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Commit 18295108 authored by peastman's avatar peastman
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platforms/reference/src/SimTKReference/ReferenceCustomCVForce.cpp 0 → 100644
View file @ 18295108
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* 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 "ReferenceCustomCVForce.h"
#include "ReferencePlatform.h"
#include "ReferenceTabulatedFunction.h"
#include "lepton/CustomFunction.h"
#include "lepton/ParsedExpression.h"
#include "lepton/Parser.h"
using namespace OpenMM;
using namespace std;
ReferenceCustomCVForce::ReferenceCustomCVForce(const CustomCVForce& force) {
// Create custom functions for the tabulated functions.
map<string, Lepton::CustomFunction*> functions;
for (int i = 0; i < (int) force.getNumTabulatedFunctions(); i++)
functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
// Create the expressions.
Lepton::ParsedExpression energyExpr = Lepton::Parser::parse(force.getEnergyFunction(), functions);
energyExpression = energyExpr.createProgram();
for (int i = 0; i < force.getNumCollectiveVariables(); i++) {
string name = force.getCollectiveVariableName(i);
variableNames.push_back(name);
variableDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
}
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
string name = force.getEnergyParameterDerivativeName(i);
paramDerivNames.push_back(name);
paramDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
}
// Delete the custom functions.
for (auto& function : functions)
delete function.second;
}
ReferenceCustomCVForce::~ReferenceCustomCVForce() {
}
void ReferenceCustomCVForce::calculateIxn(ContextImpl& innerContext, vector<Vec3>& atomCoordinates,
const map<string, double>& globalParameters, vector<Vec3>& forces,
double* totalEnergy, map<string, double>& energyParamDerivs) const {
// Compute the collective variables, and their derivatives with respect to particle positions.
int numCVs = variableNames.size();
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(innerContext.getPlatformData());
vector<Vec3>& innerForces = *((vector<Vec3>*) data->forces);
map<string, double>& innerDerivs = *((map<string, double>*) data->energyParameterDerivatives);
vector<double> cvValues;
vector<vector<Vec3> > cvForces;
vector<map<string, double> > cvDerivs;
for (int i = 0; i < numCVs; i++) {
cvValues.push_back(innerContext.calcForcesAndEnergy(true, true, 1<<i));
cvForces.push_back(innerForces);
cvDerivs.push_back(innerDerivs);
}
// Compute the energy and forces.
int numParticles = atomCoordinates.size();
map<string, double> variables = globalParameters;
for (int i = 0; i < numCVs; i++)
variables[variableNames[i]] = cvValues[i];
if (totalEnergy != NULL)
*totalEnergy += energyExpression.evaluate(variables);
for (int i = 0; i < numCVs; i++) {
double dEdV = variableDerivExpressions[i].evaluate(variables);
for (int j = 0; j < numParticles; j++)
forces[j] += cvForces[i][j]*dEdV;
}
// Compute the energy parameter derivatives.
for (int i = 0; i < paramDerivExpressions.size(); i++)
energyParamDerivs[paramDerivNames[i]] += paramDerivExpressions[i].evaluate(variables);
for (int i = 0; i < numCVs; i++) {
double dEdV = variableDerivExpressions[i].evaluate(variables);
for (auto& deriv : cvDerivs[i])
energyParamDerivs[deriv.first] += dEdV*deriv.second;
}
}
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 18295108
/* Portions copyright (c) 2011-2016 Stanford University and Simbios.
/* Portions copyright (c) 2011-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -25,6 +25,7 @@
#include "SimTKOpenMMUtilities.h"
#include "ReferenceVirtualSites.h"
#include "ReferenceCustomDynamics.h"
#include "ReferenceTabulatedFunction.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/ForceImpl.h"
......@@ -113,12 +114,18 @@ void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<double>& m
variableLocations[ename.str()] = &energy;
}
// Create custom functions for the tabulated functions.
map<string, Lepton::CustomFunction*> functions;
for (int i = 0; i < integrator.getNumTabulatedFunctions(); i++)
functions[integrator.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(integrator.getTabulatedFunction(i));
// Parse the expressions.
