/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright 1991- The GROMACS Authors
 * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
 * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * https://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at https://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
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 */
/* This file is completely threadsafe - keep it that way! */
#include "gmxpre.h"

#include "convparm.h"

#include <cassert>
#include <cmath>
#include <cstring>

#include <memory>

#include "gromacs/gmxpreprocess/gpp_atomtype.h"
#include "gromacs/gmxpreprocess/grompp_impl.h"
#include "gromacs/gmxpreprocess/topio.h"
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"

static int round_check(real r, int limit, int ftype, const char* name)
{
    const int i = gmx::roundToInt(r);

    if (r - i > 0.01 || r - i < -0.01)
    {
        gmx_fatal(FARGS,
                  "A non-integer value (%f) was supplied for '%s' in %s",
                  r,
                  name,
                  interaction_function[ftype].longname);
    }

    if (i < limit)
    {
        gmx_fatal(FARGS,
                  "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
                  name,
                  interaction_function[ftype].longname,
                  i,
                  limit);
    }

    return i;
}

static void set_ljparams(CombinationRule comb, double reppow, double v, double w, real* c6, real* c12)
{
    if (comb == CombinationRule::Arithmetic || comb == CombinationRule::GeomSigEps)
    {
        if (v >= 0)
        {
            *c6  = 4 * w * gmx::power6(v);
            *c12 = 4 * w * std::pow(v, reppow);
        }
        else
        {
            /* Interpret negative sigma as c6=0 and c12 with -sigma */
            *c6  = 0;
            *c12 = 4 * w * std::pow(-v, reppow);
        }
    }
    else
    {
        *c6  = v;
        *c12 = w;
    }
}

/* A return value of 0 means parameters were assigned successfully,
 * returning -1 means this is an all-zero interaction that should not be added.
 */
static int assign_param(t_functype                ftype,
                        t_iparams*                newparam,
                        gmx::ArrayRef<const real> old,
                        CombinationRule           comb,
                        double                    reppow)
{
    bool all_param_zero = true;

    /* Set to zero */
    for (int j = 0; (j < MAXFORCEPARAM); j++)
    {
        newparam->generic.buf[j] = 0.0;
        /* If all parameters are zero we might not add some interaction types (selected below).
         * We cannot apply this to ALL interactions, since many have valid reasons for having
         * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
         * we use it for angles and torsions that are typically generated automatically.
         */
        all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
    }

    if (all_param_zero)
    {
        if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS || ftype == F_PDIHS
            || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
        {
            return -1;
        }
    }

