CpuCustomNonbondedForce.cpp

/* Portions copyright (c) 2009-2022 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
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 * 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
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#include "CpuCustomNonbondedForce.h"
#include "openmm/internal/hardware.h"
#include <cmath>

using namespace OpenMM;
using namespace Lepton;
using namespace std;

CpuCustomNonbondedForce::ThreadData::ThreadData(const CompiledExpression& energyExpression, const CompiledVectorExpression& energyVecExpression,
            const CompiledExpression& forceExpression, const CompiledVectorExpression& forceVecExpression,
            const vector<string>& parameterNames, const std::vector<CompiledExpression> energyParamDerivExpressions,
            const vector<string>& computedValueNames, const vector<CompiledExpression> computedValueExpressions,
            vector<vector<double> >& atomComputedValues) :
            energyExpression(energyExpression), energyVecExpression(energyVecExpression), forceExpression(forceExpression),
            forceVecExpression(forceVecExpression), energyParamDerivExpressions(energyParamDerivExpressions),
            computedValueExpressions(computedValueExpressions), atomComputedValues(atomComputedValues) {
    // Prepare for passing variables to expressions.

    map<string, double*> variableLocations;
    variableLocations["r"] = &r;
    particleParam.resize(2*parameterNames.size());
    computedValues.resize(2*computedValueNames.size());
    for (int i = 0; i < parameterNames.size(); i++) {
        variableLocations[parameterNames[i]+"1"] = &particleParam[i*2];
        variableLocations[parameterNames[i]+"2"] = &particleParam[i*2+1];
    }
    for (int i = 0; i < computedValueNames.size(); i++) {
        variableLocations[computedValueNames[i]+"1"] = &computedValues[i*2];
        variableLocations[computedValueNames[i]+"2"] = &computedValues[i*2+1];
    }
    energyParamDerivs.resize(energyParamDerivExpressions.size());
    this->energyExpression.setVariableLocations(variableLocations);
    this->forceExpression.setVariableLocations(variableLocations);
    expressionSet.registerExpression(this->energyExpression);
    expressionSet.registerExpression(this->forceExpression);
    for (auto& expression : this->energyParamDerivExpressions) {
        expression.setVariableLocations(variableLocations);
        expressionSet.registerExpression(expression);
    }

    // Prepare for passing variables to vectorized expressions.

    map<string, float*> vecVariableLocations;
    int blockSize = getVectorWidth();
    rvec.resize(blockSize);
    vecParticle1Params.resize(blockSize*parameterNames.size());
    vecParticle2Params.resize(blockSize*parameterNames.size());
    vecParticle1Values.resize(blockSize*computedValueNames.size());
    vecParticle2Values.resize(blockSize*computedValueNames.size());
    vecVariableLocations["r"] = rvec.data();
    for (int i = 0; i < parameterNames.size(); i++) {
        vecVariableLocations[parameterNames[i]+"1"] = &vecParticle1Params[i*blockSize];
        vecVariableLocations[parameterNames[i]+"2"] = &vecParticle2Params[i*blockSize];
    }
    for (int i = 0; i < computedValueNames.size(); i++) {
        vecVariableLocations[computedValueNames[i]+"1"] = &vecParticle1Values[i*blockSize];
        vecVariableLocations[computedValueNames[i]+"2"] = &vecParticle2Values[i*blockSize];
    }
    this->energyVecExpression.setVariableLocations(vecVariableLocations);
    this->forceVecExpression.setVariableLocations(vecVariableLocations);

    // Prepare for passing variables to the computed value expressions.

    map<string, double*> valueVariableLocations;
    for (int i = 0; i < parameterNames.size(); i++)
        valueVariableLocations[parameterNames[i]] = &particleParam[i];
    for (auto& expression : this->computedValueExpressions) {
        expression.setVariableLocations(valueVariableLocations);
        expressionSet.registerExpression(expression);
    }
}