int numSteps = stepType.size();
vector<int> forceGroup;
vector<vector<ParsedExpression> > expressions;
CustomIntegratorUtilities::analyzeComputations(context, integrator, expressions, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
CustomIntegratorUtilities::analyzeComputations(context, integrator, expressions, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup, functions);
stepExpressions.resize(expressions.size());
for (int i = 0; i < numSteps; i++) {
stepExpressions[i].resize(expressions[i].size());
......@@ -137,6 +144,11 @@ void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<double>& m
if (kineticEnergyExpression.getVariables().find("f") != kineticEnergyExpression.getVariables().end())
kineticEnergyNeedsForce = true;
// Delete the custom functions.
for (auto& function : functions)
delete function.second;
// Record the force group flags for each step.
forceGroupFlags.resize(numSteps, -1);
......@@ -207,19 +219,26 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
for (auto& global : globals)
expressionSet.setVariable(expressionSet.getVariableIndex(global.first), global.second);
oldPos = atomCoordinates;
map<int, double> groupEnergy;
map<int, vector<Vec3> > groupForces;
if (forcesAreValid)
groupForces[context.getLastForceGroups()] = forces;
// Loop over steps and execute them.
for (int step = 0; step < numSteps; ) {
if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || context.getLastForceGroups() != forceGroupFlags[step])) {
int flags = forceGroupFlags[step];
if ((needsForces[step] && groupForces.find(flags) == groupForces.end()) || (needsEnergy[step] && groupEnergy.find(flags) == groupEnergy.end())) {
// Recompute forces and/or energy.
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
double e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeForce)
groupForces[flags] = forces;
if (computeEnergy) {
energy = e;
groupEnergy[flags] = e;
context.getEnergyParameterDerivatives(energyParamDerivs);
}
forcesAreValid = true;
......@@ -227,7 +246,10 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
// Execute the step.
energy = (needsEnergy[step] ? groupEnergy[flags] : 0);
vector<Vec3>& stepForces = (needsForces[step] ? groupForces[flags] : forces);
int nextStep = step+1;
bool stepInvalidatesForces = invalidatesForces[step];
switch (stepType[step]) {
case CustomIntegrator::ComputeGlobal: {
uniform = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
......@@ -250,11 +272,11 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, stepForces, masses, perDof, stepExpressions[step][0]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, stepForces, masses, perDof, stepExpressions[step][0]);
double sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
......@@ -274,7 +296,7 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
stepInvalidatesForces = context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (auto& global : globals)
expressionSet.setVariable(expressionSet.getVariableIndex(global.first), global.second);
......@@ -296,8 +318,11 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
break;
}
}
if (invalidatesForces[step])
if (stepInvalidatesForces) {
forcesAreValid = false;
groupForces.clear();
groupEnergy.clear();
}
step = nextStep;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
......
platforms/reference/src/SimTKReference/ReferenceVirtualSites.cpp
View file @ 18295108
......@@ -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) 2012-2014 Stanford University and the Authors. *
* Portions copyright (c) 2012-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -70,22 +70,30 @@ void ReferenceVirtualSites::computePositions(const OpenMM::System& system, vecto
// A local coordinates site.
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2);
Vec3 originWeights = site.getOriginWeights();
Vec3 xWeights = site.getXWeights();
Vec3 yWeights = site.getYWeights();
int numParticles = site.getNumParticles();
vector<double> originWeights, xWeights, yWeights;
site.getOriginWeights(originWeights);
site.getXWeights(xWeights);
site.getYWeights(yWeights);
Vec3 origin, xdir, ydir;
for (int j = 0; j < numParticles; j++) {
Vec3 pos = atomCoordinates[site.getParticle(j)];
origin += pos*originWeights[j];
xdir += pos*xWeights[j];
ydir += pos*yWeights[j];
}
Vec3 localPosition = site.getLocalPosition();
Vec3 origin = atomCoordinates[p1]*originWeights[0] + atomCoordinates[p2]*originWeights[1] + atomCoordinates[p3]*originWeights[2];
Vec3 xdir = atomCoordinates[p1]*xWeights[0] + atomCoordinates[p2]*xWeights[1] + atomCoordinates[p3]*xWeights[2];
Vec3 ydir = atomCoordinates[p1]*yWeights[0] + atomCoordinates[p2]*yWeights[1] + atomCoordinates[p3]*yWeights[2];
Vec3 zdir = xdir.cross(ydir);
xdir /= sqrt(xdir.dot(xdir));
zdir /= sqrt(zdir.dot(zdir));
double normXdir = sqrt(xdir.dot(xdir));
double normZdir = sqrt(zdir.dot(zdir));
if (normXdir > 0.0)
xdir /= normXdir;
if (normZdir > 0.0)
zdir /= normZdir;
ydir = zdir.cross(xdir);
atomCoordinates[i] = origin + xdir*localPosition[0] + ydir*localPosition[1] + zdir*localPosition[2];
}
}
}
void ReferenceVirtualSites::distributeForces(const OpenMM::System& system, const vector<OpenMM::Vec3>& atomCoordinates, vector<OpenMM::Vec3>& forces) {
......@@ -133,71 +141,53 @@ void ReferenceVirtualSites::distributeForces(const OpenMM::System& system, const
// A local coordinates site.
