(const Discrete1DFunction& function) : function(function) {
function.getFunctionParameters(values);
}
......
platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp
View file @ 4cfeb429
......@@ -244,7 +244,6 @@ 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);
......@@ -267,6 +266,55 @@ 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;
ReferencePlatform platform;
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() {
ReferencePlatform platform;
System system;
......@@ -757,6 +805,7 @@ int main() {
testCutoff();
testPeriodic();
testContinuous1DFunction();
testContinuous2DFunction();
testDiscrete1DFunction();
testDiscrete2DFunction();
testDiscrete3DFunction();
......
tests/TestSplineFitter.cpp
View file @ 4cfeb429
......@@ -103,19 +103,17 @@ void test2DSpline() {
for (int j = 0; j < ysize; j++) {
double value = SplineFitter::evaluate2DSpline(x, y, f, c, x[i], y[j]);
ASSERT_EQUAL_TOL(f[i+j*xsize], value, 1e-6);
double dx, dy;
SplineFitter::evaluate2DSplineDerivatives(x, y, f, c, x[i], y[j], dx, dy);
}
for (int i = 0; i < 10; i++) {
for (int j = 0; j < 10; j++) {
double s = x[0]+(i+1)*(x[xsize-1]-x[0])/11.0;
double t = y[0]+(j+1)*(y[ysize-1]-y[0])/11.0;
double value = SplineFitter::evaluate2DSpline(x, y, f, c, s, t);
ASSERT_EQUAL_TOL(sin(s)*cos(0.4*t), value, 0.05);
ASSERT_EQUAL_TOL(sin(s)*cos(0.4*t), value, 0.02);
double dx, dy;
SplineFitter::evaluate2DSplineDerivatives(x, y, f, c, s, t, dx, dy);
ASSERT_EQUAL_TOL(cos(s)*cos(0.4*t), dx, 0.1);
ASSERT_EQUAL_TOL(-0.4*sin(s)*sin(0.4*t), dy, 0.1);
ASSERT_EQUAL_TOL(cos(s)*cos(0.4*t), dx, 0.05);
ASSERT_EQUAL_TOL(-0.4*sin(s)*sin(0.4*t), dy, 0.05);
}
}
}
......
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