CustomManyParticleForceImpl.cpp

/* -------------------------------------------------------------------------- *
 *                                   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) 2008-2014 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
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 * The above copyright notice and this permission notice shall be included in *
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#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomManyParticleForceImpl.h"
#include "openmm/kernels.h"
#include "lepton/Operation.h"
#include "lepton/Parser.h"
#include <sstream>

using namespace OpenMM;
using Lepton::CustomFunction;
using Lepton::ExpressionTreeNode;
using Lepton::Operation;
using Lepton::ParsedExpression;
using std::map;
using std::pair;
using std::vector;
using std::set;
using std::string;
using std::stringstream;

/**
 * This class serves as a placeholder for angles and dihedrals in expressions.
 */
class CustomManyParticleForceImpl::FunctionPlaceholder : public CustomFunction {
public:
    int numArguments;
    FunctionPlaceholder(int numArguments) : numArguments(numArguments) {
    }
    int getNumArguments() const {
        return numArguments;
    }
    double evaluate(const double* arguments) const {
        return 0.0;
    }
    double evaluateDerivative(const double* arguments, const int* derivOrder) const {
        return 0.0;
    }
    CustomFunction* clone() const {
        return new FunctionPlaceholder(numArguments);
    }
};

CustomManyParticleForceImpl::CustomManyParticleForceImpl(const CustomManyParticleForce& owner) : owner(owner) {
}

CustomManyParticleForceImpl::~CustomManyParticleForceImpl() {
}

void CustomManyParticleForceImpl::initialize(ContextImpl& context) {
    kernel = context.getPlatform().createKernel(CalcCustomManyParticleForceKernel::Name(), context);

    // Check for errors in the specification of parameters and exclusions.

    const System& system = context.getSystem();
    if (owner.getNumParticles() != system.getNumParticles())
        throw OpenMMException("CustomManyParticleForce must have exactly as many particles as the System it belongs to.");
    vector<set<int> > exclusions(owner.getNumParticles());
    vector<double> parameters;
    int type;
    int numParameters = owner.getNumPerParticleParameters();
    for (int i = 0; i < owner.getNumParticles(); i++) {
        owner.getParticleParameters(i, parameters, type);
        if (parameters.size() != numParameters) {
            stringstream msg;
            msg << "CustomManyParticleForce: Wrong number of parameters for particle ";
            msg << i;
            throw OpenMMException(msg.str());
        }
    }
    for (int i = 0; i < owner.getNumExclusions(); i++) {
        int particle1, particle2;
        owner.getExclusionParticles(i, particle1, particle2);
        if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
            stringstream msg;
            msg << "CustomManyParticleForce: Illegal particle index for an exclusion: ";
            msg << particle1;
            throw OpenMMException(msg.str());
        }
        if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
            stringstream msg;
            msg << "CustomManyParticleForce: Illegal particle index for an exclusion: ";
            msg << particle2;
            throw OpenMMException(msg.str());
        }
        if (exclusions[particle1].count(particle2) > 0 || exclusions[particle2].count(particle1) > 0) {
            stringstream msg;
            msg << "CustomManyParticleForce: Multiple exclusions are specified for particles ";
            msg << particle1;
            msg << " and ";
            msg << particle2;
            throw OpenMMException(msg.str());
        }
        exclusions[particle1].insert(particle2);
        exclusions[particle2].insert(particle1);
    }
    if (owner.getNonbondedMethod() == CustomManyParticleForce::CutoffPeriodic) {
        Vec3 boxVectors[3];
        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
        double cutoff = owner.getCutoffDistance();
        if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
            throw OpenMMException("CustomManyParticleForce: The cutoff distance cannot be greater than half the periodic box size.");
    }
    kernel.getAs<CalcCustomManyParticleForceKernel>().initialize(context.getSystem(), owner);
}

double CustomManyParticleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
    if ((groups&(1<<owner.getForceGroup())) != 0)
        return kernel.getAs<CalcCustomManyParticleForceKernel>().execute(context, includeForces, includeEnergy);
    return 0.0;
}

vector<string> CustomManyParticleForceImpl::getKernelNames() {
    vector<string> names;
    names.push_back(CalcCustomManyParticleForceKernel::Name());
    return names;
}

map<string, double> CustomManyParticleForceImpl::getDefaultParameters() {
    map<string, double> parameters;
    for (int i = 0; i < owner.getNumGlobalParameters(); i++)
        parameters[owner.getGlobalParameterName(i)] = owner.getGlobalParameterDefaultValue(i);
    return parameters;
}

ParsedExpression CustomManyParticleForceImpl::prepareExpression(const CustomManyParticleForce& force, const map<string, CustomFunction*>& customFunctions, map<string, vector<int> >& distances,
        map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
    CustomManyParticleForceImpl::FunctionPlaceholder custom(1);
    CustomManyParticleForceImpl::FunctionPlaceholder distance(2);
    CustomManyParticleForceImpl::FunctionPlaceholder angle(3);
    CustomManyParticleForceImpl::FunctionPlaceholder dihedral(4);
    map<string, CustomFunction*> functions = customFunctions;
    functions["distance"] = &distance;
    functions["angle"] = &angle;
    functions["dihedral"] = &dihedral;
    ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
    map<string, int> atoms;
    for (int i = 0; i < force.getNumParticlesPerSet(); i++) {
        stringstream name;
        name << 'p' << (i+1);
        atoms[name.str()] = i;
    }
    return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals)).optimize();
}

ExpressionTreeNode CustomManyParticleForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
    const Operation& op = node.getOperation();
    if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
    {
        // This is not an angle or dihedral, so process its children.

        vector<ExpressionTreeNode> children;
        for (int i = 0; i < (int) node.getChildren().size(); i++)
            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals));
        return ExpressionTreeNode(op.clone(), children);
    }
    const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

    // Identify the atoms this term is based on.

    int numArgs = custom.getNumArguments();
    vector<int> indices(numArgs);
    for (int i = 0; i < numArgs; i++) {
        map<string, int>::const_iterator iter = atoms.find(node.getChildren()[i].getOperation().getName());
        if (iter == atoms.end())
            throw OpenMMException("CustomManyParticleForce: Unknown particle '"+node.getChildren()[i].getOperation().getName()+"'");
        indices[i] = iter->second;
    }
    
    // Select a name for the variable and add it to the appropriate map.
    
    stringstream variable;
    if (numArgs == 2)
        variable << "distance";
    else if (numArgs == 3)
        variable << "angle";
    else
        variable << "dihedral";
    for (int i = 0; i < numArgs; i++)
        variable << indices[i];
    string name = variable.str();
    if (numArgs == 2)
        distances[name] = indices;
    else if (numArgs == 3)
        angles[name] = indices;
    else
        dihedrals[name] = indices;
    
    // Return a new node that represents it as a simple variable.
    
    return ExpressionTreeNode(new Operation::Variable(name));
}

void CustomManyParticleForceImpl::updateParametersInContext(ContextImpl& context) {
    kernel.getAs<CalcCustomManyParticleForceKernel>().copyParametersToContext(context, owner);
}