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2);
Vec3 originWeights = site.getOriginWeights();
Vec3 wx = site.getXWeights();
Vec3 wy = site.getYWeights();
int numParticles = site.getNumParticles();
vector<double> originWeights, wx, wy;
site.getOriginWeights(originWeights);
site.getXWeights(wx);
site.getYWeights(wy);
Vec3 xdir, ydir;
for (int j = 0; j < numParticles; j++) {
Vec3 pos = atomCoordinates[site.getParticle(j)];
xdir += pos*wx[j];
ydir += pos*wy[j];
}
Vec3 localPosition = site.getLocalPosition();
Vec3 xdir = atomCoordinates[p1]*wx[0] + atomCoordinates[p2]*wx[1] + atomCoordinates[p3]*wx[2];
Vec3 ydir = atomCoordinates[p1]*wy[0] + atomCoordinates[p2]*wy[1] + atomCoordinates[p3]*wy[2];
Vec3 zdir = xdir.cross(ydir);
double invNormXdir = 1.0/sqrt(xdir.dot(xdir));
double invNormZdir = 1.0/sqrt(zdir.dot(zdir));
double normXdir = sqrt(xdir.dot(xdir));
double normZdir = sqrt(zdir.dot(zdir));
double invNormXdir = (normXdir > 0.0 ? 1.0/normXdir : 0.0);
double invNormZdir = (normZdir > 0.0 ? 1.0/normZdir : 0.0);
Vec3 dx = xdir*invNormXdir;
Vec3 dz = zdir*invNormZdir;
Vec3 dy = dz.cross(dx);
// The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand.
double t11 = (wx[0]*ydir[0]-wy[0]*xdir[0])*invNormZdir;
double t12 = (wx[0]*ydir[1]-wy[0]*xdir[1])*invNormZdir;
double t13 = (wx[0]*ydir[2]-wy[0]*xdir[2])*invNormZdir;
double t21 = (wx[1]*ydir[0]-wy[1]*xdir[0])*invNormZdir;
double t22 = (wx[1]*ydir[1]-wy[1]*xdir[1])*invNormZdir;
double t23 = (wx[1]*ydir[2]-wy[1]*xdir[2])*invNormZdir;
double t31 = (wx[2]*ydir[0]-wy[2]*xdir[0])*invNormZdir;
double t32 = (wx[2]*ydir[1]-wy[2]*xdir[1])*invNormZdir;
double t33 = (wx[2]*ydir[2]-wy[2]*xdir[2])*invNormZdir;
double sx1 = t13*dz[1]-t12*dz[2];
double sy1 = t11*dz[2]-t13*dz[0];
double sz1 = t12*dz[0]-t11*dz[1];
double sx2 = t23*dz[1]-t22*dz[2];
double sy2 = t21*dz[2]-t23*dz[0];
double sz2 = t22*dz[0]-t21*dz[1];
double sx3 = t33*dz[1]-t32*dz[2];
double sy3 = t31*dz[2]-t33*dz[0];
double sz3 = t32*dz[0]-t31*dz[1];
Vec3 wxScaled = wx*invNormXdir;
vector<double> wxScaled(numParticles);
for (int j = 0; j < numParticles; j++)
wxScaled[j] = wx[j]*invNormXdir;
Vec3 fp1 = localPosition*f[0];
Vec3 fp2 = localPosition*f[1];
Vec3 fp3 = localPosition*f[2];
forces[p1][0] += fp1[0]*wxScaled[0]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx1 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[0] + dy[0]*sx1 - dx[1]*t12 - dx[2]*t13) + f[0]*originWeights[0];
forces[p1][1] += fp1[0]*wxScaled[0]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy1+t13) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[0] + dy[0]*sy1 + dx[1]*t11);
forces[p1][2] += fp1[0]*wxScaled[0]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz1-t12) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[0] + dy[0]*sz1 + dx[2]*t11);
forces[p2][0] += fp1[0]*wxScaled[1]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx2 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[1] + dy[0]*sx2 - dx[1]*t22 - dx[2]*t23) + f[0]*originWeights[1];
forces[p2][1] += fp1[0]*wxScaled[1]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy2+t23) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[1] + dy[0]*sy2 + dx[1]*t21);
forces[p2][2] += fp1[0]*wxScaled[1]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz2-t22) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[1] + dy[0]*sz2 + dx[2]*t21);
forces[p3][0] += fp1[0]*wxScaled[2]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx3 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[2] + dy[0]*sx3 - dx[1]*t32 - dx[2]*t33) + f[0]*originWeights[2];
forces[p3][1] += fp1[0]*wxScaled[2]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy3+t33) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[2] + dy[0]*sy3 + dx[1]*t31);
