NoseHooverIntegrator.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) 2019-2020 Stanford University and the Authors.      *
 * Authors: Andreas Krämer and Andrew C. Simmonett                            *
 * Contributors: Peter Eastman                                                *
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#include "openmm/NoseHooverIntegrator.h"
#include "openmm/Context.h"
#include "openmm/Force.h"
#include "openmm/System.h"
#include "openmm/NoseHooverChain.h"
#include "openmm/OpenMMException.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/kernels.h"
#include <iostream>
#include <string>
#include <algorithm>

using namespace OpenMM;
using std::string;
using std::vector;

NoseHooverIntegrator::NoseHooverIntegrator(double stepSize):
    forcesAreValid(false),
    hasSubsystemThermostats_(true)
{
    setStepSize(stepSize);
    setConstraintTolerance(1e-5);
    setMaximumPairDistance(0.0);
}
NoseHooverIntegrator::NoseHooverIntegrator(double temperature, double collisionFrequency, double stepSize,
                                           int chainLength, int numMTS, int numYoshidaSuzuki) : 
    forcesAreValid(false),
    hasSubsystemThermostats_(false) {

    setStepSize(stepSize);
    setConstraintTolerance(1e-5);
    setMaximumPairDistance(0.0);
    addThermostat(temperature, collisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
}

NoseHooverIntegrator::~NoseHooverIntegrator() {}

int NoseHooverIntegrator::addThermostat(double temperature, double collisionFrequency,
                                        int chainLength, int numMTS, int numYoshidaSuzuki) {
    if (temperature < 0)
        throw OpenMMException("NoseHooverIntegrator: temperature cannot be negative");
    if (collisionFrequency <= 0)
        throw OpenMMException("NoseHooverIntegrator: collisionFrequency must be positive");
    if (chainLength <= 0)
        throw OpenMMException("NoseHooverIntegrator: chainLength must be positive");
    if (numMTS < 0)
        throw OpenMMException("NoseHooverIntegrator: numMTS must be positive");
    if (numYoshidaSuzuki != 1 && numYoshidaSuzuki != 3 && numYoshidaSuzuki != 5 && numYoshidaSuzuki != 7)
        throw OpenMMException("NoseHooverIntegrator: numYoshidaSuzuki must be 1, 3, 5, or 7");
    hasSubsystemThermostats_ = false;
    return addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int, int>>(), temperature,
                                  collisionFrequency, temperature, collisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
}

int NoseHooverIntegrator::addSubsystemThermostat(const std::vector<int>& thermostatedParticles,
                                                 const std::vector< std::pair< int, int> > &thermostatedPairs,
                                                 double temperature, double collisionFrequency,
                                                 double relativeTemperature, double relativeCollisionFrequency,
                                                 int chainLength, int numMTS, int numYoshidaSuzuki) {
    if (temperature < 0)
        throw OpenMMException("NoseHooverIntegrator: temperature cannot be negative");
    if (relativeTemperature < 0)
        throw OpenMMException("NoseHooverIntegrator: relativeTemperature cannot be negative");
    if (collisionFrequency <= 0)
        throw OpenMMException("NoseHooverIntegrator: collisionFrequency must be positive");
    if (relativeCollisionFrequency <= 0)
        throw OpenMMException("NoseHooverIntegrator: relativeCollisionFrequency must be positive");
    if (chainLength <= 0)
        throw OpenMMException("NoseHooverIntegrator: chainLength must be positive");
    if (numMTS < 0)
        throw OpenMMException("NoseHooverIntegrator: numMTS must be positive");
    if (numYoshidaSuzuki != 1 && numYoshidaSuzuki != 3 && numYoshidaSuzuki != 5 && numYoshidaSuzuki != 7)
        throw OpenMMException("NoseHooverIntegrator: numYoshidaSuzuki must be 1, 3, 5, or 7");
    int chainID = noseHooverChains.size();
    // check if one thermostat already applies to all atoms or pairs
    if ( (chainID > 0) && (noseHooverChains[0].getThermostatedAtoms().size()+noseHooverChains[0].getThermostatedPairs().size() == 0) ) {
        throw OpenMMException(
            "Cannot add thermostat, since one of the thermostats already in the integrator applies to all particles. "
            "To manually add thermostats, use the constructor that takes only the "
            "step size as an input argument."
        );
    }
    int nDOF = 0; // is set in initializeThermostats()
    noseHooverChains.emplace_back(temperature, relativeTemperature,
                                 collisionFrequency, relativeCollisionFrequency,
                                 nDOF, chainLength, numMTS,
                                 numYoshidaSuzuki, chainID,
                                 thermostatedParticles, thermostatedPairs);
    return chainID;
}