    switch (ftype)
    {
        case F_G96ANGLES:
            /* Post processing of input data: store cosine iso angle itself */
            newparam->harmonic.rA  = cos(old[0] * gmx::c_deg2Rad);
            newparam->harmonic.krA = old[1];
            newparam->harmonic.rB  = cos(old[2] * gmx::c_deg2Rad);
            newparam->harmonic.krB = old[3];
            break;
        case F_G96BONDS:
            /* Post processing of input data: store square of length itself */
            newparam->harmonic.rA  = gmx::square(old[0]);
            newparam->harmonic.krA = old[1];
            newparam->harmonic.rB  = gmx::square(old[2]);
            newparam->harmonic.krB = old[3];
            break;
        case F_FENEBONDS:
            newparam->fene.bm = old[0];
            newparam->fene.kb = old[1];
            break;
        case F_RESTRBONDS:
            newparam->restraint.lowA = old[0];
            newparam->restraint.up1A = old[1];
            newparam->restraint.up2A = old[2];
            newparam->restraint.kA   = old[3];
            newparam->restraint.lowB = old[4];
            newparam->restraint.up1B = old[5];
            newparam->restraint.up2B = old[6];
            newparam->restraint.kB   = old[7];
            break;
        case F_TABBONDS:
        case F_TABBONDSNC:
        case F_TABANGLES:
        case F_TABDIHS:
            newparam->tab.table = round_check(old[0], 0, ftype, "table index");
            newparam->tab.kA    = old[1];
            newparam->tab.kB    = old[3];
            break;
        case F_CROSS_BOND_BONDS:
            newparam->cross_bb.r1e = old[0];
            newparam->cross_bb.r2e = old[1];
            newparam->cross_bb.krr = old[2];
            break;
        case F_CROSS_BOND_ANGLES:
            newparam->cross_ba.r1e = old[0];
            newparam->cross_ba.r2e = old[1];
            newparam->cross_ba.r3e = old[2];
            newparam->cross_ba.krt = old[3];
            break;
        case F_UREY_BRADLEY:
            newparam->u_b.thetaA  = old[0];
            newparam->u_b.kthetaA = old[1];
            newparam->u_b.r13A    = old[2];
            newparam->u_b.kUBA    = old[3];
            newparam->u_b.thetaB  = old[4];
            newparam->u_b.kthetaB = old[5];
            newparam->u_b.r13B    = old[6];
            newparam->u_b.kUBB    = old[7];
            break;
        case F_QUARTIC_ANGLES:
            newparam->qangle.theta = old[0];
            for (int i = 0; i < 5; i++)
            {
                newparam->qangle.c[i] = old[i + 1];
            }
            break;
        case F_LINEAR_ANGLES:
            newparam->linangle.aA    = old[0];
            newparam->linangle.klinA = old[1];
            newparam->linangle.aB    = old[2];
            newparam->linangle.klinB = old[3];
            break;
        case F_BONDS:
        case F_ANGLES:
        case F_HARMONIC:
        case F_IDIHS:
            newparam->harmonic.rA  = old[0];
            newparam->harmonic.krA = old[1];
            newparam->harmonic.rB  = old[2];
            newparam->harmonic.krB = old[3];
            break;
        case F_RESTRANGLES:
            newparam->harmonic.rA  = old[0];
            newparam->harmonic.krA = old[1];
            break;
        case F_MORSE:
            newparam->morse.b0A   = old[0];
            newparam->morse.cbA   = old[1];
            newparam->morse.betaA = old[2];
            newparam->morse.b0B   = old[3];
            newparam->morse.cbB   = old[4];
            newparam->morse.betaB = old[5];
            break;
        case F_CUBICBONDS:
            newparam->cubic.b0   = old[0];
            newparam->cubic.kb   = old[1];
            newparam->cubic.kcub = old[2];
            break;
        case F_CONNBONDS: break;
        case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
        case F_ANHARM_POL:
            newparam->anharm_polarize.alpha = old[0];
            newparam->anharm_polarize.drcut = old[1];
            newparam->anharm_polarize.khyp  = old[2];
            break;
        case F_WATER_POL:
            newparam->wpol.al_x = old[0];
            newparam->wpol.al_y = old[1];
            newparam->wpol.al_z = old[2];
            newparam->wpol.rOH  = old[3];
            newparam->wpol.rHH  = old[4];
            newparam->wpol.rOD  = old[5];
            break;
        case F_THOLE_POL:
            newparam->thole.a      = old[0];
            newparam->thole.alpha1 = old[1];
            newparam->thole.alpha2 = old[2];
            break;
        case F_BHAM:
            newparam->bham.a = old[0];
            newparam->bham.b = old[1];
            newparam->bham.c = old[2];
            break;
        case F_LJ14:
            set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
            set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
            break;
        case F_LJC14_Q:
            newparam->ljc14.fqq = old[0];
            newparam->ljc14.qi  = old[1];
            newparam->ljc14.qj  = old[2];
            set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
            break;
        case F_LJC_PAIRS_NB:
            newparam->ljcnb.qi = old[0];
            newparam->ljcnb.qj = old[1];
            set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
            break;
        case F_LJ:
            set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
            break;
        case F_PDIHS:
        case F_PIDIHS:
        case F_ANGRES:
        case F_ANGRESZ:
            newparam->pdihs.phiA = old[0];
            newparam->pdihs.cpA  = old[1];

