Convert gmx_mtop_t to C++

[gromacs.git] / src / gromacs / listed-forces / orires.cpp

/*
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 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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 * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
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#include "gmxpre.h"

#include "orires.h"

#include <climits>
#include <cmath>

#include "gromacs/gmxlib/network.h"
#include "gromacs/linearalgebra/nrjac.h"
#include "gromacs/math/do_fit.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/main.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"

// TODO This implementation of ensemble orientation restraints is nasty because
// a user can't just do multi-sim with single-sim orientation restraints.

void init_orires(FILE                 *fplog,
                 const gmx_mtop_t     *mtop,
                 const t_inputrec     *ir,
                 const t_commrec      *cr,
                 const gmx_multisim_t *ms,
                 t_state              *globalState,
                 t_oriresdata         *od)
{
    od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
    if (0 == od->nr)
    {
        /* Not doing orientation restraints */
        return;
    }

    const int numFitParams = 5;
    if (od->nr <= numFitParams)
    {
        gmx_fatal(FARGS, "The system has %d orientation restraints, but at least %d are required, since there are %d fitting parameters.",
                  od->nr, numFitParams + 1, numFitParams);
    }

    if (ir->bPeriodicMols)
    {
        /* Since we apply fitting, we need to make molecules whole and this
         * can not be done when periodic molecules are present.
         */
        gmx_fatal(FARGS, "Orientation restraints can not be applied when periodic molecules are present in the system");
    }

    if (PAR(cr))
    {
        gmx_fatal(FARGS, "Orientation restraints do not work with MPI parallelization. Choose 1 MPI rank, if possible.");
    }

    GMX_RELEASE_ASSERT(globalState != nullptr, "We need a valid global state in init_orires");

    od->fc  = ir->orires_fc;
    od->nex = 0;
    od->S   = nullptr;
    od->M   = nullptr;
    od->eig = nullptr;
    od->v   = nullptr;

    int                  *nr_ex   = nullptr;
    int                   typeMin = INT_MAX;
    int                   typeMax = 0;
    gmx_mtop_ilistloop_t  iloop   = gmx_mtop_ilistloop_init(mtop);
    const t_ilist        *il;
    int                   nmol;
    while (gmx_mtop_ilistloop_next(iloop, &il, &nmol))
    {
        if (nmol > 1)
        {
            gmx_fatal(FARGS, "Found %d copies of a molecule with orientation restrains while the current code only supports a single copy. If you want to ensemble average, run multiple copies of the system using the multi-sim feature of mdrun.", nmol);
        }

        for (int i = 0; i < il[F_ORIRES].nr; i += 3)
        {
            int type = il[F_ORIRES].iatoms[i];
            int ex   = mtop->ffparams.iparams[type].orires.ex;
            if (ex >= od->nex)
            {
                srenew(nr_ex, ex+1);
                for (int j = od->nex; j < ex+1; j++)
                {
                    nr_ex[j] = 0;
                }
                od->nex = ex+1;
            }
            GMX_ASSERT(nr_ex, "Check for allocated nr_ex to keep the static analyzer happy");
            nr_ex[ex]++;

            typeMin = std::min(typeMin, type);
            typeMax = std::max(typeMax, type);
        }
    }
    /* With domain decomposition we use the type index for indexing in global arrays */
    GMX_RELEASE_ASSERT(typeMax - typeMin + 1 == od->nr, "All orientation restraint parameter entries in the topology should be consecutive");
    /* Store typeMin so we can index array with the type offset */
    od->typeMin = typeMin;

    snew(od->S, od->nex);
    /* When not doing time averaging, the instaneous and time averaged data
     * are indentical and the pointers can point to the same memory.
     */
    snew(od->Dinsl, od->nr);

    if (ms)
    {
        snew(od->Dins, od->nr);
    }
    else
    {
        od->Dins = od->Dinsl;
    }

    if (ir->orires_tau == 0)
    {
        od->Dtav  = od->Dins;
        od->edt   = 0.0;
        od->edt_1 = 1.0;
    }
    else
    {
        snew(od->Dtav, od->nr);
        od->edt   = std::exp(-ir->delta_t/ir->orires_tau);
        od->edt_1 = 1.0 - od->edt;

