Fix GPU X buffer ops with empty domain

[gromacs.git] / src / gromacs / gmxpreprocess / gen_ad.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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
 * top-level source directory and at http://www.gromacs.org.
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/* This file is completely threadsafe - keep it that way! */
#include "gmxpre.h"

#include "gen_ad.h"

#include <cctype>
#include <cmath>
#include <cstdlib>
#include <cstring>

#include <algorithm>
#include <numeric>

#include "gromacs/fileio/confio.h"
#include "gromacs/gmxpreprocess/gpp_nextnb.h"
#include "gromacs/gmxpreprocess/grompp_impl.h"
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/gmxpreprocess/pgutil.h"
#include "gromacs/gmxpreprocess/topio.h"
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"

#include "hackblock.h"
#include "resall.h"

#define DIHEDRAL_WAS_SET_IN_RTP 0
static bool was_dihedral_set_in_rtp(const InteractionOfType &dih)
{
    // This is a bad way to check this, but I don't know how to make this better now.
    gmx::ArrayRef<const real> forceParam = dih.forceParam();
    return forceParam[MAXFORCEPARAM-1] == DIHEDRAL_WAS_SET_IN_RTP;
}

typedef bool (*peq)(const InteractionOfType &p1, const InteractionOfType &p2);

static bool acomp(const InteractionOfType &a1, const InteractionOfType &a2)
{
    int            ac;

    if ((ac = (a1.aj()-a2.aj())) != 0)
    {
        return ac < 0;
    }
    else if ((ac = (a1.ai()-a2.ai())) != 0)
    {
        return ac < 0;
    }
    else
    {
        return (a1.ak() < a2.ak());
    }
}

static bool pcomp(const InteractionOfType &a1, const InteractionOfType &a2)
{
    int            pc;

    if ((pc = (a1.ai()-a2.ai())) != 0)
    {
        return pc < 0;
    }
    else
    {
        return (a1.aj() < a2.aj());
    }
}

static bool dcomp(const InteractionOfType &d1, const InteractionOfType &d2)
{
    int            dc;

    /* First sort by J & K (the two central) atoms */
    if ((dc = (d1.aj()-d2.aj())) != 0)
    {
        return dc < 0;
    }
    else if ((dc = (d1.ak()-d2.ak())) != 0)
    {
        return dc < 0;
    }
    /* Then make sure to put rtp dihedrals before generated ones */
    else if (was_dihedral_set_in_rtp(d1) &&
             !was_dihedral_set_in_rtp(d2))
    {
        return true;
    }
    else if (!was_dihedral_set_in_rtp(d1) &&
             was_dihedral_set_in_rtp(d2))
    {
        return false;
    }
    /* Then sort by I and J (two outer) atoms */
    else if ((dc = (d1.ai()-d2.ai())) != 0)
    {
        return dc < 0;
    }
    else if ((dc = (d1.al()-d2.al())) != 0)
    {
        return dc < 0;
    }
    else
    {
        // AMBER force fields with type 9 dihedrals can reach here, where we sort on
        // the contents of the string that names the macro for the parameters.
        return std::lexicographical_compare(d1.interactionTypeName().begin(),
                                            d1.interactionTypeName().end(),
                                            d2.interactionTypeName().begin(),
                                            d2.interactionTypeName().end());
    }
}


static bool is_dihedral_on_same_bond(const InteractionOfType &p1, const InteractionOfType &p2)
{
    return ((p1.aj() == p2.aj()) && (p1.ak() == p2.ak())) ||
           ((p1.aj() == p2.ak()) && (p1.ak() == p2.aj()));
}


static bool preq(const InteractionOfType &p1, const InteractionOfType &p2)
{
    return (p1.ai() == p2.ai()) && (p1.aj() == p2.aj());
}

static void rm2par(std::vector<InteractionOfType> *p, peq eq)
{
    if (p->empty())
    {
        return;
    }

    for (auto param = p->begin() + 1; param != p->end(); )
    {
        auto prev = param - 1;
        if (eq(*param, *prev))
        {
            param = p->erase(param);
        }
        else
        {
            ++param;
        }
    }
}

static void cppar(gmx::ArrayRef<const InteractionOfType>          types,
                  gmx::ArrayRef<InteractionsOfType>               plist,
                  int                                             ftype)
{
    /* Keep old stuff */
    for (const auto &type : types)
    {
        plist[ftype].interactionTypes.push_back(type);
    }
}

