src/gromacs/selection/tests/toputils.cpp

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  36 /*! \internal \file
  37  * \brief
  38  * Implements test helper routines from toputils.h.
  39  *
  40  * \author Teemu Murtola <teemu.murtola@gmail.com>
  41  * \ingroup module_selection
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "toputils.h"
  46
  47 #include <cstring>
  48
  49 #include <algorithm>
  50 #include <memory>
  51 #include <numeric>
  52
  53 #include "gromacs/fileio/confio.h"
  54 #include "gromacs/fileio/trxio.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/topology/atoms.h"
  57 #include "gromacs/topology/mtop_util.h"
  58 #include "gromacs/topology/topology.h"
  59 #include "gromacs/trajectory/trajectoryframe.h"
  60 #include "gromacs/utility/arrayref.h"
  61 #include "gromacs/utility/cstringutil.h"
  62 #include "gromacs/utility/gmxassert.h"
  63 #include "gromacs/utility/smalloc.h"
  64
  65 #include "testutils/testfilemanager.h"
  66
  67 namespace gmx
  68 {
  69 namespace test
  70 {
  71
  72 TopologyManager::TopologyManager() : frame_(nullptr) {}
  73
  74 TopologyManager::~TopologyManager()
  75 {
  76     if (frame_ != nullptr)
  77     {
  78         sfree(frame_->x);
  79         sfree(frame_->v);
  80         sfree(frame_->f);
  81         sfree(frame_->index);
  82         sfree(frame_);
  83     }
  84
  85     for (char* atomtype : atomtypes_)
  86     {
  87         sfree(atomtype);
  88     }
  89 }
  90
  91 void TopologyManager::requestFrame()
  92 {
  93     GMX_RELEASE_ASSERT(mtop_ == nullptr, "Frame must be requested before initializing topology");
  94     if (frame_ == nullptr)
  95     {
  96         snew(frame_, 1);
  97     }
  98 }
  99
 100 void TopologyManager::requestVelocities()
 101 {
 102     GMX_RELEASE_ASSERT(frame_ != nullptr, "Velocities requested before requesting a frame");
 103     frame_->bV = TRUE;
 104     if (frame_->natoms > 0)
 105     {
 106         snew(frame_->v, frame_->natoms);
 107     }
 108 }
 109
 110 void TopologyManager::requestForces()
 111 {
 112     GMX_RELEASE_ASSERT(frame_ != nullptr, "Forces requested before requesting a frame");
 113     frame_->bF = TRUE;
 114     if (frame_->natoms > 0)
 115     {
 116         snew(frame_->f, frame_->natoms);
 117     }
 118 }
 119
 120 void TopologyManager::loadTopology(const char* filename)
 121 {
 122     bool   fullTopology;
 123     int    ePBC;
 124     rvec*  xtop = nullptr;
 125     matrix box;
 126
 127     GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
 128     mtop_ = std::make_unique<gmx_mtop_t>();
 129     readConfAndTopology(gmx::test::TestFileManager::getInputFilePath(filename).c_str(), &fullTopology,
 130                         mtop_.get(), &ePBC, frame_ != nullptr ? &xtop : nullptr, nullptr, box);
 131
 132     if (frame_ != nullptr)
 133     {
 134         GMX_ASSERT(xtop != nullptr, "Keep the static analyzer happy");
 135         frame_->natoms = mtop_->natoms;
 136         frame_->bX     = TRUE;
 137         snew(frame_->x, frame_->natoms);
 138         std::memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
 139         frame_->bBox = TRUE;
 140         copy_mat(box, frame_->box);
 141     }
 142
 143     sfree(xtop);
 144 }
 145
 146 void TopologyManager::initAtoms(int count)
 147 {
 148     GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
 149     mtop_ = std::make_unique<gmx_mtop_t>();
 150     mtop_->moltype.resize(1);
 151     init_t_atoms(&mtop_->moltype[0].atoms, count, FALSE);
 152     mtop_->molblock.resize(1);
 153     mtop_->molblock[0].type = 0;
 154     mtop_->molblock[0].nmol = 1;
 155     mtop_->natoms           = count;
 156     mtop_->maxres_renum     = 0;
 157     gmx_mtop_finalize(mtop_.get());
 158     GMX_RELEASE_ASSERT(mtop_->maxres_renum == 0,
 159                        "maxres_renum in mtop can be modified by an env.var., that is not supported "
 160                        "in this test");
 161     t_atoms& atoms = this->atoms();
 162     for (int i = 0; i < count; ++i)
 163     {
 164         atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
 165     }
 166     atoms.haveMass = TRUE;
 167     if (frame_ != nullptr)
 168     {
 169         frame_->natoms = count;
 170         frame_->bX     = TRUE;
 171         snew(frame_->x, count);
 172         if (frame_->bV)
 173         {
 174             snew(frame_->v, count);
 175         }
 176         if (frame_->bF)
 177         {
 178             snew(frame_->f, count);
 179         }
 180     }
 181 }
 182
 183 void TopologyManager::initAtomTypes(const ArrayRef<const char* const>& types)
 184 {
 185     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 186     atomtypes_.reserve(types.size());
 187     for (const char* type : types)
 188     {
 189         atomtypes_.push_back(gmx_strdup(type));
 190     }
 191     t_atoms& atoms = this->atoms();
 192     snew(atoms.atomtype, atoms.nr);
