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Commit 91deada7 authored by peastman's avatar peastman
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Merge pull request #341 from peastman/master 

Fixed compilation errors on Windows
parents 492f2c1b 8381aaa8
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platforms/reference/src/ReferenceTabulatedFunction.cpp
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/* -------------------------------------------------------------------------- *
* 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) 2014 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. *
* -------------------------------------------------------------------------- */
#include "ReferenceTabulatedFunction.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/SplineFitter.h"
#include <cmath>
using namespace OpenMM;
using namespace std;
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 Continuous3DFunction*>(&function) != NULL)
return new ReferenceContinuous3DFunction(dynamic_cast<const Continuous3DFunction&>(function));
if (dynamic_cast<const Discrete1DFunction*>(&function) != NULL)
return new ReferenceDiscrete1DFunction(dynamic_cast<const Discrete1DFunction&>(function));
if (dynamic_cast<const Discrete2DFunction*>(&function) != NULL)
return new ReferenceDiscrete2DFunction(dynamic_cast<const Discrete2DFunction&>(function));
if (dynamic_cast<const Discrete3DFunction*>(&function) != NULL)
return new ReferenceDiscrete3DFunction(dynamic_cast<const Discrete3DFunction&>(function));
throw OpenMMException("createReferenceTabulatedFunction: Unknown function type");
}
ReferenceContinuous1DFunction::ReferenceContinuous1DFunction(const Continuous1DFunction& function) : function(function) {
function.getFunctionParameters(values, min, max);
int numValues = values.size();
x.resize(numValues);
for (int i = 0; i < numValues; i++)
x[i] = min+i*(max-min)/(numValues-1);
SplineFitter::createNaturalSpline(x, values, derivs);
}
int ReferenceContinuous1DFunction::getNumArguments() const {
return 1;
}
double ReferenceContinuous1DFunction::evaluate(const double* arguments) const {
double t = arguments[0];
if (t < min || t > max)
return 0.0;
return SplineFitter::evaluateSpline(x, values, derivs, t);
}
double ReferenceContinuous1DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
double t = arguments[0];
if (t < min || t > max)
return 0.0;
return SplineFitter::evaluateSplineDerivative(x, values, derivs, t);
}
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);
}
ReferenceContinuous3DFunction::ReferenceContinuous3DFunction(const Continuous3DFunction& function) : function(function) {
function.getFunctionParameters(xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax);
x.resize(xsize);
y.resize(ysize);
z.resize(zsize);
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);
for (int i = 0; i < zsize; i++)
z[i] = zmin+i*(zmax-zmin)/(zsize-1);
SplineFitter::create3DNaturalSpline(x, y, z, values, c);
}
int ReferenceContinuous3DFunction::getNumArguments() const {
return 3;
}
double ReferenceContinuous3DFunction::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;
double w = arguments[2];
if (w < zmin || w > zmax)
return 0.0;
return SplineFitter::evaluate3DSpline(x, y, z, values, c, u, v, w);
}
double ReferenceContinuous3DFunction::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 w = arguments[2];
if (w < zmin || w > zmax)
return 0.0;
double dx, dy, dz;
SplineFitter::evaluate3DSplineDerivatives(x, y, z, values, c, u, v, w, dx, dy, dz);
if (derivOrder[0] == 1 && derivOrder[1] == 0 && derivOrder[2] == 0)
return dx;
if (derivOrder[0] == 0 && derivOrder[1] == 1 && derivOrder[2] == 0)
return dy;
if (derivOrder[0] == 0 && derivOrder[1] == 0 && derivOrder[2] == 1)
return dz;
throw OpenMMException("ReferenceContinuous3DFunction: Unsupported derivative order");
}
CustomFunction* ReferenceContinuous3DFunction::clone() const {
return new ReferenceContinuous3DFunction(function);
}
ReferenceDiscrete1DFunction::ReferenceDiscrete1DFunction(const Discrete1DFunction& function) : function(function) {