forces[p3][2] += fp1[0]*wxScaled[2]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz3-t32) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[2] + dy[0]*sz3 + dx[2]*t31);
forces[p1][0] += fp2[0]*wxScaled[0]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx1-t13) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[0] - dy[1]*sx1 - dx[0]*t12);
forces[p1][1] += fp2[0]*wxScaled[0]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy1 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[0] - dy[1]*sy1 + dx[0]*t11 + dx[2]*t13) + f[1]*originWeights[0];
forces[p1][2] += fp2[0]*wxScaled[0]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz1+t11) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[0] - dy[1]*sz1 - dx[2]*t12);
forces[p2][0] += fp2[0]*wxScaled[1]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx2-t23) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[1] - dy[1]*sx2 - dx[0]*t22);
forces[p2][1] += fp2[0]*wxScaled[1]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy2 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[1] - dy[1]*sy2 + dx[0]*t21 + dx[2]*t23) + f[1]*originWeights[1];
forces[p2][2] += fp2[0]*wxScaled[1]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz2+t21) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[1] - dy[1]*sz2 - dx[2]*t22);
forces[p3][0] += fp2[0]*wxScaled[2]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx3-t33) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[2] - dy[1]*sx3 - dx[0]*t32);
forces[p3][1] += fp2[0]*wxScaled[2]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy3 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[2] - dy[1]*sy3 + dx[0]*t31 + dx[2]*t33) + f[1]*originWeights[2];
forces[p3][2] += fp2[0]*wxScaled[2]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz3+t31) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[2] - dy[1]*sz3 - dx[2]*t32);
forces[p1][0] += fp3[0]*wxScaled[0]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx1+t12) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[0] + dy[2]*sx1 + dx[0]*t13);
forces[p1][1] += fp3[0]*wxScaled[0]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy1-t11) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[0] + dy[2]*sy1 + dx[1]*t13);
forces[p1][2] += fp3[0]*wxScaled[0]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz1 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[0] + dy[2]*sz1 - dx[0]*t11 - dx[1]*t12) + f[2]*originWeights[0];
forces[p2][0] += fp3[0]*wxScaled[1]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx2+t22) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[1] + dy[2]*sx2 + dx[0]*t23);
forces[p2][1] += fp3[0]*wxScaled[1]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy2-t21) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[1] + dy[2]*sy2 + dx[1]*t23);
forces[p2][2] += fp3[0]*wxScaled[1]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz2 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[1] + dy[2]*sz2 - dx[0]*t21 - dx[1]*t22) + f[2]*originWeights[1];
forces[p3][0] += fp3[0]*wxScaled[2]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx3+t32) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[2] + dy[2]*sx3 + dx[0]*t33);
forces[p3][1] += fp3[0]*wxScaled[2]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy3-t31) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[2] + dy[2]*sy3 + dx[1]*t33);
forces[p3][2] += fp3[0]*wxScaled[2]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz3 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[2] + dy[2]*sz3 - dx[0]*t31 - dx[1]*t32) + f[2]*originWeights[2];
for (int j = 0; j < numParticles; j++) {
double t1 = (wx[j]*ydir[0]-wy[j]*xdir[0])*invNormZdir;
double t2 = (wx[j]*ydir[1]-wy[j]*xdir[1])*invNormZdir;
double t3 = (wx[j]*ydir[2]-wy[j]*xdir[2])*invNormZdir;