static bool idcomp(const InteractionOfType &a, const InteractionOfType &b)
{
    int            d;

    if ((d = (a.ai()-b.ai())) != 0)
    {
        return d < 0;
    }
    else if ((d = (a.al()-b.al())) != 0)
    {
        return d < 0;
    }
    else if ((d = (a.aj()-b.aj())) != 0)
    {
        return d < 0;
    }
    else
    {
        return (a.ak() < b.ak());
    }
}

static void sort_id(gmx::ArrayRef<InteractionOfType> ps)
{
    if (ps.size() > 1)
    {
        for (auto &parm : ps)
        {
            parm.sortAtomIds();
        }
        std::sort(ps.begin(), ps.end(), idcomp);
    }
}

static int n_hydro(gmx::ArrayRef<const int> a, char ***atomname)
{
    int  nh = 0;

    for (auto atom = a.begin(); atom < a.end(); atom += 3)
    {
        const char *aname = *atomname[*atom];
        char        c0    = toupper(aname[0]);
        if (c0 == 'H')
        {
            nh++;
        }
        else if ((static_cast<int>(strlen(aname)) > 1) && (c0 >= '0') && (c0 <= '9'))
        {
            char c1 = toupper(aname[1]);
            if (c1 == 'H')
            {
                nh++;
            }
        }
    }
    return nh;
}

/* Clean up the dihedrals (both generated and read from the .rtp
 * file). */
static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
                                                gmx::ArrayRef<const InteractionOfType> improper,
                                                t_atoms *atoms, bool bKeepAllGeneratedDihedrals,
                                                bool bRemoveDihedralIfWithImproper)
{
    /* Construct the list of the indices of the dihedrals
     * (i.e. generated or read) that might be kept. */
    std::vector < std::pair < InteractionOfType, int>> newDihedrals;
    if (bKeepAllGeneratedDihedrals)
    {
        fprintf(stderr, "Keeping all generated dihedrals\n");
        int i = 0;
        for (const auto &dihedral : dih)
        {
            newDihedrals.emplace_back(std::pair<InteractionOfType, int>(dihedral, i++));
        }
    }
    else
    {
        /* Check if generated dihedral i should be removed. The
         * dihedrals have been sorted by dcomp() above, so all those
         * on the same two central atoms are together, with those from
         * the .rtp file preceding those that were automatically
         * generated. We remove the latter if the former exist. */
        int i = 0;
        for (auto dihedral = dih.begin(); dihedral != dih.end(); dihedral++)
        {
            /* Keep the dihedrals that were defined in the .rtp file,
             * and the dihedrals that were generated and different
             * from the last one (whether it was generated or not). */
            if (was_dihedral_set_in_rtp(*dihedral) ||
                dihedral == dih.begin() ||
                !is_dihedral_on_same_bond(*dihedral, *(dihedral-1)))
            {
                newDihedrals.emplace_back(std::pair<InteractionOfType, int>(*dihedral, i++));
            }
        }
    }
    int k = 0;
    for (auto dihedral = newDihedrals.begin(); dihedral != newDihedrals.end(); )
    {
        bool bWasSetInRTP = was_dihedral_set_in_rtp(dihedral->first);
        bool bKeep        = true;
        if (!bWasSetInRTP && bRemoveDihedralIfWithImproper)
        {
            /* Remove the dihedral if there is an improper on the same
             * bond. */
            for (auto imp = improper.begin(); imp != improper.end() && bKeep; ++imp)
            {
                bKeep = !is_dihedral_on_same_bond(dihedral->first, *imp);
            }
        }

        if (bKeep)
        {
            /* If we don't want all dihedrals, we want to select the
             * ones with the fewest hydrogens. Note that any generated
             * dihedrals on the same bond as an .rtp dihedral may have
             * been already pruned above in the construction of
             * index[]. However, their parameters are still present,
             * and l is looping over this dihedral and all of its
             * pruned siblings. */
            int bestl = dihedral->second;
            if (!bKeepAllGeneratedDihedrals && !bWasSetInRTP)
            {
                /* Minimum number of hydrogens for i and l atoms */
                int minh = 2;
                int next = dihedral->second + 1;
                for (int l = dihedral->second;
                     (l < next &&
                      is_dihedral_on_same_bond(dihedral->first, dih[l]));
                     l++)
                {
                    int nh = n_hydro(dih[l].atoms(), atoms->atomname);
                    if (nh < minh)
                    {
                        minh  = nh;
                        bestl = l;
                    }
                    if (0 == minh)
                    {
                        break;
                    }
                }
                dihedral->first = dih[bestl];
            }
            if (k == bestl)
            {
                ++dihedral;
            }
            k++;
        }
        else
        {
            dihedral = newDihedrals.erase(dihedral);
        }
    }
    std::vector<InteractionOfType> finalDihedrals;
    finalDihedrals.reserve(newDihedrals.size());
    for (const auto &param : newDihedrals)
    {
        finalDihedrals.emplace_back(param.first);
    }
    return finalDihedrals;
}