CpuCustomNonbondedForce::CpuCustomNonbondedForce(ThreadPool& threads, const CpuNeighborList& neighbors) : cutoff(false), useSwitch(false),
        periodic(false), useInteractionGroups(false), threads(threads), neighborList(&neighbors) {
}

void CpuCustomNonbondedForce::initialize(const ParsedExpression& energyExpression,
            const ParsedExpression& forceExpression, const vector<string>& parameterNames, const vector<set<int> >& exclusions,
            const vector<ParsedExpression> energyParamDerivExpressions, const vector<string>& computedValueNames,
            const vector<ParsedExpression> computedValueExpressions) {
    this->paramNames = parameterNames;
    this->exclusions = exclusions;
    this->computedValueNames = computedValueNames;
    CompiledExpression compiledEnergyExpression = energyExpression.createCompiledExpression();
    CompiledExpression compiledForceExpression = forceExpression.createCompiledExpression();
    CompiledVectorExpression energyVecExpression = energyExpression.createCompiledVectorExpression(getVectorWidth());
    CompiledVectorExpression forceVecExpression = forceExpression.createCompiledVectorExpression(getVectorWidth());
    vector<CompiledExpression> compiledDerivExpressions, compiledValueExpressions;
    for (auto& exp : energyParamDerivExpressions)
        compiledDerivExpressions.push_back(exp.createCompiledExpression());
    for (auto& exp : computedValueExpressions)
        compiledValueExpressions.push_back(exp.createCompiledExpression());
    for (int i = 0; i < threads.getNumThreads(); i++)
        threadData.push_back(new ThreadData(compiledEnergyExpression, energyVecExpression, compiledForceExpression, forceVecExpression, parameterNames,
                compiledDerivExpressions, computedValueNames, compiledValueExpressions, atomComputedValues));
}

CpuCustomNonbondedForce::~CpuCustomNonbondedForce() {
    for (auto data : threadData)
        delete data;
}

void CpuCustomNonbondedForce::setUseCutoff(double distance) {
    cutoff = true;
    cutoffDistance = distance;
  }

void CpuCustomNonbondedForce::setInteractionGroups(const vector<pair<set<int>, set<int> > >& groups) {
    useInteractionGroups = true;
    for (auto& group : groups) {
        const set<int>& set1 = group.first;
        const set<int>& set2 = group.second;
        for (set<int>::const_iterator atom1 = set1.begin(); atom1 != set1.end(); ++atom1) {
            for (set<int>::const_iterator atom2 = set2.begin(); atom2 != set2.end(); ++atom2) {
                if (*atom1 == *atom2 || exclusions[*atom1].find(*atom2) != exclusions[*atom1].end())
                    continue; // This is an excluded interaction.
                if (*atom1 > *atom2 && set1.find(*atom2) != set1.end() && set2.find(*atom1) != set2.end())
                    continue; // Both atoms are in both sets, so skip duplicate interactions.
                groupInteractions.push_back(make_pair(*atom1, *atom2));
            }
        }
    }
}

void CpuCustomNonbondedForce::setUseSwitchingFunction(double distance) {
    useSwitch = true;
    switchingDistance = distance;
}

void CpuCustomNonbondedForce::setPeriodic(Vec3* periodicBoxVectors) {
    assert(cutoff);
    assert(periodicBoxVectors[0][0] >= 2.0*cutoffDistance);
    assert(periodicBoxVectors[1][1] >= 2.0*cutoffDistance);
    assert(periodicBoxVectors[2][2] >= 2.0*cutoffDistance);
    periodic = true;
    this->periodicBoxVectors[0] = periodicBoxVectors[0];
    this->periodicBoxVectors[1] = periodicBoxVectors[1];
    this->periodicBoxVectors[2] = periodicBoxVectors[2];
    recipBoxSize[0] = (float) (1.0/periodicBoxVectors[0][0]);
    recipBoxSize[1] = (float) (1.0/periodicBoxVectors[1][1]);
    recipBoxSize[2] = (float) (1.0/periodicBoxVectors[2][2]);
    periodicBoxVec4.resize(3);
    periodicBoxVec4[0] = fvec4(periodicBoxVectors[0][0], periodicBoxVectors[0][1], periodicBoxVectors[0][2], 0);
    periodicBoxVec4[1] = fvec4(periodicBoxVectors[1][0], periodicBoxVectors[1][1], periodicBoxVectors[1][2], 0);
    periodicBoxVec4[2] = fvec4(periodicBoxVectors[2][0], periodicBoxVectors[2][1], periodicBoxVectors[2][2], 0);
    triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
                 periodicBoxVectors[1][0] != 0.0 || periodicBoxVectors[1][2] != 0.0 ||
                 periodicBoxVectors[2][0] != 0.0 || periodicBoxVectors[2][1] != 0.0);
}


void CpuCustomNonbondedForce::calculatePairIxn(int numberOfAtoms, float* posq, vector<Vec3>& atomCoordinates, vector<vector<double> >& atomParameters,
                                               const map<string, double>& globalParameters, vector<AlignedArray<float> >& threadForce,
                                               bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs) {
    // Record the parameters for the threads.
    