            /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
             * so I have changed the lower limit to -99 /EL
             */
            newparam->pdihs.phiB = old[3];
            newparam->pdihs.cpB  = old[4];
            /* If both force constants are zero there is no interaction. Return -1 to signal
             * this entry should NOT be added.
             */
            if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
            {
                return -1;
            }

            newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");

            break;
        case F_RESTRDIHS:
            newparam->pdihs.phiA = old[0];
            newparam->pdihs.cpA  = old[1];
            break;
        case F_POSRES:
            newparam->posres.fcA[XX]   = old[0];
            newparam->posres.fcA[YY]   = old[1];
            newparam->posres.fcA[ZZ]   = old[2];
            newparam->posres.fcB[XX]   = old[3];
            newparam->posres.fcB[YY]   = old[4];
            newparam->posres.fcB[ZZ]   = old[5];
            newparam->posres.pos0A[XX] = old[6];
            newparam->posres.pos0A[YY] = old[7];
            newparam->posres.pos0A[ZZ] = old[8];
            newparam->posres.pos0B[XX] = old[9];
            newparam->posres.pos0B[YY] = old[10];
            newparam->posres.pos0B[ZZ] = old[11];
            break;
        case F_FBPOSRES:
            newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
            if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
            {
                gmx_fatal(FARGS,
                          "Invalid geometry for flat-bottomed position restraint.\n"
                          "Expected number between 1 and %d. Found %d\n",
                          efbposresNR - 1,
                          newparam->fbposres.geom);
            }
            newparam->fbposres.r        = old[1];
            newparam->fbposres.k        = old[2];
            newparam->fbposres.pos0[XX] = old[3];
            newparam->fbposres.pos0[YY] = old[4];
            newparam->fbposres.pos0[ZZ] = old[5];
            break;
        case F_DISRES:
            newparam->disres.label = round_check(old[0], 0, ftype, "label");
            newparam->disres.type  = round_check(old[1], 1, ftype, "type'");
            newparam->disres.low   = old[2];
            newparam->disres.up1   = old[3];
            newparam->disres.up2   = old[4];
            newparam->disres.kfac  = old[5];
            break;
        case F_ORIRES:
            newparam->orires.ex    = round_check(old[0], 1, ftype, "experiment") - 1;
            newparam->orires.label = round_check(old[1], 1, ftype, "label");
            newparam->orires.power = round_check(old[2], 0, ftype, "power");
            newparam->orires.c     = old[3];
            newparam->orires.obs   = old[4];
            newparam->orires.kfac  = old[5];
            break;
        case F_DIHRES:
            newparam->dihres.phiA  = old[0];
            newparam->dihres.dphiA = old[1];
            newparam->dihres.kfacA = old[2];
            newparam->dihres.phiB  = old[3];
            newparam->dihres.dphiB = old[4];
            newparam->dihres.kfacB = old[5];
            break;
        case F_RBDIHS:
            for (int i = 0; (i < NR_RBDIHS); i++)
            {
                newparam->rbdihs.rbcA[i] = old[i];
                newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
            }
            break;
        case F_CBTDIHS:
            for (int i = 0; (i < NR_CBTDIHS); i++)
            {
                newparam->cbtdihs.cbtcA[i] = old[i];
            }
            break;
        case F_FOURDIHS:
            /* Read the dihedral parameters to temporary arrays,
             * and convert them to the computationally faster
             * Ryckaert-Bellemans form.
             */
            /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
            newparam->rbdihs.rbcA[0] = old[1] + 0.5 * (old[0] + old[2]);
            newparam->rbdihs.rbcA[1] = 0.5 * (3.0 * old[2] - old[0]);
            newparam->rbdihs.rbcA[2] = 4.0 * old[3] - old[1];
            newparam->rbdihs.rbcA[3] = -2.0 * old[2];
            newparam->rbdihs.rbcA[4] = -4.0 * old[3];
            newparam->rbdihs.rbcA[5] = 0.0;

