Introduce SimulatorBuilder

[gromacs.git] / src / gromacs / restraint / restraintmdmodule.cpp

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#include "gmxpre.h"

#include "restraintmdmodule.h"

#include <memory>

#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/iforceprovider.h"

#include "restraintmdmodule_impl.h"

namespace gmx
{

RestraintForceProvider::RestraintForceProvider(std::shared_ptr<IRestraintPotential> restraint,
                                               const std::vector<int>              &sites) :
    restraint_ {std::move(restraint)}
{
    GMX_ASSERT(restraint_, "Valid RestraintForceProviders wrap non-null restraints.");
    GMX_ASSERT(sites_.empty(), "");
    for (auto && site : sites)
    {
        sites_.emplace_back(site);
    }
    if (sites_.size() < 2)
    {
        GMX_THROW(InvalidInputError("Restraints require at least two sites to calculate forces."));
    }
}

void RestraintForceProvider::calculateForces(const ForceProviderInput &forceProviderInput,
                                             ForceProviderOutput     * forceProviderOutput)
{
    GMX_ASSERT(restraint_, "Restraint must be initialized.");

    const auto &mdatoms = forceProviderInput.mdatoms_;
    GMX_ASSERT(mdatoms.homenr >= 0, "number of home atoms must be non-negative.");

    const auto &box = forceProviderInput.box_;
    GMX_ASSERT(check_box(-1, box) == nullptr, "Invalid box.");
    t_pbc       pbc {};
    set_pbc(&pbc,
            -1,
            box);

    const auto &x  = forceProviderInput.x_;
    const auto &cr = forceProviderInput.cr_;
    const auto &t  = forceProviderInput.t_;
    // Cooperatively get Cartesian coordinates for center of mass of each site
    RVec        r1 = sites_[0].centerOfMass(cr,
                                            static_cast<size_t>(mdatoms.homenr),
                                            x,
                                            t);
    // r2 is to be constructed as
    // r2 = (site[N] - site[N-1]) + (site_{N-1} - site_{N-2}) + ... + (site_2 - site_1) + site_1
    // where the minimum image convention is applied to each path but not to the overall sum.
    // It is redundant to pass both r1 and r2 to called code, and potentially confusing, since
    // r1 may refer to an actual coordinate in the simulation while r2 may be in an expanded
    // Cartesian coordinate system. Called code should not use r1 and r2 to attempt to identify
    // sites in the simulation. If we need that functionality, we should do it separately by
    // allowing called code to look up atoms by tag or global index.
    RVec r2 = {r1[0], r1[1], r1[2]};
    rvec dr = {0, 0, 0};
    // Build r2 by following a path of difference vectors that are each presumed to be less than
    // a half-box apart, in case we are battling periodic boundary conditions along the lines of
    // a big molecule in a small box.
    for (size_t i = 0; i < sites_.size() - 1; ++i)
    {
        RVec a = sites_[i].centerOfMass(cr,
                                        static_cast<size_t>(mdatoms.homenr),
                                        x,
                                        t);
        RVec b = sites_[i + 1].centerOfMass(cr,
                                            static_cast<size_t>(mdatoms.homenr),
                                            x,
                                            t);
        // dr = minimum_image_vector(b - a)
        pbc_dx(&pbc,
               b,
               a,
               dr);
        r2[0] += dr[0];
        r2[1] += dr[1];
        r2[2] += dr[2];
    }
    // In the case of a single-atom site, r1 and r2 are now correct if local or [0,0,0] if not local.


    // Master rank update call-back. This needs to be moved to a discrete place in the
    // time step to avoid extraneous barriers. The code would be prettier with "futures"...
    if ((cr.dd == nullptr) || MASTER(&cr))
    {
        restraint_->update(RVec(r1),
                           r2,
                           t);
    }
    // All ranks wait for the update to finish.
    // tMPI ranks are depending on structures that may have just been updated.
    if (DOMAINDECOMP(&cr))
    {
        // Note: this assumes that all ranks are hitting this line, which is not generally true.
        // I need to find the right subcommunicator. What I really want is a _scoped_ communicator...
        gmx_barrier(&cr);
    }

    // Apply restraint on all thread ranks only after any updates have been made.
    auto result = restraint_->evaluate(RVec(r1),
                                       r2,
                                       t);

    // This can easily be generalized for pair restraints that apply to selections instead of
    // individual indices, or to restraints that aren't pair restraints.
    const int  site1  = static_cast<int>(sites_.front().index());
    const int* aLocal = &site1;
    // Set forces using index `site1` if no domain decomposition, otherwise set with local index if available.
    auto      &force = forceProviderOutput->forceWithVirial_.force_;
    if ((cr.dd == nullptr) || (aLocal = cr.dd->ga2la->findHome(site1)))
    {
        force[static_cast<size_t>(*aLocal)] += result.force;
    }

    // Note: Currently calculateForces is called once per restraint and each restraint
    // applies to a pair of atoms. Future optimizations may consolidate multiple restraints
    // with possibly duplicated sites, in which case we may prefer to iterate over non-frozen
    // sites to apply forces without explicitly expressing pairwise symmetry as in the
    // following logic.
    const int  site2  = static_cast<int>(sites_.back().index());
    const int* bLocal = &site2;
    if ((cr.dd == nullptr) || (bLocal = cr.dd->ga2la->findHome(site2)))
    {
        force[static_cast<size_t>(*bLocal)] -= result.force;
    }
}

RestraintMDModuleImpl::~RestraintMDModuleImpl() = default;

RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr<IRestraintPotential> restraint,
                                             const std::vector<int>              &sites) :
    forceProvider_(std::make_unique<RestraintForceProvider>(restraint,
                                                            sites))
{
    GMX_ASSERT(forceProvider_, "Class invariant implies non-null ForceProvider.");
}

IMdpOptionProvider* RestraintMDModuleImpl::mdpOptionProvider()
{
    return nullptr;
}

IMDOutputProvider* RestraintMDModuleImpl::outputProvider()
{
    return nullptr;
}

void RestraintMDModuleImpl::initForceProviders(ForceProviders* forceProviders)
{
    GMX_ASSERT(forceProvider_, "Class invariant implies non-null ForceProvider member.");
    GMX_ASSERT(forceProviders, "Provided ForceProviders* assumed to be non-null.");
    forceProviders->addForceProvider(forceProvider_.get());
}


// Needs to be defined after implementation type is complete in order to have unique_ptr member.
RestraintMDModule::~RestraintMDModule() = default;


IMdpOptionProvider* RestraintMDModule::mdpOptionProvider()
{
    return nullptr;
}

IMDOutputProvider* RestraintMDModule::outputProvider()
{
    return nullptr;
}

void RestraintMDModule::initForceProviders(ForceProviders* forceProviders)
{
    GMX_ASSERT(impl_, "Class invariant implies non-null implementation member.");
    impl_->initForceProviders(forceProviders);
}

std::unique_ptr<RestraintMDModule>
RestraintMDModule::create(std::shared_ptr<IRestraintPotential>  restraint,
                          const std::vector<int>               &sites)
{
    auto implementation = std::make_unique<RestraintMDModuleImpl>(std::move(restraint),
                                                                  sites);
    auto newModule = std::make_unique<RestraintMDModule>(std::move(implementation));
    return newModule;
}

// private constructor to implement static create() method.
RestraintMDModule::RestraintMDModule(std::unique_ptr<RestraintMDModuleImpl> restraint) :
    impl_ {std::move(restraint)}
{
}

} // end namespace gmx