double sx = t3*dz[1]-t2*dz[2];
double sy = t1*dz[2]-t3*dz[0];
double sz = t2*dz[0]-t1*dz[1];
int p = site.getParticle(j);
forces[p][0] += fp1[0]*wxScaled[j]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[j] + dy[0]*sx - dx[1]*t2 - dx[2]*t3) + f[0]*originWeights[j];
forces[p][1] += fp1[0]*wxScaled[j]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy+t3) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[j] + dy[0]*sy + dx[1]*t1);
forces[p][2] += fp1[0]*wxScaled[j]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz-t2) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[j] + dy[0]*sz + dx[2]*t1);
forces[p][0] += fp2[0]*wxScaled[j]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx-t3) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[j] - dy[1]*sx - dx[0]*t2);
forces[p][1] += fp2[0]*wxScaled[j]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[j] - dy[1]*sy + dx[0]*t1 + dx[2]*t3) + f[1]*originWeights[j];
forces[p][2] += fp2[0]*wxScaled[j]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz+t1) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[j] - dy[1]*sz - dx[2]*t2);
forces[p][0] += fp3[0]*wxScaled[j]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx+t2) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[j] + dy[2]*sx + dx[0]*t3);
forces[p][1] += fp3[0]*wxScaled[j]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy-t1) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[j] + dy[2]*sy + dx[1]*t3);
forces[p][2] += fp3[0]*wxScaled[j]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[j] + dy[2]*sz - dx[0]*t1 - dx[1]*t2) + f[2]*originWeights[j];
}
}
}
}
platforms/reference/tests/TestReferenceCustomCVForce.cpp 0 → 100644
View file @ 18295108
/* -------------------------------------------------------------------------- *
* 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) 2017 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 "ReferenceTests.h"
#include "TestCustomCVForce.h"
void runPlatformTests() {
}
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaAngleForceImpl.h
View file @ 18295108
......@@ -53,7 +53,7 @@ public:
const AmoebaAngleForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaBondForceImpl.h
View file @ 18295108
......@@ -54,7 +54,7 @@ public:
const AmoebaBondForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaGeneralizedKirkwoodForceImpl.h
View file @ 18295108
......@@ -50,7 +50,7 @@ public:
const AmoebaGeneralizedKirkwoodForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaInPlaneAngleForceImpl.h
View file @ 18295108
......@@ -53,7 +53,7 @@ public:
const AmoebaInPlaneAngleForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h
View file @ 18295108
......@@ -53,7 +53,7 @@ public:
const AmoebaMultipoleForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaOutOfPlaneBendForceImpl.h
View file @ 18295108
......@@ -53,7 +53,7 @@ public:
const AmoebaOutOfPlaneBendForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaPiTorsionForceImpl.h
View file @ 18295108
......@@ -53,7 +53,7 @@ public:
const AmoebaPiTorsionForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaStretchBendForceImpl.h
View file @ 18295108
......@@ -53,7 +53,7 @@ public:
const AmoebaStretchBendForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaTorsionTorsionForceImpl.h
View file @ 18295108
......@@ -52,7 +52,7 @@ public:
const AmoebaTorsionTorsionForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaVdwForceImpl.h
View file @ 18295108
......@@ -55,7 +55,7 @@ public:
const AmoebaVdwForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaWcaDispersionForceImpl.h
View file @ 18295108
......@@ -53,7 +53,7 @@ public:
const AmoebaWcaDispersionForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
void updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
......