        /* Extend the state with the orires history */
        globalState->flags           |= (1<<estORIRE_INITF);
        globalState->hist.orire_initf = 1;
        globalState->flags           |= (1<<estORIRE_DTAV);
        globalState->hist.norire_Dtav = od->nr*5;
        snew(globalState->hist.orire_Dtav, globalState->hist.norire_Dtav);
    }

    snew(od->oinsl, od->nr);
    if (ms)
    {
        snew(od->oins, od->nr);
    }
    else
    {
        od->oins = od->oinsl;
    }
    if (ir->orires_tau == 0)
    {
        od->otav = od->oins;
    }
    else
    {
        snew(od->otav, od->nr);
    }
    snew(od->tmpEq, od->nex);

    od->nref = 0;
    for (int i = 0; i < mtop->natoms; i++)
    {
        if (ggrpnr(&mtop->groups, egcORFIT, i) == 0)
        {
            od->nref++;
        }
    }
    snew(od->mref, od->nref);
    snew(od->xref, od->nref);
    snew(od->xtmp, od->nref);

    snew(od->eig, od->nex*12);

    /* Determine the reference structure on the master node.
     * Copy it to the other nodes after checking multi compatibility,
     * so we are sure the subsystems match before copying.
     */
    rvec                     com   = { 0, 0, 0 };
    double                   mtot  = 0.0;
    int                      j     = 0;
    gmx_mtop_atomloop_all_t  aloop = gmx_mtop_atomloop_all_init(mtop);
    int                      i     = -1;
    const t_atom            *atom;
    while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
    {
        if (mtop->groups.grpnr[egcORFIT] == nullptr ||
            mtop->groups.grpnr[egcORFIT][i] == 0)
        {
            /* Not correct for free-energy with changing masses */
            od->mref[j] = atom->m;
            // Note that only one rank per sim is supported.
            if (isMasterSim(ms))
            {
                copy_rvec(globalState->x[i], od->xref[j]);
                for (int d = 0; d < DIM; d++)
                {
                    com[d] += od->mref[j]*globalState->x[i][d];
                }
            }
            mtot += od->mref[j];
            j++;
        }
    }
    svmul(1.0/mtot, com, com);
    if (isMasterSim(ms))
    {
        for (int j = 0; j < od->nref; j++)
        {
            rvec_dec(od->xref[j], com);
        }
    }

    fprintf(fplog, "Found %d orientation experiments\n", od->nex);
    for (int i = 0; i < od->nex; i++)
    {
        fprintf(fplog, "  experiment %d has %d restraints\n", i+1, nr_ex[i]);
    }

    sfree(nr_ex);

    fprintf(fplog, "  the fit group consists of %d atoms and has total mass %g\n",
            od->nref, mtot);

    if (ms)
    {
        fprintf(fplog, "  the orientation restraints are ensemble averaged over %d systems\n", ms->nsim);

        check_multi_int(fplog, ms, od->nr,
                        "the number of orientation restraints",
                        FALSE);
        check_multi_int(fplog, ms, od->nref,
                        "the number of fit atoms for orientation restraining",
                        FALSE);
        check_multi_int(fplog, ms, ir->nsteps, "nsteps", FALSE);
        /* Copy the reference coordinates from the master to the other nodes */
        gmx_sum_sim(DIM*od->nref, od->xref[0], ms);
    }

    please_cite(fplog, "Hess2003");
}

void diagonalize_orires_tensors(t_oriresdata *od)
{
    if (od->M == nullptr)
    {
        snew(od->M, DIM);
        for (int i = 0; i < DIM; i++)
        {
            snew(od->M[i], DIM);
        }
        snew(od->eig_diag, DIM);
        snew(od->v, DIM);
        for (int i = 0; i < DIM; i++)
        {
            snew(od->v[i], DIM);
        }
    }

    for (int ex = 0; ex < od->nex; ex++)
    {
        /* Rotate the S tensor back to the reference frame */
        matrix S, TMP;
        mmul(od->R, od->S[ex], TMP);
        mtmul(TMP, od->R, S);
        for (int i = 0; i < DIM; i++)
        {
            for (int j = 0; j < DIM; j++)
            {
                od->M[i][j] = S[i][j];
            }
        }

        int nrot;
        jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);

        int ord[DIM];
        for (int i = 0; i < DIM; i++)
        {
            ord[i] = i;
        }
        for (int i = 0; i < DIM; i++)
        {
            for (int j = i+1; j < DIM; j++)
            {
                if (gmx::square(od->eig_diag[ord[j]]) > gmx::square(od->eig_diag[ord[i]]))
                {
                    int t  = ord[i];
                    ord[i] = ord[j];
                    ord[j] = t;
                }
            }
        }