static std::vector<InteractionOfType> get_impropers(t_atoms                             *atoms,
                                                    gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
                                                    bool                                 bAllowMissing)
{
    std::vector<InteractionOfType> improper;

    /* Add all the impropers from the residue database to the list. */
    int start     = 0;
    if (!globalPatches.empty())
    {
        for (int i = 0; (i < atoms->nres); i++)
        {
            BondedInteractionList *impropers = &globalPatches[i].rb[ebtsIDIHS];
            for (const auto &bondeds : impropers->b)
            {
                bool                     bStop = false;
                std::vector<int>         ai;
                for (int k = 0; (k < 4) && !bStop; k++)
                {
                    int entry = search_atom(bondeds.a[k].c_str(), start,
                                            atoms, "improper", bAllowMissing);

                    if (entry != -1)
                    {
                        ai.emplace_back(entry);
                    }
                    else
                    {
                        bStop = true;
                    }
                }
                if (!bStop)
                {
                    /* Not broken out */
                    improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
                }
            }
            while ((start < atoms->nr) && (atoms->atom[start].resind == i))
            {
                start++;
            }
        }
    }

    return improper;
}

static int nb_dist(t_nextnb *nnb, int ai, int aj)
{
    int  nre, nrx, NRE;
    int *nrexcl;
    int *a;

    if (ai == aj)
    {
        return 0;
    }

    NRE    = -1;
    nrexcl = nnb->nrexcl[ai];
    for (nre = 1; (nre < nnb->nrex); nre++)
    {
        a = nnb->a[ai][nre];
        for (nrx = 0; (nrx < nrexcl[nre]); nrx++)
        {
            if ((aj == a[nrx]) && (NRE == -1))
            {
                NRE = nre;
            }
        }
    }
    return NRE;
}

static bool is_hydro(t_atoms *atoms, int ai)
{
    return ((*(atoms->atomname[ai]))[0] == 'H');
}

static void get_atomnames_min(int n, gmx::ArrayRef<std::string> anm,
                              int resind, t_atoms *atoms, gmx::ArrayRef<const int> a)
{
    /* Assume ascending residue numbering */
    for (int m = 0; m < n; m++)
    {
        if (atoms->atom[a[m]].resind < resind)
        {
            anm[m] = "-";
        }
        else if (atoms->atom[a[m]].resind > resind)
        {
            anm[m] = "+";
        }
        else
        {
            anm[m] = "";
        }
        anm[m].append(*(atoms->atomname[a[m]]));
    }
}

static void gen_excls(t_atoms                             *atoms,
                      t_excls                             *excls,
                      gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
                      bool                                 bAllowMissing)
{
    int astart = 0;
    for (int a = 0; a < atoms->nr; a++)
    {
        int r = atoms->atom[a].resind;
        if (a == atoms->nr-1 || atoms->atom[a+1].resind != r)
        {
            BondedInteractionList *hbexcl = &globalPatches[r].rb[ebtsEXCLS];

            for (const auto &bondeds : hbexcl->b)
            {
                const char *anm = bondeds.a[0].c_str();
                int         i1  = search_atom(anm, astart, atoms,
                                              "exclusion", bAllowMissing);
                anm = bondeds.a[1].c_str();
                int i2  = search_atom(anm, astart, atoms,
                                      "exclusion", bAllowMissing);
                if (i1 != -1 && i2 != -1)
                {
                    if (i1 > i2)
                    {
                        int itmp = i1;
                        i1   = i2;
                        i2   = itmp;
                    }
                    srenew(excls[i1].e, excls[i1].nr+1);
                    excls[i1].e[excls[i1].nr] = i2;
                    excls[i1].nr++;
                }
            }