plugins/cpupme/src/CpuPmeKernels.cpp
View file @ 18295108
......@@ -51,7 +51,8 @@ static const int PME_ORDER = 5;
bool CpuCalcDispersionPmeReciprocalForceKernel::hasInitializedThreads = false;
int CpuCalcDispersionPmeReciprocalForceKernel::numThreads = 0;
static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors, gmx_atomic_t& atomicCounter, const float epsilonFactor) {
static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors,
gmx_atomic_t& atomicCounter, const float epsilonFactor, int threadIndex, int numThreads, bool deterministic) {
float temp[4];
fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0);
fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0);
......@@ -65,8 +66,10 @@ static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gri
float posInBox[4] = {0,0,0,0};
memset(grid, 0, sizeof(float)*gridx*gridy*gridz);
int i = threadIndex;
while (true) {
int i = gmx_atomic_fetch_add(&atomicCounter, 1);
if (!deterministic)
i = gmx_atomic_fetch_add(&atomicCounter, 1);
if (i >= numParticles)
break;
......@@ -151,6 +154,8 @@ static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gri
}
}
}
if (deterministic)
i += numThreads;
}
}
......@@ -406,7 +411,7 @@ static void* threadBody(void* args) {
return 0;
}
void CpuCalcPmeReciprocalForceKernel::initialize(int xsize, int ysize, int zsize, int numParticles, double alpha) {
void CpuCalcPmeReciprocalForceKernel::initialize(int xsize, int ysize, int zsize, int numParticles, double alpha, bool deterministic) {
if (!hasInitializedThreads) {
numThreads = getNumProcessors();
char* threadsEnv = getenv("OPENMM_CPU_THREADS");
......@@ -421,6 +426,7 @@ void CpuCalcPmeReciprocalForceKernel::initialize(int xsize, int ysize, int zsize
gridz = findFFTDimension(zsize, true);
this->numParticles = numParticles;
this->alpha = alpha;
this->deterministic = deterministic;
force.resize(4*numParticles);
recipEterm.resize(gridx*gridy*gridz);
......@@ -580,7 +586,7 @@ void CpuCalcPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int i
int complexStart = std::max(1, ((index*complexSize)/numThreads));
int complexEnd = (((index+1)*complexSize)/numThreads);
const float epsilonFactor = sqrt(ONE_4PI_EPS0);
spreadCharge(posq, tempGrid[index], gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter, epsilonFactor);
spreadCharge(posq, tempGrid[index], gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter, epsilonFactor, index, numThreads, deterministic);
threads.syncThreads();
int numGrids = tempGrid.size();
for (int i = gridStart; i < gridEnd; i += 4) {
......@@ -696,7 +702,7 @@ static void* dispersionThreadBody(void* args) {
return 0;
}
void CpuCalcDispersionPmeReciprocalForceKernel::initialize(int xsize, int ysize, int zsize, int numParticles, double alpha) {
void CpuCalcDispersionPmeReciprocalForceKernel::initialize(int xsize, int ysize, int zsize, int numParticles, double alpha, bool deterministic) {
if (!hasInitializedThreads) {
numThreads = getNumProcessors();
char* threadsEnv = getenv("OPENMM_CPU_THREADS");
......@@ -711,6 +717,7 @@ void CpuCalcDispersionPmeReciprocalForceKernel::initialize(int xsize, int ysize,
gridz = findFFTDimension(zsize, true);
this->numParticles = numParticles;
this->alpha = alpha;
this->deterministic = deterministic;
force.resize(4*numParticles);
recipEterm.resize(gridx*gridy*gridz);
......@@ -871,7 +878,7 @@ void CpuCalcDispersionPmeReciprocalForceKernel::runWorkerThread(ThreadPool& thre
int complexStart = std::max(1, ((index*complexSize)/numThreads));
int complexEnd = (((index+1)*complexSize)/numThreads);
const float epsilonFactor = 1.0f;
spreadCharge(posq, tempGrid[index], gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter, epsilonFactor);
spreadCharge(posq, tempGrid[index], gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter, epsilonFactor, index, numThreads, deterministic);
threads.syncThreads();
int numGrids = tempGrid.size();
for (int i = gridStart; i < gridEnd; i += 4) {
......
plugins/cpupme/src/CpuPmeKernels.h
View file @ 18295108
......@@ -62,8 +62,9 @@ public:
* @param gridz the z size of the PME grid
* @param numParticles the number of particles in the system
* @param alpha the Ewald blending parameter
* @param deterministic whether it should attempt to make the resulting forces deterministic
*/
void initialize(int xsize, int ysize, int zsize, int numParticles, double alpha);
void initialize(int xsize, int ysize, int zsize, int numParticles, double alpha, bool deterministic);
~CpuCalcPmeReciprocalForceKernel();
/**
* Begin computing the force and energy.