const NoseHooverChain& NoseHooverIntegrator::getThermostat(int chainID) const {
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    return noseHooverChains[chainID];
}

void NoseHooverIntegrator::initializeThermostats(const System &system) {

    allAtoms.clear();
    allPairs.clear();
    std::set<int> allAtomsSet;
    for (int atom = 0; atom < system.getNumParticles(); ++atom) allAtomsSet.insert(atom);

    for (auto &thermostat : noseHooverChains) {
        const auto &thermostatedParticles = thermostat.getThermostatedAtoms();
        const auto &thermostatedPairs = thermostat.getThermostatedPairs();

        for( auto& pair : thermostatedPairs ) {
            allAtomsSet.erase(pair.first);
            allAtomsSet.erase(pair.second);
            allPairs.emplace_back(pair.first, pair.second, thermostat.getRelativeTemperature());
        }

        // figure out the number of DOFs
        int nDOF = 3*(thermostatedParticles.size() + thermostatedPairs.size());
        for (int constraintNum = 0; constraintNum < system.getNumConstraints(); constraintNum++) {
            int particle1, particle2;
            double distance;
            system.getConstraintParameters(constraintNum, particle1, particle2, distance);
            bool particle1_in_thermostatedParticles = ((std::find(thermostatedParticles.begin(),
                                                                  thermostatedParticles.end(), particle1)
                                                                    != thermostatedParticles.end())) ||
                                                      (std::find_if(thermostatedPairs.begin(),
                                                                    thermostatedPairs.end(),
                                                                    [&particle1](const std::pair<int, int>& pair){
                                                                           return pair.first == particle1 || pair.second == particle1;})
                                                                      != thermostatedPairs.end());
            bool particle2_in_thermostatedParticles = ((std::find(thermostatedParticles.begin(),
                                                                  thermostatedParticles.end(), particle2)
                                                                    != thermostatedParticles.end())) ||
                                                      (std::find_if(thermostatedPairs.begin(),
                                                                    thermostatedPairs.end(),
                                                                    [&particle2](const std::pair<int, int>& pair){
                                                                           return pair.first == particle2 || pair.second == particle2;})
                                                                      != thermostatedPairs.end());
            if ((system.getParticleMass(particle1) > 0) && (system.getParticleMass(particle2) > 0)){
                if ((particle1_in_thermostatedParticles && !particle2_in_thermostatedParticles) ||
                     (!particle1_in_thermostatedParticles && particle2_in_thermostatedParticles)){
                    throw OpenMMException("Cannot add only one of particles " + std::to_string(particle1) + " and " + std::to_string(particle2)
                                            + " to NoseHooverChain, because they are connected by a constraint.");
                }
                if (particle1_in_thermostatedParticles && particle2_in_thermostatedParticles){
                    nDOF -= 1;
                }
            }
        }

        // remove 3 degrees of freedom from thermostats that act on absolute motions
        int numForces = system.getNumForces();
        if (thermostatedPairs.size() == 0){
            for (int forceNum = 0; forceNum < numForces; ++forceNum) {
                if (dynamic_cast<const CMMotionRemover*>(&system.getForce(forceNum))) nDOF -= 3;
            }
        }

        // set number of DoFs for chain 
        thermostat.setNumDegreesOfFreedom(nDOF);
    }


    for (int chain1 = 0; chain1 < noseHooverChains.size(); ++chain1){
        const auto& nhc = noseHooverChains[chain1];