 193     index j = 0;
 194     for (int i = 0; i < atoms.nr; ++i, ++j)
 195     {
 196         if (j == types.ssize())
 197         {
 198             j = 0;
 199         }
 200         atoms.atomtype[i] = &atomtypes_[j];
 201     }
 202     atoms.haveType = TRUE;
 203 }
 204
 205 void TopologyManager::initTopology(const int numMoleculeTypes, const int numMoleculeBlocks)
 206 {
 207     GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
 208     mtop_ = std::make_unique<gmx_mtop_t>();
 209     mtop_->moltype.resize(numMoleculeTypes);
 210     mtop_->molblock.resize(numMoleculeBlocks);
 211 }
 212
 213 void TopologyManager::setMoleculeType(const int moleculeTypeIndex, const ArrayRef<const int> residueSizes)
 214 {
 215     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 216
 217     // Make a molecule block that refers to a new molecule type
 218     auto& newMoleculeType = mtop_->moltype[moleculeTypeIndex];
 219     auto& atoms           = newMoleculeType.atoms;
 220
 221     auto numAtomsInMolecule = std::accumulate(residueSizes.begin(), residueSizes.end(), 0);
 222     init_t_atoms(&atoms, numAtomsInMolecule, FALSE);
 223     atoms.nres = residueSizes.size();
 224
 225     // Fill the residues in the molecule type
 226     int  residueIndex = 0;
 227     auto residueSize  = std::begin(residueSizes);
 228     for (int i = 0; i < atoms.nr && residueSize != std::end(residueSizes); ++residueSize, ++residueIndex)
 229     {
 230         for (int j = 0; i < atoms.nr && j < *residueSize; ++i, ++j)
 231         {
 232             atoms.atom[i].resind = residueIndex;
 233             atoms.atom[i].m      = (i % 3 == 0 ? 2.0 : 1.0);
 234         }
 235     }
 236     atoms.nres     = residueIndex;
 237     atoms.haveMass = true;
 238 }
 239
 240 void TopologyManager::setMoleculeBlock(const int moleculeBlockIndex,
 241                                        const int moleculeTypeIndex,
 242                                        const int numMoleculesToAdd)
 243 {
 244     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 245
 246     auto& newMoleculeBlock = mtop_->molblock[moleculeBlockIndex];
 247     newMoleculeBlock.type  = moleculeTypeIndex;
 248     newMoleculeBlock.nmol  = numMoleculesToAdd;
 249
 250     mtop_->natoms += numMoleculesToAdd * mtop_->moltype[moleculeTypeIndex].atoms.nr;
 251 }
 252
 253 void TopologyManager::finalizeTopology()
 254 {
 255     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 256
 257     mtop_->maxres_renum        = 0;
 258     mtop_->haveMoleculeIndices = true;
 259     gmx_mtop_finalize(mtop_.get());
 260 }
 261
 262 void TopologyManager::initUniformResidues(int residueSize)
 263 {
 264     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 265     t_atoms& atoms        = this->atoms();
 266     int      residueIndex = -1;
 267     for (int i = 0; i < atoms.nr; ++i)
 268     {
 269         if (i % residueSize == 0)
 270         {
 271             ++residueIndex;
 272         }
 273         atoms.atom[i].resind = residueIndex;
 274     }
 275     atoms.nres = residueIndex;
 276 }
 277
 278 void TopologyManager::initUniformMolecules(int moleculeSize)
 279 {
 280     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 281     GMX_RELEASE_ASSERT(mtop_->molblock.size() == 1,
 282                        "initUniformMolecules only implemented for a single molblock");
 283     gmx_molblock_t& molblock = mtop_->molblock[0];
 284     t_atoms&        atoms    = mtop_->moltype[molblock.type].atoms;
 285     GMX_RELEASE_ASSERT(atoms.nr % moleculeSize == 0,
 286                        "The number of atoms should be a multiple of moleculeSize");
 287     molblock.nmol  = atoms.nr / moleculeSize;
 288     atoms.nr       = moleculeSize;
 289     const int nres = atoms.atom[atoms.nr].resind;
 290     GMX_RELEASE_ASSERT(atoms.atom[atoms.nr - 1].resind != nres,
 291                        "The residues should break at molecule boundaries");
 292     atoms.nres                 = nres;
 293     mtop_->haveMoleculeIndices = true;
 294     gmx_mtop_finalize(mtop_.get());
 295 }
 296
 297 void TopologyManager::initFrameIndices(const ArrayRef<const int>& index)
 298 {
 299     GMX_RELEASE_ASSERT(frame_ != nullptr, "Frame not initialized");
 300     GMX_RELEASE_ASSERT(!frame_->bIndex, "Frame atom indices can only be set once");
 301
 302     frame_->bIndex = TRUE;
 303     snew(frame_->index, index.size());
 304     std::copy(index.begin(), index.end(), frame_->index);
 305
 306     frame_->natoms = index.size();
 307 }
 308
 309 t_atoms& TopologyManager::atoms()
 310 {
 311     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 312     GMX_RELEASE_ASSERT(mtop_->natoms == mtop_->moltype[0].atoms.nr,
 313                        "Test setup assumes all atoms in a single molecule type");
 314     return mtop_->moltype[0].atoms;
 315 }
 316
 317 } // namespace test
 318 } // namespace gmx