            astart = a+1;
        }
    }

    for (int a = 0; a < atoms->nr; a++)
    {
        if (excls[a].nr > 1)
        {
            std::sort(excls[a].e, excls[a].e+excls[a].nr);
        }
    }
}

static void remove_excl(t_excls *excls, int remove)
{
    int i;

    for (i = remove+1; i < excls->nr; i++)
    {
        excls->e[i-1] = excls->e[i];
    }

    excls->nr--;
}

void clean_excls(t_nextnb *nnb, int nrexcl, t_excls excls[])
{
    int      i, j, j1, k, k1, l, l1, e;
    t_excls *excl;

    if (nrexcl >= 1)
    {
        /* extract all i-j-k-l neighbours from nnb struct */
        for (i = 0; (i < nnb->nr); i++)
        {
            /* For all particles */
            excl = &excls[i];

            for (j = 0; (j < nnb->nrexcl[i][1]); j++)
            {
                /* For all first neighbours */
                j1 = nnb->a[i][1][j];

                for (e = 0; e < excl->nr; e++)
                {
                    if (excl->e[e] == j1)
                    {
                        remove_excl(excl, e);
                    }
                }

                if (nrexcl >= 2)
                {
                    for (k = 0; (k < nnb->nrexcl[j1][1]); k++)
                    {
                        /* For all first neighbours of j1 */
                        k1 = nnb->a[j1][1][k];

                        for (e = 0; e < excl->nr; e++)
                        {
                            if (excl->e[e] == k1)
                            {
                                remove_excl(excl, e);
                            }
                        }

                        if (nrexcl >= 3)
                        {
                            for (l = 0; (l < nnb->nrexcl[k1][1]); l++)
                            {
                                /* For all first neighbours of k1 */
                                l1 = nnb->a[k1][1][l];

                                for (e = 0; e < excl->nr; e++)
                                {
                                    if (excl->e[e] == l1)
                                    {
                                        remove_excl(excl, e);
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
    }
}

void generate_excls(t_nextnb *nnb, int nrexcl, t_excls excls[])
{
    int      i, j, n, N;
    t_excls *excl;

    for (N = 1; (N < std::min(nrexcl, nnb->nrex)); N++)
    {
        /* extract all i-j-k-l neighbours from nnb struct */
        for (i = 0; (i < nnb->nr); i++)
        {
            /* For all particles */
            excl      = &excls[i];
            n         = excl->nr;
            excl->nr += nnb->nrexcl[i][N];
            srenew(excl->e, excl->nr);
            for (j = 0; (j < nnb->nrexcl[i][N]); j++)
            {
                /* For all first neighbours */
                if (nnb->a[i][N][j] != i)
                {
                    excl->e[n++] = nnb->a[i][N][j];
                }
            }
        }
    }
}

/* Generate pairs, angles and dihedrals from .rtp settings */
void gen_pad(t_nextnb *nnb, t_atoms *atoms, gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
             gmx::ArrayRef<InteractionsOfType> plist, t_excls excls[], gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
             bool bAllowMissing)
{
    /* These are the angles, dihedrals and pairs that we generate
     * from the bonds. The ones that are already there from the rtp file
     * will be retained.
     */
    std::vector<InteractionOfType>   ang;
    std::vector<InteractionOfType>   dih;
    std::vector<InteractionOfType>   pai;
    std::vector<InteractionOfType>   improper;

    std::array<std::string, 4>       anm;

    if (!globalPatches.empty())
    {
        gen_excls(atoms, excls, globalPatches, bAllowMissing);
        /* mark all entries as not matched yet */
        for (int i = 0; i < atoms->nres; i++)
        {
            for (int j = 0; j < ebtsNR; j++)
            {
                for (auto &bondeds : globalPatches[i].rb[j].b)
                {
                    bondeds.match = false;
                }
            }
        }
    }