        for (int i = 0; i < DIM; i++)
        {
            od->eig[ex*12 + i] = od->eig_diag[ord[i]];
        }
        for (int i = 0; i < DIM; i++)
        {
            for (int j = 0; j < DIM; j++)
            {
                od->eig[ex*12 + 3 + 3*i + j] = od->v[j][ord[i]];
            }
        }
    }
}

void print_orires_log(FILE *log, t_oriresdata *od)
{
    real *eig;

    diagonalize_orires_tensors(od);

    for (int ex = 0; ex < od->nex; ex++)
    {
        eig = od->eig + ex*12;
        fprintf(log, "  Orientation experiment %d:\n", ex+1);
        fprintf(log, "    order parameter: %g\n", eig[0]);
        for (int i = 0; i < DIM; i++)
        {
            fprintf(log, "    eig: %6.3f   %6.3f %6.3f %6.3f\n",
                    (eig[0] != 0) ? eig[i]/eig[0] : eig[i],
                    eig[DIM+i*DIM+XX],
                    eig[DIM+i*DIM+YY],
                    eig[DIM+i*DIM+ZZ]);
        }
        fprintf(log, "\n");
    }
}

real calc_orires_dev(const gmx_multisim_t *ms,
                     int nfa, const t_iatom forceatoms[], const t_iparams ip[],
                     const t_mdatoms *md, const rvec x[], const t_pbc *pbc,
                     t_fcdata *fcd, history_t *hist)
{
    int              nref;
    real             edt, edt_1, invn, pfac, r2, invr, corrfac, wsv2, sw, dev;
    OriresMatEq     *matEq;
    real            *mref;
    double           mtot;
    rvec            *xref, *xtmp, com, r_unrot, r;
    t_oriresdata    *od;
    gmx_bool         bTAV;
    const real       two_thr = 2.0/3.0;

    od = &(fcd->orires);

    if (od->nr == 0)
    {
        /* This means that this is not the master node */
        gmx_fatal(FARGS, "Orientation restraints are only supported on the master rank, use fewer ranks");
    }

    bTAV  = (od->edt != 0);
    edt   = od->edt;
    edt_1 = od->edt_1;
    matEq = od->tmpEq;
    nref  = od->nref;
    mref  = od->mref;
    xref  = od->xref;
    xtmp  = od->xtmp;

    if (bTAV)
    {
        od->exp_min_t_tau = hist->orire_initf*edt;

        /* Correction factor to correct for the lack of history
         * at short times.
         */
        corrfac = 1.0/(1.0 - od->exp_min_t_tau);
    }
    else
    {
        corrfac = 1.0;
    }

    if (ms)
    {
        invn = 1.0/ms->nsim;
    }
    else
    {
        invn = 1.0;
    }

    clear_rvec(com);
    mtot  = 0;
    int j = 0;
    for (int i = 0; i < md->nr; i++)
    {
        if (md->cORF[i] == 0)
        {
            copy_rvec(x[i], xtmp[j]);
            mref[j] = md->massT[i];
            for (int d = 0; d < DIM; d++)
            {
                com[d] += mref[j]*xtmp[j][d];
            }
            mtot += mref[j];
            j++;
        }
    }
    svmul(1.0/mtot, com, com);
    for (int j = 0; j < nref; j++)
    {
        rvec_dec(xtmp[j], com);
    }
    /* Calculate the rotation matrix to rotate x to the reference orientation */
    calc_fit_R(DIM, nref, mref, xref, xtmp, od->R);

    for (int fa = 0; fa < nfa; fa += 3)
    {
        const int type           = forceatoms[fa];
        const int restraintIndex = type - od->typeMin;
        if (pbc)
        {
            pbc_dx_aiuc(pbc, x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
        }
        else
        {
            rvec_sub(x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
        }
        mvmul(od->R, r_unrot, r);
        r2   = norm2(r);
        invr = gmx::invsqrt(r2);
        /* Calculate the prefactor for the D tensor, this includes the factor 3! */
        pfac = ip[type].orires.c*invr*invr*3;
        for (int i = 0; i < ip[type].orires.power; i++)
        {
            pfac *= invr;
        }
        rvec5 &Dinsl = od->Dinsl[restraintIndex];
        Dinsl[0] = pfac*(2*r[0]*r[0] + r[1]*r[1] - r2);
        Dinsl[1] = pfac*(2*r[0]*r[1]);
        Dinsl[2] = pfac*(2*r[0]*r[2]);
        Dinsl[3] = pfac*(2*r[1]*r[1] + r[0]*r[0] - r2);
        Dinsl[4] = pfac*(2*r[1]*r[2]);