function.getFunctionParameters(values);
}
int ReferenceDiscrete1DFunction::getNumArguments() const {
return 1;
}
double ReferenceDiscrete1DFunction::evaluate(const double* arguments) const {
int i = (int) round(arguments[0]);
if (i < 0 || i >= values.size())
throw OpenMMException("ReferenceDiscrete1DFunction: argument out of range");
return values[i];
}
double ReferenceDiscrete1DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
return 0.0;
}
CustomFunction* ReferenceDiscrete1DFunction::clone() const {
return new ReferenceDiscrete1DFunction(function);
}
ReferenceDiscrete2DFunction::ReferenceDiscrete2DFunction(const Discrete2DFunction& function) : function(function) {
function.getFunctionParameters(xsize, ysize, values);
}
int ReferenceDiscrete2DFunction::getNumArguments() const {
return 2;
}
double ReferenceDiscrete2DFunction::evaluate(const double* arguments) const {
int i = (int) round(arguments[0]);
int j = (int) round(arguments[1]);
if (i < 0 || i >= xsize || j < 0 || j >= ysize)
throw OpenMMException("ReferenceDiscrete2DFunction: argument out of range");
return values[i+j*xsize];
}
double ReferenceDiscrete2DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
return 0.0;
}
CustomFunction* ReferenceDiscrete2DFunction::clone() const {
return new ReferenceDiscrete2DFunction(function);
}
ReferenceDiscrete3DFunction::ReferenceDiscrete3DFunction(const Discrete3DFunction& function) : function(function) {
function.getFunctionParameters(xsize, ysize, zsize, values);
}
int ReferenceDiscrete3DFunction::getNumArguments() const {
return 3;
}
double ReferenceDiscrete3DFunction::evaluate(const double* arguments) const {
int i = (int) round(arguments[0]);
int j = (int) round(arguments[1]);
int k = (int) round(arguments[2]);
if (i < 0 || i >= xsize || j < 0 || j >= ysize || k < 0 || k >= zsize)
throw OpenMMException("ReferenceDiscrete3DFunction: argument out of range");
return values[i+(j+k*ysize)*xsize];
}
double ReferenceDiscrete3DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
return 0.0;
}
CustomFunction* ReferenceDiscrete3DFunction::clone() const {
return new ReferenceDiscrete3DFunction(function);
}
/* -------------------------------------------------------------------------- *
* 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) 2014 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. *
* -------------------------------------------------------------------------- */
#include "ReferenceTabulatedFunction.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/SplineFitter.h"
using namespace OpenMM;
using namespace std;
using Lepton::CustomFunction;
/**
* We need to define this ourselves, since Visual Studio is missing round() from cmath.
*/
static int round(double x) {
return (int) (x+0.5);
}
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 Continuous3DFunction*>(&function) != NULL)
return new ReferenceContinuous3DFunction(dynamic_cast<const Continuous3DFunction&>(function));
if (dynamic_cast<const Discrete1DFunction*>(&function) != NULL)
return new ReferenceDiscrete1DFunction(dynamic_cast<const Discrete1DFunction&>(function));
if (dynamic_cast<const Discrete2DFunction*>(&function) != NULL)
return new ReferenceDiscrete2DFunction(dynamic_cast<const Discrete2DFunction&>(function));
if (dynamic_cast<const Discrete3DFunction*>(&function) != NULL)
return new ReferenceDiscrete3DFunction(dynamic_cast<const Discrete3DFunction&>(function));
throw OpenMMException("createReferenceTabulatedFunction: Unknown function type");
}
ReferenceContinuous1DFunction::ReferenceContinuous1DFunction(const Continuous1DFunction& function) : function(function) {
function.getFunctionParameters(values, min, max);
int numValues = values.size();
x.resize(numValues);
for (int i = 0; i < numValues; i++)
x[i] = min+i*(max-min)/(numValues-1);
SplineFitter::createNaturalSpline(x, values, derivs);
}
int ReferenceContinuous1DFunction::getNumArguments() const {
return 1;
}
double ReferenceContinuous1DFunction::evaluate(const double* arguments) const {
double t = arguments[0];
if (t < min || t > max)
return 0.0;