    /* Extract all i-j-k-l neighbours from nnb struct to generate all
     * angles and dihedrals. */
    for (int i = 0; (i < nnb->nr); i++)
    {
        /* For all particles */
        for (int j = 0; (j < nnb->nrexcl[i][1]); j++)
        {
            /* For all first neighbours */
            int j1 = nnb->a[i][1][j];
            for (int k = 0; (k < nnb->nrexcl[j1][1]); k++)
            {
                /* For all first neighbours of j1 */
                int k1 = nnb->a[j1][1][k];
                if (k1 != i)
                {
                    /* Generate every angle only once */
                    if (i < k1)
                    {
                        std::vector<int> atomNumbers = {i, j1, k1};
                        std::string      name;
                        if (!globalPatches.empty())
                        {
                            int minres = atoms->atom[i].resind;
                            int maxres = minres;
                            for (int m = 1; m < 3; m++)
                            {
                                minres = std::min(minres, atoms->atom[atomNumbers[m]].resind);
                                maxres = std::max(maxres, atoms->atom[atomNumbers[m]].resind);
                            }
                            int res = 2*minres-maxres;
                            do
                            {
                                res += maxres-minres;
                                get_atomnames_min(3, anm, res, atoms, atomNumbers);
                                BondedInteractionList *hbang = &globalPatches[res].rb[ebtsANGLES];
                                for (auto &bondeds : hbang->b)
                                {
                                    if (anm[1] == bondeds.aj())
                                    {
                                        bool bFound = false;
                                        for (int m = 0; m < 3; m += 2)
                                        {
                                            bFound = (bFound ||
                                                      ((anm[m] == bondeds.ai()) &&
                                                       (anm[2-m] == bondeds.ak())));
                                        }
                                        if (bFound)
                                        {
                                            name = bondeds.s;
                                            /* Mark that we found a match for this entry */
                                            bondeds.match = true;
                                        }
                                    }
                                }
                            }
                            while (res < maxres);
                        }
                        ang.push_back(InteractionOfType(atomNumbers, {}, name));
                    }
                    /* Generate every dihedral, 1-4 exclusion and 1-4 interaction
                       only once */
                    if (j1 < k1)
                    {
                        for (int l = 0; (l < nnb->nrexcl[k1][1]); l++)
                        {
                            /* For all first neighbours of k1 */
                            int l1 = nnb->a[k1][1][l];
                            if ((l1 != i) && (l1 != j1))
                            {
                                std::vector<int> atomNumbers = {i, j1, k1, l1};
                                std::string      name;
                                int              nFound = 0;
                                if (!globalPatches.empty())
                                {
                                    int minres = atoms->atom[i].resind;
                                    int maxres = minres;
                                    for (int m = 1; m < 4; m++)
                                    {
                                        minres = std::min(
                                                    minres,
                                                    atoms->atom[atomNumbers[m]].resind);
                                        maxres = std::max(
                                                    maxres,
                                                    atoms->atom[atomNumbers[m]].resind);
                                    }
                                    int res = 2*minres-maxres;
                                    do
                                    {
                                        res += maxres-minres;
                                        get_atomnames_min(4, anm, res, atoms, atomNumbers);
                                        BondedInteractionList *hbdih = &globalPatches[res].rb[ebtsPDIHS];
                                        for (auto &bondeds : hbdih->b)
                                        {
                                            bool bFound = false;
                                            for (int m = 0; m < 2; m++)
                                            {
                                                bFound = (bFound ||
                                                          ((anm[3*m] == bondeds.ai()) &&
                                                           (anm[1+m] == bondeds.aj()) &&
                                                           (anm[2-m] == bondeds.ak()) &&
                                                           (anm[3-3*m] == bondeds.al())));
                                            }
                                            if (bFound)
                                            {
                                                name = bondeds.s;
                                                /* Mark that we found a match for this entry */
                                                bondeds.match = true;

                                                /* Set the last parameter to be able to see
                                                   if the dihedral was in the rtp list.
                                                 */
                                                nFound++;
                                                dih.push_back(InteractionOfType(atomNumbers, {}, name));
                                                dih.back().setForceParameter(MAXFORCEPARAM-1, DIHEDRAL_WAS_SET_IN_RTP);
                                            }
                                        }
                                    }
                                    while (res < maxres);
                                }
                                if (nFound == 0)
                                {
                                    std::vector<int> atoms = {i, j1, k1, l1};
                                    dih.push_back(InteractionOfType(atoms, {},   ""));
                                }