    this->numberOfAtoms = numberOfAtoms;
    this->posq = posq;
    this->atomCoordinates = &atomCoordinates[0];
    this->atomParameters = &atomParameters[0];
    this->globalParameters = &globalParameters;
    this->threadForce = &threadForce;
    this->includeForce = includeForce;
    this->includeEnergy = includeEnergy;
    threadEnergy.resize(threads.getNumThreads());
    atomComputedValues.resize(computedValueNames.size(), vector<double>(numberOfAtoms));
    atomicCounter = 0;
    
    // Signal the threads to start running and wait for them to finish.
    
    threads.execute([&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex); });
    threads.waitForThreads(); // Computed values
    threads.resumeThreads();
    threads.waitForThreads(); // Interactions
    
    // Combine the energies from all the threads.
    
    int numThreads = threads.getNumThreads();
    if (includeEnergy) {
        for (int i = 0; i < numThreads; i++)
            totalEnergy += threadEnergy[i];
    }

    // Combine the energy derivatives from all threads.
    
    int numDerivs = threadData[0]->energyParamDerivs.size();
    for (int i = 0; i < numThreads; i++)
        for (int j = 0; j < numDerivs; j++)
            energyParamDerivs[j] += threadData[i]->energyParamDerivs[j];
}

void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
    int numThreads = threads.getNumThreads();
    int blockSize = getVectorWidth();
    ThreadData& data = *threadData[threadIndex];
    for (auto& param : *globalParameters) {
        data.expressionSet.setVariable(data.expressionSet.getVariableIndex(param.first), param.second);
        try {
            float* p = data.energyVecExpression.getVariablePointer(param.first);
            for (int i = 0; i < blockSize; i++)
                p[i] = param.second;
        }
        catch (...) {
            // The expression doesn't use this parameter.
        }
        try {
            float* p = data.forceVecExpression.getVariablePointer(param.first);
            for (int i = 0; i < blockSize; i++)
                p[i] = param.second;
        }
        catch (...) {
            // The expression doesn't use this parameter.
        }
    }

    // Process computed values for this thread's subset of interactions.

    int numComputedValues = atomComputedValues.size();
    if (numComputedValues > 0) {
        int start = threadIndex*numberOfAtoms/numThreads;
        int end = (threadIndex+1)*numberOfAtoms/numThreads;
        for (int i = start; i < end; i++) {
            for (int j = 0; j < paramNames.size(); j++)
                data.particleParam[j] = atomParameters[i][j];
            for (int j = 0; j < numComputedValues; j++)
                atomComputedValues[j][i] = data.computedValueExpressions[j].evaluate();
        }
    }
    threads.syncThreads();

    // Compute this thread's subset of interactions.

    threadEnergy[threadIndex] = 0;
    double& energy = threadEnergy[threadIndex];
    float* forces = &(*threadForce)[threadIndex][0];
    for (auto& deriv : data.energyParamDerivs)
        deriv = 0.0;
    fvec4 boxSize(periodicBoxVectors[0][0], periodicBoxVectors[1][1], periodicBoxVectors[2][2], 0);
    fvec4 invBoxSize(recipBoxSize[0], recipBoxSize[1], recipBoxSize[2], 0);
    if (useInteractionGroups) {
        // The user has specified interaction groups, so compute only the requested interactions.
        