       // make sure that thermostats do not overlap
        for (int chain2 = 0; chain2 < chain1; ++chain2){
            const auto& other_nhc = noseHooverChains[chain2];
            for (auto &particle: nhc.getThermostatedAtoms()){
                bool isParticleInOtherChain = (std::find(other_nhc.getThermostatedAtoms().begin(),
                                                         other_nhc.getThermostatedAtoms().end(),
                                                         particle) != other_nhc.getThermostatedAtoms().end()) ||
                                              (std::find_if(other_nhc.getThermostatedPairs().begin(),
                                                            other_nhc.getThermostatedPairs().end(),
                                               [&particle](const std::pair<int, int>& pair){ return pair.first == particle || pair.second == particle;})
                                                  != other_nhc.getThermostatedPairs().end());
                if (isParticleInOtherChain){
                    throw OpenMMException("Found particle " + std::to_string(particle) + "in a different NoseHooverChain, "
                                          "but particles can only be thermostated by one thermostat.");
                }
            }
            for (auto &pair: nhc.getThermostatedPairs()){
                bool isParticleInOtherChain = (std::find(other_nhc.getThermostatedAtoms().begin(),
                                                         other_nhc.getThermostatedAtoms().end(),
                                                         pair.first) != other_nhc.getThermostatedAtoms().end()) ||
                                              (std::find(other_nhc.getThermostatedAtoms().begin(),
                                                         other_nhc.getThermostatedAtoms().end(),
                                                         pair.second) != other_nhc.getThermostatedAtoms().end()) ||
                                              (std::find_if(other_nhc.getThermostatedPairs().begin(),
                                                            other_nhc.getThermostatedPairs().end(),
                                               [&pair](const std::pair<int, int>& other_pair){
                                                        return pair.first == other_pair.first || pair.first == other_pair.second ||
                                                               pair.second == other_pair.first || pair.second == other_pair.second;})
                                                  != other_nhc.getThermostatedPairs().end());
                if (isParticleInOtherChain){
                    throw OpenMMException("Found pair " + std::to_string(pair.first) + "," +
                                          std::to_string(pair.second) + " in a different NoseHooverChain, "
                                          "but particles can only be thermostated by one thermostat.");
                }
            }
        }

        // make sure that massless particles are not thermostated
        for(auto particle: nhc.getThermostatedAtoms()){
            double mass = system.getParticleMass(particle);
            if (mass == 0.0) {
                throw OpenMMException("Found a particle with no mass (" + std::to_string(particle) + ") in a thermostat. Massless particles cannot be thermostated.");
            }
        }
    }

    for(const auto& atom : allAtomsSet) allAtoms.push_back(atom);
}

double NoseHooverIntegrator::getTemperature(int chainID) const {
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    return noseHooverChains[chainID].getTemperature();
}

void NoseHooverIntegrator::setTemperature(double temperature, int chainID){
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    noseHooverChains[chainID].setTemperature(temperature);

}

double NoseHooverIntegrator::getRelativeTemperature(int chainID) const {
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    return noseHooverChains[chainID].getRelativeTemperature();
}

void NoseHooverIntegrator::setRelativeTemperature(double temperature, int chainID){
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    noseHooverChains[chainID].setRelativeTemperature(temperature);

}

double NoseHooverIntegrator::getCollisionFrequency(int chainID) const {
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    return noseHooverChains[chainID].getCollisionFrequency();
}

void NoseHooverIntegrator::setCollisionFrequency(double frequency, int chainID){
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    noseHooverChains[chainID].setCollisionFrequency(frequency);
}

double NoseHooverIntegrator::getRelativeCollisionFrequency(int chainID) const {
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    return noseHooverChains[chainID].getRelativeCollisionFrequency();
}

void NoseHooverIntegrator::setRelativeCollisionFrequency(double frequency, int chainID){
    ASSERT_VALID_INDEX(chainID, noseHooverChains);
    noseHooverChains[chainID].setRelativeCollisionFrequency(frequency);
}

double NoseHooverIntegrator::computeKineticEnergy() {
    forcesAreValid = false;
    double kE = 0.0;
    if(noseHooverChains.size() > 0) {
        for (const auto &nhc: noseHooverChains){
            kE += kernel.getAs<IntegrateNoseHooverStepKernel>().computeMaskedKineticEnergy(*context, nhc, true).first;
        }
    } else {
        kE = kernel.getAs<IntegrateNoseHooverStepKernel>().computeKineticEnergy(*context, *this);
    }
    return kE;
}

bool NoseHooverIntegrator::kineticEnergyRequiresForce() const {
    return false;
}