                                int nbd = nb_dist(nnb, i, l1);
                                if (nbd == 3)
                                {
                                    int  i1    = std::min(i, l1);
                                    int  i2    = std::max(i, l1);
                                    bool bExcl = false;
                                    for (int m = 0; m < excls[i1].nr; m++)
                                    {
                                        bExcl = bExcl || excls[i1].e[m] == i2;
                                    }
                                    if (!bExcl)
                                    {
                                        if (rtpFFDB[0].bGenerateHH14Interactions ||
                                            !(is_hydro(atoms, i1) && is_hydro(atoms, i2)))
                                        {
                                            std::vector<int> atoms = {i1, i2};
                                            pai.push_back(InteractionOfType(atoms, {}, ""));
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
    }

    if (!globalPatches.empty())
    {
        /* The above approach is great in that we double-check that e.g. an angle
         * really corresponds to three atoms connected by bonds, but this is not
         * generally true. Go through the angle and dihedral hackblocks to add
         * entries that we have not yet marked as matched when going through bonds.
         */
        for (int i = 0; i < atoms->nres; i++)
        {
            /* Add remaining angles from hackblock */
            BondedInteractionList *hbang = &globalPatches[i].rb[ebtsANGLES];
            for (auto &bondeds : hbang->b)
            {
                if (bondeds.match)
                {
                    /* We already used this entry, continue to the next */
                    continue;
                }
                /* Hm - entry not used, let's see if we can find all atoms */
                std::vector<int> atomNumbers;
                bool             bFound = true;
                for (int k = 0; k < 3 && bFound; k++)
                {
                    const char *p   = bondeds.a[k].c_str();
                    int         res = i;
                    if (p[0] == '-')
                    {
                        p++;
                        res--;
                    }
                    else if (p[0] == '+')
                    {
                        p++;
                        res++;
                    }
                    atomNumbers.emplace_back(search_res_atom(p, res, atoms, "angle", TRUE));
                    bFound            = (atomNumbers.back() != -1);
                }

                if (bFound)
                {
                    bondeds.match = true;
                    /* Incrementing nang means we save this angle */
                    ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
                }
            }

            /* Add remaining dihedrals from hackblock */
            BondedInteractionList *hbdih = &globalPatches[i].rb[ebtsPDIHS];
            for (auto &bondeds : hbdih->b)
            {
                if (bondeds.match)
                {
                    /* We already used this entry, continue to the next */
                    continue;
                }
                /* Hm - entry not used, let's see if we can find all atoms */
                std::vector<int> atomNumbers;
                bool             bFound = true;
                for (int k = 0; k < 4 && bFound; k++)
                {
                    const char *p   = bondeds.a[k].c_str();
                    int         res = i;
                    if (p[0] == '-')
                    {
                        p++;
                        res--;
                    }
                    else if (p[0] == '+')
                    {
                        p++;
                        res++;
                    }
                    atomNumbers.emplace_back(search_res_atom(p, res, atoms, "dihedral", TRUE));
                    bFound               = (atomNumbers.back() != -1);
                }

                if (bFound)
                {
                    bondeds.match = true;
                    /* Incrementing ndih means we save this dihedral */
                    dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
                }
            }
        }
    }

    /* Sort angles with respect to j-i-k (middle atom first) */
    if (ang.size() > 1)
    {
        std::sort(ang.begin(), ang.end(), acomp);
    }

    /* Sort dihedrals with respect to j-k-i-l (middle atoms first) */
    if (dih.size() > 1)
    {
        std::sort(dih.begin(), dih.end(), dcomp);
    }

    /* Sort the pairs */
    if (pai.size() > 1)
    {
        std::sort(pai.begin(), pai.end(), pcomp);
    }
    if (!pai.empty())
    {
        /* Remove doubles, could occur in 6-rings, such as phenyls,
           maybe one does not want this when fudgeQQ < 1.
         */
        fprintf(stderr, "Before cleaning: %zu pairs\n", pai.size());
        rm2par(&pai, preq);
    }

    /* Get the impropers from the database */
    improper = get_impropers(atoms, globalPatches, bAllowMissing);

    /* Sort the impropers */
    sort_id(improper);

    if (!dih.empty())
    {
        fprintf(stderr, "Before cleaning: %zu dihedrals\n", dih.size());
        dih = clean_dih(dih, improper, atoms,
                        rtpFFDB[0].bKeepAllGeneratedDihedrals,
                        rtpFFDB[0].bRemoveDihedralIfWithImproper);
    }

    /* Now we have unique lists of angles and dihedrals
     * Copy them into the destination struct
     */
    cppar(ang, plist, F_ANGLES);
    cppar(dih, plist, F_PDIHS);
    cppar(improper, plist, F_IDIHS);
    cppar(pai, plist, F_LJ14);

    /* Remove all exclusions which are within nrexcl */
    clean_excls(nnb, rtpFFDB[0].nrexcl, excls);
}