        int start = threadIndex*groupInteractions.size()/numThreads;
        int end = (threadIndex+1)*groupInteractions.size()/numThreads;
        for (int i = start; i < end; i++) {
            int atom1 = groupInteractions[i].first;
            int atom2 = groupInteractions[i].second;
            for (int j = 0; j < paramNames.size(); j++) {
                data.particleParam[j*2] = atomParameters[atom1][j];
                data.particleParam[j*2+1] = atomParameters[atom2][j];
            }
            for (int j = 0; j < computedValueNames.size(); j++) {
                data.computedValues[j*2] = atomComputedValues[j][atom1];
                data.computedValues[j*2+1] = atomComputedValues[j][atom2];
            }
            calculateOneIxn(atom1, atom2, data, forces, energy, boxSize, invBoxSize);
        }
    }
    else {
        // Get the interactions from the neighbor list.

        while (true) {
            int blockIndex = atomicCounter++;
            if (blockIndex >= neighborList->getNumBlocks())
                break;
            if (data.energyParamDerivs.size() == 0)
                calculateBlockIxn(data, blockIndex, forces, energy, boxSize, invBoxSize);
            else {
                const int blockSize = neighborList->getBlockSize();
                const int32_t* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
                CpuNeighborList::NeighborIterator neighbors = neighborList->getNeighborIterator(blockIndex);
                while (neighbors.next()) {
                    int first = neighbors.getNeighbor();
                    for (int j = 0; j < paramNames.size(); j++)
                        data.particleParam[j*2] = atomParameters[first][j];
                    for (int j = 0; j < computedValueNames.size(); j++)
                        data.computedValues[j*2] = atomComputedValues[j][first];
                    auto exclusions = neighbors.getExclusions();
                    for (int k = 0; k < blockSize; k++) {
                        if ((exclusions & (1<<k)) == 0) {
                            int second = blockAtom[k];
                            for (int j = 0; j < paramNames.size(); j++)
                                data.particleParam[j*2+1] = atomParameters[second][j];
                            for (int j = 0; j < computedValueNames.size(); j++)
                                data.computedValues[j*2+1] = atomComputedValues[j][second];
                            calculateOneIxn(first, second, data, forces, energy, boxSize, invBoxSize);
                        }
                    }
                }
            }
        }
    }
}

void CpuCustomNonbondedForce::calculateOneIxn(int ii, int jj, ThreadData& data, 
        float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
    // Get deltaR, R2, and R between 2 atoms

    fvec4 deltaR;
    fvec4 posI(posq+4*ii);
    fvec4 posJ(posq+4*jj);
    float r2;
    getDeltaR(posI, posJ, deltaR, r2, boxSize, invBoxSize);
    if (cutoff && r2 >= cutoffDistance*cutoffDistance)
        return;
    float r = sqrtf(r2);
    data.r = r;

    // accumulate forces

    double dEdR = (includeForce ? data.forceExpression.evaluate()/r : 0.0);
    double energy = 0.0;
    if (includeEnergy || (useSwitch && r > switchingDistance))
        energy = data.energyExpression.evaluate();
    double switchValue = 1.0;
    if (useSwitch) {
        if (r > switchingDistance) {
            double t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
            switchValue = 1+t*t*t*(-10+t*(15-t*6));
            double switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
            dEdR = switchValue*dEdR + energy*switchDeriv/r;
            energy *= switchValue;
        }
    }
    fvec4 result = deltaR*dEdR;
    (fvec4(forces+4*ii)+result).store(forces+4*ii);
    (fvec4(forces+4*jj)-result).store(forces+4*jj);

    // accumulate energies

    totalEnergy += energy;
    
    // Accumulate energy derivatives.

    for (int i = 0; i < data.energyParamDerivExpressions.size(); i++)
        data.energyParamDerivs[i] += switchValue*data.energyParamDerivExpressions[i].evaluate();
}

void CpuCustomNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, const fvec4& boxSize, const fvec4& invBoxSize) const {
    deltaR = posJ-posI;
    if (periodic) {
        if (triclinic) {
            deltaR -= periodicBoxVec4[2]*floorf(deltaR[2]*recipBoxSize[2]+0.5f);
            deltaR -= periodicBoxVec4[1]*floorf(deltaR[1]*recipBoxSize[1]+0.5f);
            deltaR -= periodicBoxVec4[0]*floorf(deltaR[0]*recipBoxSize[0]+0.5f);
        }
        else {
            fvec4 base = round(deltaR*invBoxSize)*boxSize;
            deltaR = deltaR-base;
        }
    }
    r2 = dot3(deltaR, deltaR);
}