            newparam->rbdihs.rbcB[0] =
                    old[NR_FOURDIHS + 1] + 0.5 * (old[NR_FOURDIHS + 0] + old[NR_FOURDIHS + 2]);
            newparam->rbdihs.rbcB[1] = 0.5 * (3.0 * old[NR_FOURDIHS + 2] - old[NR_FOURDIHS + 0]);
            newparam->rbdihs.rbcB[2] = 4.0 * old[NR_FOURDIHS + 3] - old[NR_FOURDIHS + 1];
            newparam->rbdihs.rbcB[3] = -2.0 * old[NR_FOURDIHS + 2];
            newparam->rbdihs.rbcB[4] = -4.0 * old[NR_FOURDIHS + 3];
            newparam->rbdihs.rbcB[5] = 0.0;
            break;
        case F_CONSTR:
        case F_CONSTRNC:
            newparam->constr.dA = old[0];
            newparam->constr.dB = old[1];
            break;
        case F_SETTLE:
            newparam->settle.doh = old[0];
            newparam->settle.dhh = old[1];
            break;
        case F_VSITE1:
        case F_VSITE2:
        case F_VSITE2FD:
        case F_VSITE3:
        case F_VSITE3FD:
        case F_VSITE3OUT:
        case F_VSITE4FD:
        case F_VSITE4FDN:
            newparam->vsite.a = old[0];
            newparam->vsite.b = old[1];
            newparam->vsite.c = old[2];
            newparam->vsite.d = old[3];
            newparam->vsite.e = old[4];
            newparam->vsite.f = old[5];
            break;
        case F_VSITE3FAD:
            newparam->vsite.a = old[1] * cos(gmx::c_deg2Rad * old[0]);
            newparam->vsite.b = old[1] * sin(gmx::c_deg2Rad * old[0]);
            newparam->vsite.c = old[2];
            newparam->vsite.d = old[3];
            newparam->vsite.e = old[4];
            newparam->vsite.f = old[5];
            break;
        case F_VSITEN:
            newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
            newparam->vsiten.a = old[1];
            break;
        case F_CMAP:
            newparam->cmap.cmapA = static_cast<int>(old[0]);
            newparam->cmap.cmapB = static_cast<int>(old[1]);
            break;
        case F_GB12_NOLONGERUSED:
        case F_GB13_NOLONGERUSED:
        case F_GB14_NOLONGERUSED: break;
        default:
            gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
    }
    return 0;
}

static int enter_params(gmx_ffparams_t*           ffparams,
                        t_functype                ftype,
                        gmx::ArrayRef<const real> forceparams,
                        CombinationRule           comb,
                        real                      reppow,
                        int                       start,
                        bool                      bAppend)
{
    t_iparams newparam;
    int       rc;

    if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
    {
        /* -1 means this interaction is all-zero and should not be added */
        return rc;
    }

    if (!bAppend)
    {
        if (ftype != F_DISRES)
        {
            for (int type = start; type < ffparams->numTypes(); type++)
            {
                // Note that the first condition is always met by starting the loop at start
                if (ffparams->functype[type] == ftype
                    && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
                {
                    return type;
                }
            }
        }
        else
        {
            // Distance restraints should have unique labels and pairs with the same label
            // should be consecutive, so we here we only need to check the last type in the list.
            // This changes the complexity from quadratic to linear in the number of restraints.
            const int type = ffparams->numTypes() - 1;
            if (type >= 0 && ffparams->functype[type] == ftype
                && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
            {
                return type;
            }
        }
    }

    const int type = ffparams->numTypes();

    ffparams->iparams.push_back(newparam);
    ffparams->functype.push_back(ftype);

    GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");

    return type;
}

static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
{
    ilist->iatoms.push_back(type);
    for (const auto& atom : a)
    {
        ilist->iatoms.push_back(atom);
    }
}

static void enter_function(const InteractionsOfType* p,
                           t_functype                ftype,
                           CombinationRule           comb,
                           real                      reppow,
                           gmx_ffparams_t*           ffparams,
                           InteractionList*          il,
                           bool                      bNB,
                           bool                      bAppend)
{
    int start = ffparams->numTypes();

    for (const auto& parm : p->interactionTypes)
    {
        int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
        /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
        if (!bNB && type >= 0)
        {
            GMX_RELEASE_ASSERT(il, "Need valid interaction list");
            GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
                               "Need to have correct number of atoms for the parameter");
            append_interaction(il, type, parm.atoms());
        }
    }
}

void convertInteractionsOfType(int                                      atnr,
                               gmx::ArrayRef<const InteractionsOfType>  nbtypes,
                               gmx::ArrayRef<const MoleculeInformation> mi,
                               const MoleculeInformation*               intermolecular_interactions,
                               CombinationRule                          comb,
                               double                                   reppow,
                               real                                     fudgeQQ,
                               gmx_mtop_t*                              mtop)
{
    int             i;
    unsigned long   flags;
    gmx_ffparams_t* ffp;
    gmx_moltype_t*  molt;

    ffp       = &mtop->ffparams;
    ffp->atnr = atnr;
    ffp->functype.clear();
    ffp->iparams.clear();
    ffp->reppow = reppow;

    enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
    enter_function(
            &(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr, TRUE, TRUE);

    for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
    {
        molt = &mtop->moltype[mt];
        for (i = 0; (i < F_NRE); i++)
        {
            molt->ilist[i].iatoms.clear();

            gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;

            flags = interaction_function[i].flags;
            if ((i != F_LJ) && (i != F_BHAM)
                && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
            {
                enter_function(&(interactions[i]),
                               static_cast<t_functype>(i),
                               comb,
                               reppow,
                               ffp,
                               &molt->ilist[i],
                               FALSE,
                               (i == F_POSRES || i == F_FBPOSRES));
            }
        }
    }

    mtop->bIntermolecularInteractions = FALSE;
    if (intermolecular_interactions != nullptr)
    {
        /* Process the intermolecular interaction list */
        mtop->intermolecular_ilist = std::make_unique<InteractionLists>();

        for (i = 0; (i < F_NRE); i++)
        {
            (*mtop->intermolecular_ilist)[i].iatoms.clear();

            gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;

            if (!interactions[i].interactionTypes.empty())
            {
                flags = interaction_function[i].flags;
                /* For intermolecular interactions we (currently)
                 * only support potentials.
                 * Constraints and virtual sites would be possible,
                 * but require a lot of extra (bug-prone) code.
                 */
                if (!(flags & IF_BOND))
                {
                    gmx_fatal(FARGS,
                              "The intermolecular_interaction section may only contain bonded "
                              "potentials");
                }
                else if (NRAL(i) == 1) /* e.g. position restraints */
                {
                    gmx_fatal(FARGS,
                              "Single atom interactions don't make sense in the "
                              "intermolecular_interaction section, you can put them in the "
                              "moleculetype section");
                }
                else if (flags & IF_CHEMBOND)
                {
                    gmx_fatal(FARGS,
                              "The intermolecular_interaction can not contain chemically bonding "
                              "interactions");
                }
                else
                {
                    enter_function(&(interactions[i]),
                                   static_cast<t_functype>(i),
                                   comb,
                                   reppow,
                                   ffp,
                                   &(*mtop->intermolecular_ilist)[i],
                                   FALSE,
                                   FALSE);

                    mtop->bIntermolecularInteractions = TRUE;
                }
            }
        }

        if (!mtop->bIntermolecularInteractions)
        {
            mtop->intermolecular_ilist.reset(nullptr);
        }
    }

    ffp->fudgeQQ = fudgeQQ;
}