        if (ms)
        {
            for (int i = 0; i < 5; i++)
            {
                od->Dins[restraintIndex][i] = Dinsl[i]*invn;
            }
        }
    }

    if (ms)
    {
        gmx_sum_sim(5*od->nr, od->Dins[0], ms);
    }

    /* Calculate the order tensor S for each experiment via optimization */
    for (int ex = 0; ex < od->nex; ex++)
    {
        for (int i = 0; i < 5; i++)
        {
            matEq[ex].rhs[i] = 0;
            for (int j = 0; j <= i; j++)
            {
                matEq[ex].mat[i][j] = 0;
            }
        }
    }

    for (int fa = 0; fa < nfa; fa += 3)
    {
        const int  type           = forceatoms[fa];
        const int  restraintIndex = type - od->typeMin;
        rvec5     &Dtav           = od->Dtav[restraintIndex];
        if (bTAV)
        {
            /* Here we update Dtav in t_fcdata using the data in history_t.
             * Thus the results stay correct when this routine
             * is called multiple times.
             */
            for (int i = 0; i < 5; i++)
            {
                Dtav[i] =
                    edt*hist->orire_Dtav[restraintIndex*5 + i] +
                    edt_1*od->Dins[restraintIndex][i];
            }
        }

        int  ex     = ip[type].orires.ex;
        real weight = ip[type].orires.kfac;
        /* Calculate the vector rhs and half the matrix T for the 5 equations */
        for (int i = 0; i < 5; i++)
        {
            matEq[ex].rhs[i] += Dtav[i]*ip[type].orires.obs*weight;
            for (int j = 0; j <= i; j++)
            {
                matEq[ex].mat[i][j] += Dtav[i]*Dtav[j]*weight;
            }
        }
    }
    /* Now we have all the data we can calculate S */
    for (int ex = 0; ex < od->nex; ex++)
    {
        OriresMatEq &eq = matEq[ex];
        /* Correct corrfac and copy one half of T to the other half */
        for (int i = 0; i < 5; i++)
        {
            eq.rhs[i]    *= corrfac;
            eq.mat[i][i] *= gmx::square(corrfac);
            for (int j = 0; j < i; j++)
            {
                eq.mat[i][j] *= gmx::square(corrfac);
                eq.mat[j][i]  = eq.mat[i][j];
            }
        }
        m_inv_gen(&eq.mat[0][0], 5, &eq.mat[0][0]);
        /* Calculate the orientation tensor S for this experiment */
        matrix &S = od->S[ex];
        S[0][0] = 0;
        S[0][1] = 0;
        S[0][2] = 0;
        S[1][1] = 0;
        S[1][2] = 0;
        for (int i = 0; i < 5; i++)
        {
            S[0][0] += 1.5*eq.mat[0][i]*eq.rhs[i];
            S[0][1] += 1.5*eq.mat[1][i]*eq.rhs[i];
            S[0][2] += 1.5*eq.mat[2][i]*eq.rhs[i];
            S[1][1] += 1.5*eq.mat[3][i]*eq.rhs[i];
            S[1][2] += 1.5*eq.mat[4][i]*eq.rhs[i];
        }
        S[1][0] = S[0][1];
        S[2][0] = S[0][2];
        S[2][1] = S[1][2];
        S[2][2] = -S[0][0] - S[1][1];
    }

    const matrix *S = od->S;

    wsv2            = 0;
    sw              = 0;

    for (int fa = 0; fa < nfa; fa += 3)
    {
        const int    type           = forceatoms[fa];
        const int    restraintIndex = type - od->typeMin;
        const int    ex             = ip[type].orires.ex;

        const rvec5 &Dtav           = od->Dtav[restraintIndex];
        od->otav[restraintIndex]    = two_thr*
            corrfac*(S[ex][0][0]*Dtav[0] + S[ex][0][1]*Dtav[1] +
                     S[ex][0][2]*Dtav[2] + S[ex][1][1]*Dtav[3] +
                     S[ex][1][2]*Dtav[4]);
        if (bTAV)
        {
            const rvec5 &Dins = od->Dins[restraintIndex];
            od->oins[restraintIndex] = two_thr*
                (S[ex][0][0]*Dins[0] + S[ex][0][1]*Dins[1] +
                 S[ex][0][2]*Dins[2] + S[ex][1][1]*Dins[3] +
                 S[ex][1][2]*Dins[4]);
        }
        if (ms)
        {
            /* When ensemble averaging is used recalculate the local orientation
             * for output to the energy file.
             */
            const rvec5 &Dinsl = od->Dinsl[restraintIndex];
            od->oinsl[restraintIndex] = two_thr*
                (S[ex][0][0]*Dinsl[0] + S[ex][0][1]*Dinsl[1] +
                 S[ex][0][2]*Dinsl[2] + S[ex][1][1]*Dinsl[3] +
                 S[ex][1][2]*Dinsl[4]);
        }

