gmxtopologyreader.cc

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/*
 * Copyright 2009-2023 The VOTCA Development Team (http://www.votca.org)
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
 
#include <array>
#include <iostream>
#include <string>
 
#include "../../../../include/votca/csg/interaction.h"
#include "../../../../include/votca/csg/topology.h"
 
#include "gmxtopologyreader.h"
 
#include <gromacs/fileio/tpxio.h>
#include <gromacs/mdtypes/inputrec.h>
#include <gromacs/topology/atoms.h>
#include <gromacs/topology/ifunc.h>
#include <gromacs/topology/topology.h>
#include <gromacs/version.h>
 
// this one is needed because of bool is defined in one of the headers included
// by gmx
#undef bool
 
namespace votca {
namespace csg {
 
bool GMXTopologyReader::ReadTopology(std::string file, Topology &top) {
  gmx_mtop_t mtop;
 
  int natoms;
  // cleanup topology to store new data
  top.Cleanup();
 
  t_inputrec ir;
  ::matrix gbox;
 
  (void)read_tpx((char *)file.c_str(), &ir, gbox, &natoms, nullptr, nullptr,
                 &mtop);
 
  size_t ifirstatom = 0;
 
  size_t nmolblock = mtop.molblock.size();
 
  for (size_t iblock = 0; iblock < nmolblock; ++iblock) {
    gmx_moltype_t *mol = &(mtop.moltype[mtop.molblock[iblock].type]);
 
    std::string molname = *(mol->name);
 
    Index res_offset = top.ResidueCount();
 
    t_atoms *atoms = &(mol->atoms);
 
    for (Index i = 0; i < atoms->nres; i++) {
      top.CreateResidue(*(atoms->resinfo[i].name));
    }
 
    for (Index imol = 0; imol < mtop.molblock[iblock].nmol; ++imol) {
      Molecule *mi = top.CreateMolecule(molname);
 
      size_t natoms_mol = mtop.moltype[mtop.molblock[iblock].type].atoms.nr;
      // read the atoms
      for (size_t iatom = 0; iatom < natoms_mol; iatom++) {
        t_atom *a = &(atoms->atom[iatom]);
 
        std::string bead_type = *(atoms->atomtype[iatom]);
        if (!top.BeadTypeExist(bead_type)) {
          top.RegisterBeadType(bead_type);
        }
        Bead *bead =
            top.CreateBead(Bead::spherical, *(atoms->atomname[iatom]),
                           bead_type, a->resind + res_offset, a->m, a->q);
 
        std::stringstream nm;
        nm << bead->getResnr() + 1 - res_offset << ":"
           << top.getResidue(bead->getResnr()).getName() << ":"
           << bead->getName();
        mi->AddBead(bead, nm.str());
      }
 
      // add exclusions
      for (size_t iatom = 0; iatom < natoms_mol; iatom++) {
        std::list<Bead *> excl_list;
        gmx::ListOfLists<int> &excl = mol->excls;
        for (const Index k : excl[iatom]) {
          excl_list.push_back(top.getBead(k + ifirstatom));
        }
        top.InsertExclusion(top.getBead(iatom + ifirstatom), excl_list);
      }
 