double NoseHooverIntegrator::computeHeatBathEnergy() {
    double energy = 0;
    for(auto &nhc : noseHooverChains) {
        if (context && (nhc.getNumDegreesOfFreedom() > 0)) {
            energy += kernel.getAs<IntegrateNoseHooverStepKernel>().computeHeatBathEnergy(*context, nhc);
        }
    }
    return energy;
}

void NoseHooverIntegrator::initialize(ContextImpl& contextRef) {
    if (owner != NULL && &contextRef.getOwner() != owner)
        throw OpenMMException("This Integrator is already bound to a context");

    context = &contextRef;
    const System& system = context->getSystem();
    owner = &contextRef.getOwner();
    kernel = context->getPlatform().createKernel(IntegrateNoseHooverStepKernel::Name(), contextRef);
    kernel.getAs<IntegrateNoseHooverStepKernel>().initialize(contextRef.getSystem(), *this);
    forcesAreValid = false;

    // check for drude particles and build the Nose-Hoover Chains
    for (auto& thermostat: noseHooverChains){
        // if there are no thermostated particles or pairs in the lists this is a regular thermostat for the whole (non-Drude) system
        if ( (thermostat.getThermostatedAtoms().size() == 0) && (thermostat.getThermostatedPairs().size() == 0) ){
            std::vector<int> thermostatedParticles;
            for(int particle = 0; particle < system.getNumParticles(); ++particle) {
                double mass = system.getParticleMass(particle);
                if ( (mass > 0) && (mass < 0.8) ){
                    std::cout << "Warning: Found particles with mass between 0.0 and 0.8 dalton. Did you mean to make a DrudeNoseHooverIntegrator instead? "
                                 "The thermostat you are about to use will not treat these particles as Drude particles!" << std::endl;
                }
                if(system.getParticleMass(particle) > 0) {
                   thermostatedParticles.push_back(particle);
                }
            }
            thermostat.setThermostatedAtoms(thermostatedParticles);
        }
    }

    initializeThermostats(system);
}

void NoseHooverIntegrator::cleanup() {
    kernel = Kernel();
}

vector<string> NoseHooverIntegrator::getKernelNames() {
    std::vector<std::string> names;
    names.push_back(IntegrateNoseHooverStepKernel::Name());
    return names;
}

void NoseHooverIntegrator::step(int steps) {
    if (context == NULL)
        throw OpenMMException("This Integrator is not bound to a context!");
    for (int i = 0; i < steps; ++i) {
        if(context->updateContextState())
            forcesAreValid = false;
        context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
        kernel.getAs<IntegrateNoseHooverStepKernel>().execute(*context, *this, forcesAreValid);
    }
}

void NoseHooverIntegrator::createCheckpoint(std::ostream& stream) const {
    kernel.getAs<IntegrateNoseHooverStepKernel>().createCheckpoint(*context, stream);
}

void NoseHooverIntegrator::loadCheckpoint(std::istream& stream) {
    kernel.getAs<IntegrateNoseHooverStepKernel>().loadCheckpoint(*context, stream);
}

void NoseHooverIntegrator::serializeParameters(SerializationNode& node) const {
    node.setIntProperty("version", 1);
    vector<vector<double> > positions, velocities;
    kernel.getAs<IntegrateNoseHooverStepKernel>().getChainStates(*context, positions, velocities);
    for (int i = 0; i < positions.size(); i++) {
        SerializationNode& chain = node.createChildNode("Chain");
        for (int j = 0; j < positions[i].size(); j++)
            chain.createChildNode("Bead").setDoubleProperty("position", positions[i][j]).setDoubleProperty("velocity", velocities[i][j]);
    }
}

void NoseHooverIntegrator::deserializeParameters(const SerializationNode& node) {
    if (node.getIntProperty("version") != 1)
        throw OpenMMException("Unsupported version number");
    int numChains = node.getChildren().size();
    vector<vector<double> > positions(numChains), velocities(numChains);
    for (int i = 0; i < numChains; i++) {
        auto& chain = node.getChildren()[i];
        for (auto& bead : chain.getChildren()) {
            positions[i].push_back(bead.getDoubleProperty("position"));
            velocities[i].push_back(bead.getDoubleProperty("velocity"));
        }
    }
    kernel.getAs<IntegrateNoseHooverStepKernel>().setChainStates(*context, positions, velocities);
}