        dev = od->otav[restraintIndex] - ip[type].orires.obs;

        wsv2 += ip[type].orires.kfac*gmx::square(dev);
        sw   += ip[type].orires.kfac;
    }
    od->rmsdev = std::sqrt(wsv2/sw);

    /* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
    for (int ex = 0; ex < od->nex; ex++)
    {
        matrix RS;
        tmmul(od->R, od->S[ex], RS);
        mmul(RS, od->R, od->S[ex]);
    }

    return od->rmsdev;

    /* Approx. 120*nfa/3 flops */
}

real orires(int nfa, const t_iatom forceatoms[], const t_iparams ip[],
            const rvec x[], rvec4 f[], rvec fshift[],
            const t_pbc *pbc, const t_graph *g,
            real gmx_unused lambda, real gmx_unused *dvdlambda,
            const t_mdatoms gmx_unused *md, t_fcdata *fcd,
            int gmx_unused *global_atom_index)
{
    int                 ex, power, ki = CENTRAL;
    ivec                dt;
    real                r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
    rvec                r, Sr, fij;
    real                vtot;
    const t_oriresdata *od;
    gmx_bool            bTAV;

    vtot = 0;
    od   = &(fcd->orires);

    if (od->fc != 0)
    {
        bTAV = (od->edt != 0);

        smooth_fc = od->fc;
        if (bTAV)
        {
            /* Smoothly switch on the restraining when time averaging is used */
            smooth_fc *= (1.0 - od->exp_min_t_tau);
        }

        for (int fa = 0; fa < nfa; fa += 3)
        {
            const int type           = forceatoms[fa];
            const int ai             = forceatoms[fa + 1];
            const int aj             = forceatoms[fa + 2];
            const int restraintIndex = type - od->typeMin;
            if (pbc)
            {
                ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
            }
            else
            {
                rvec_sub(x[ai], x[aj], r);
            }
            r2    = norm2(r);
            invr  = gmx::invsqrt(r2);
            invr2 = invr*invr;
            ex    = ip[type].orires.ex;
            power = ip[type].orires.power;
            fc    = smooth_fc*ip[type].orires.kfac;
            dev   = od->otav[restraintIndex] - ip[type].orires.obs;

            /* NOTE:
             * there is no real potential when time averaging is applied
             */
            vtot += 0.5*fc*gmx::square(dev);

            if (bTAV)
            {
                /* Calculate the force as the sqrt of tav times instantaneous */
                devins = od->oins[restraintIndex] - ip[type].orires.obs;
                if (dev*devins <= 0)
                {
                    dev = 0;
                }
                else
                {
                    dev = std::sqrt(dev*devins);
                    if (devins < 0)
                    {
                        dev = -dev;
                    }
                }
            }

            pfac  = fc*ip[type].orires.c*invr2;
            for (int i = 0; i < power; i++)
            {
                pfac *= invr;
            }
            mvmul(od->S[ex], r, Sr);
            for (int i = 0; i < DIM; i++)
            {
                fij[i] =
                    -pfac*dev*(4*Sr[i] - 2*(2+power)*invr2*iprod(Sr, r)*r[i]);
            }

            if (g)
            {
                ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
                ki = IVEC2IS(dt);
            }

            for (int i = 0; i < DIM; i++)
            {
                f[ai][i]           += fij[i];
                f[aj][i]           -= fij[i];
                fshift[ki][i]      += fij[i];
                fshift[CENTRAL][i] -= fij[i];
            }
        }
    }

    return vtot;

    /* Approx. 80*nfa/3 flops */
}

void update_orires_history(t_fcdata *fcd, history_t *hist)
{
    t_oriresdata *od = &(fcd->orires);

    if (od->edt != 0)
    {
        /* Copy the new time averages that have been calculated
         *  in calc_orires_dev.
         */
        hist->orire_initf = od->exp_min_t_tau;
        for (int pair = 0; pair < od->nr; pair++)
        {
            for (int i = 0; i < 5; i++)
            {
                hist->orire_Dtav[pair*5+i] = od->Dtav[pair][i];
            }
        }
    }
}