return SplineFitter::evaluateSpline(x, values, derivs, t);
}
double ReferenceContinuous1DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
double t = arguments[0];
if (t < min || t > max)
return 0.0;
return SplineFitter::evaluateSplineDerivative(x, values, derivs, t);
}
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);
}
ReferenceContinuous3DFunction::ReferenceContinuous3DFunction(const Continuous3DFunction& function) : function(function) {
function.getFunctionParameters(xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax);
x.resize(xsize);
y.resize(ysize);
z.resize(zsize);
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);
for (int i = 0; i < zsize; i++)
z[i] = zmin+i*(zmax-zmin)/(zsize-1);
SplineFitter::create3DNaturalSpline(x, y, z, values, c);
}
int ReferenceContinuous3DFunction::getNumArguments() const {
return 3;
}
double ReferenceContinuous3DFunction::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;
double w = arguments[2];
if (w < zmin || w > zmax)
return 0.0;
return SplineFitter::evaluate3DSpline(x, y, z, values, c, u, v, w);
}
double ReferenceContinuous3DFunction::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 w = arguments[2];
if (w < zmin || w > zmax)
return 0.0;
double dx, dy, dz;
SplineFitter::evaluate3DSplineDerivatives(x, y, z, values, c, u, v, w, dx, dy, dz);
if (derivOrder[0] == 1 && derivOrder[1] == 0 && derivOrder[2] == 0)
return dx;
if (derivOrder[0] == 0 && derivOrder[1] == 1 && derivOrder[2] == 0)
return dy;
if (derivOrder[0] == 0 && derivOrder[1] == 0 && derivOrder[2] == 1)
return dz;
throw OpenMMException("ReferenceContinuous3DFunction: Unsupported derivative order");
}
CustomFunction* ReferenceContinuous3DFunction::clone() const {
return new ReferenceContinuous3DFunction(function);
}
ReferenceDiscrete1DFunction::ReferenceDiscrete1DFunction(const Discrete1DFunction& function) : function(function) {
function.getFunctionParameters(values);
}
int ReferenceDiscrete1DFunction::getNumArguments() const {
return 1;
}
double ReferenceDiscrete1DFunction::evaluate(const double* arguments) const {
int i = round(arguments[0]);
if (i < 0 || i >= values.size())
throw OpenMMException("ReferenceDiscrete1DFunction: argument out of range");
return values[i];
}
double ReferenceDiscrete1DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
return 0.0;
}
CustomFunction* ReferenceDiscrete1DFunction::clone() const {
return new ReferenceDiscrete1DFunction(function);
}
ReferenceDiscrete2DFunction::ReferenceDiscrete2DFunction(const Discrete2DFunction& function) : function(function) {
function.getFunctionParameters(xsize, ysize, values);
}
int ReferenceDiscrete2DFunction::getNumArguments() const {
return 2;
}
double ReferenceDiscrete2DFunction::evaluate(const double* arguments) const {
int i = round(arguments[0]);
int j = round(arguments[1]);
if (i < 0 || i >= xsize || j < 0 || j >= ysize)
throw OpenMMException("ReferenceDiscrete2DFunction: argument out of range");
return values[i+j*xsize];
}
double ReferenceDiscrete2DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
return 0.0;
}
CustomFunction* ReferenceDiscrete2DFunction::clone() const {
return new ReferenceDiscrete2DFunction(function);
}
ReferenceDiscrete3DFunction::ReferenceDiscrete3DFunction(const Discrete3DFunction& function) : function(function) {
function.getFunctionParameters(xsize, ysize, zsize, values);
}
int ReferenceDiscrete3DFunction::getNumArguments() const {
return 3;
}
double ReferenceDiscrete3DFunction::evaluate(const double* arguments) const {
int i = round(arguments[0]);
int j = round(arguments[1]);
int k = round(arguments[2]);
if (i < 0 || i >= xsize || j < 0 || j >= ysize || k < 0 || k >= zsize)
throw OpenMMException("ReferenceDiscrete3DFunction: argument out of range");
return values[i+(j+k*ysize)*xsize];
}
double ReferenceDiscrete3DFunction::evaluateDerivative(const double* arguments, const int* derivOrder) const {
return 0.0;
}
CustomFunction* ReferenceDiscrete3DFunction::clone() const {
return new ReferenceDiscrete3DFunction(function);
}
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