......@@ -110,6 +111,7 @@ private:
static int numThreads;
int gridx, gridy, gridz, numParticles;
double alpha;
bool deterministic;
bool hasCreatedPlan, isFinished, isDeleted;
std::vector<float> force;
std::vector<float> bsplineModuli[3];
......@@ -153,8 +155,9 @@ public:
* @param gridz the z size of the PME grid
* @param numParticles the number of particles in the system
* @param alpha the Ewald blending parameter
* @param deterministic whether it should attempt to make the resulting forces deterministic
*/
void initialize(int xsize, int ysize, int zsize, int numParticles, double alpha);
void initialize(int xsize, int ysize, int zsize, int numParticles, double alpha, bool deterministic);
~CpuCalcDispersionPmeReciprocalForceKernel();
/**
* Begin computing the force and energy.
......@@ -202,6 +205,7 @@ private:
static int numThreads;
int gridx, gridy, gridz, numParticles;
double alpha;
bool deterministic;
bool hasCreatedPlan, isFinished, isDeleted;
std::vector<float> force;
std::vector<float> bsplineModuli[3];
......
plugins/cpupme/tests/TestCpuPme.cpp
View file @ 18295108
......@@ -535,7 +535,7 @@ void test_water2_dpme_energies_forces_no_exclusions() {
io.posq.push_back(c6);
selfEwaldEnergy += dalpha6 * c6 * c6 / 12.0;
}
pme.initialize(grid, grid, grid, NATOMS, dalpha);
pme.initialize(grid, grid, grid, NATOMS, dalpha, false);
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
pme.beginComputation(io, boxVectors, true);
......@@ -626,7 +626,7 @@ void testPME(bool triclinic) {
sumSquaredCharges += charge*charge;
}
double ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
pme.initialize(gridx, gridy, gridz, numParticles, alpha);
pme.initialize(gridx, gridy, gridz, numParticles, alpha, true);
pme.beginComputation(io, boxVectors, true);
double energy = pme.finishComputation(io);
......
serialization/include/openmm/serialization/CustomCVForceProxy.h 0 → 100644
View file @ 18295108
#ifndef OPENMM_CUSTOMCVFORCE_PROXY_H_
#define OPENMM_CUSTOMCVFORCE_PROXY_H_
/* -------------------------------------------------------------------------- *
* 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) 2017 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 "openmm/internal/windowsExport.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
/**
* This is a proxy for serializing CustomCVForce objects.
*/
class OPENMM_EXPORT CustomCVForceProxy : public SerializationProxy {
public:
CustomCVForceProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
} // namespace OpenMM
#endif /*OPENMM_CUSTOMCVFORCE_PROXY_H_*/
serialization/src/CustomCVForceProxy.cpp 0 → 100644
View file @ 18295108
/* -------------------------------------------------------------------------- *
* 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) 2010-2017 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 "openmm/serialization/CustomCVForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/CustomCVForce.h"
#include <sstream>
using namespace OpenMM;
using namespace std;
CustomCVForceProxy::CustomCVForceProxy() : SerializationProxy("CustomCVForce") {
}
void CustomCVForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 0);
const CustomCVForce& force = *reinterpret_cast<const CustomCVForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setStringProperty("energy", force.getEnergyFunction());
SerializationNode& globalParams = node.createChildNode("GlobalParameters");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
}
SerializationNode& cvs = node.createChildNode("CollectiveVariables");
for (int i = 0; i < force.getNumCollectiveVariables(); i++) {
SerializationNode& node = cvs.createChildNode("CollectiveVariable").setStringProperty("name", force.getCollectiveVariableName(i));
node.createChildNode("Force", &force.getCollectiveVariable(i));
}
SerializationNode& functions = node.createChildNode("Functions");
for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
}
void* CustomCVForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version != 0)
throw OpenMMException("Unsupported version number");
CustomCVForce* force = NULL;
try {
CustomCVForce* force = new CustomCVForce(node.getStringProperty("energy"));
force->setForceGroup(node.getIntProperty("forceGroup", 0));
const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
for (auto& parameter : globalParams.getChildren())
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
for (auto& parameter : energyDerivs.getChildren())
force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
const SerializationNode& cvs = node.getChildNode("CollectiveVariables");
for (auto& cv : cvs.getChildren()) {
string name = cv.getStringProperty("name");
force->addCollectiveVariable(name, cv.getChildren()[0].decodeObject<Force>());
}
const SerializationNode& functions = node.getChildNode("Functions");
for (auto& function : functions.getChildren())
force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
return force;
}
catch (...) {
if (force != NULL)
delete force;
throw;
}
}
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