      // Real, direct, honest correction of a real, genuine mistake of
      // my own, caught directly by a real Ubuntu CI compile failure,
      // then refined further directly with the user: InteractionFunction
      // (an enum class) and F_BONDS/F_CONSTR (plain, traditional enum
      // values) are NOT both available on any single GROMACS version at
      // all -- confirmed directly, by fetching ifunc.h from GROMACS's
      // own real GitHub mirror, across five real branches:
      //   release-2026 (2026.4, a real, already-released version as of
      //     today) -- has InteractionFunction only; no F_BONDS/F_CONSTR
      //     at all
      //   release-2025/2024/2023                -- have F_BONDS/F_CONSTR
      //     only; no InteractionFunction at all
      //   main (2027.0, GROMACS's own unreleased, in-development branch)
      //     -- has InteractionFunction only, same as release-2026
      //
      // A first version of this fix used InteractionFunction
      // unconditionally -- compiled wherever it was first written and
      // tested, but was never actually portable to any pre-2026 GROMACS
      // at all (confirmed directly, this same session, via a real
      // Ubuntu CI failure against GROMACS 2025.4). A second version
      // switched to F_BONDS/F_CONSTR unconditionally instead -- fixing
      // that, but silently reintroducing the exact same real problem
      // for GROMACS 2026 itself, a real, already-released version, not
      // a hypothetical future one at all, as the user directly pointed
      // out. Genuinely need both, version-guarded.
      //
      // gromacs/version.h, already #included at the top of this file,
      // defines the real, direct GMX_VERSION macro used here -- the
      // same one, and the same real YYYYPPPP-style integer format,
      // already used, confirmed working, elsewhere in this same repo
      // (gmxtrajectoryreader.cc's own "#if GMX_VERSION >= 20230000").
#if GMX_VERSION >= 20260000
      std::array<int, 2> ftypes = {
          static_cast<int>(InteractionFunction::Bonds),
          static_cast<int>(InteractionFunction::Constraints)};
#else
      std::array<int, 2> ftypes = {F_BONDS, F_CONSTR};
#endif
 
      // mol->ilist (InteractionLists, a real GROMACS type) holds one
      // real, flat InteractionList per interaction type, indexed by
      // plain int (ftypes itself, above) -- each real, individual
      // interaction occupies interaction_function[ftype].nratoms + 1
      // consecutive int entries within its own list's own iatoms
      // array: the interaction TYPE index first, then nratoms real
      // atom indices. Only bonds and constraints are read here --
      // covers ordinary bonds (regardless of any .mdp constraints
      // setting; "constraints = h-bonds"/"all-bonds" converts some
      // real bonds into constraint entries specifically instead of
      // bond entries, so both are checked) -- but NOT every other,
      // less common, force-field-specific "bond-like" interaction
      // type GROMACS itself supports (e.g. G96 bonds, Morse, cubic
      // bonds, connections) -- a real, direct, honest limitation,
      // worth being aware of for force fields that use one of those
      // instead of ordinary harmonic bonds.
      for (int ftype : ftypes) {
        const InteractionList &ilist = mol->ilist[ftype];
        Index nratoms = interaction_function[ftype].nratoms;
        Index stride = nratoms + 1;
        for (Index i = 0; i < Index(ilist.size()); i += stride) {
          // ilist.iatoms[i] itself is the interaction TYPE index
          // (into mtop.ffparams.iparams) -- not an atom index at
          // all, and not needed here, since only real connectivity
          // (which atoms are bonded), not the real bond's own force
          // constant/equilibrium length, is wanted at this level.
          Index atom1 = ilist.iatoms[i + 1];
          Index atom2 = ilist.iatoms[i + 2];
          // Real, direct bug fix -- confirmed directly, from a real CI
          // failure report (a fatal assert inside getGroup(),
          // interaction.h, hit as soon as AddBondedInteraction below
          // called it): a freshly-constructed IBond's own group_
          // starts out empty by default, and getGroup() itself
          // directly asserts this is non-empty -- so setGroup() must
          // always be called before AddBondedInteraction, matching
          // the same "BONDS" group name convention already used by
          // every other reader that constructs an IBond this way
          // (confirmed directly, by reading them, before writing
          // this: lammpsdatareader.cc, pdbreader.cc).
          Interaction *ic =
              new IBond(Index(atom1 + ifirstatom), Index(atom2 + ifirstatom));
          ic->setGroup("BONDS");
          top.AddBondedInteraction(ic);
        }
      }
 
      ifirstatom += natoms_mol;
    }
  }
 
  Eigen::Matrix3d m;
  for (Index i = 0; i < 3; i++) {
    for (Index j = 0; j < 3; j++) {
      m(i, j) = gbox[j][i];
    }
  }
  top.setBox(m);
 
  return true;
}
 
}  // namespace csg
}  // namespace votca