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     PbcType pbcType;
 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(), &pbcType, 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_->finalize();
 157     GMX_RELEASE_ASSERT(mtop_->maxResiduesPerMoleculeToTriggerRenumber() == 0,
 158                        "maxres_renum in mtop can be modified by an env.var., that is not supported "
 159                        "in this test");
 160     t_atoms& atoms = this->atoms();
 161     for (int i = 0; i < count; ++i)
 162     {
 163         atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
 164     }
 165     atoms.haveMass = TRUE;
 166     if (frame_ != nullptr)
 167     {
 168         frame_->natoms = count;
 169         frame_->bX     = TRUE;
 170         snew(frame_->x, count);
 171         if (frame_->bV)
 172         {
 173             snew(frame_->v, count);
 174         }
 175         if (frame_->bF)
 176         {
 177             snew(frame_->f, count);
 178         }
 179     }
 180 }
 181
 182 void TopologyManager::initAtomTypes(const ArrayRef<const char* const>& types)
 183 {
 184     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 185     atomtypes_.reserve(types.size());
 186     for (const char* type : types)
 187     {
 188         atomtypes_.push_back(gmx_strdup(type));
 189     }
 190     t_atoms& atoms = this->atoms();
 191     snew(atoms.atomtype, atoms.nr);
 192     index j = 0;
 193     for (int i = 0; i < atoms.nr; ++i, ++j)
 194     {
 195         if (j == types.ssize())
 196         {
 197             j = 0;
 198         }
 199         atoms.atomtype[i] = &atomtypes_[j];
 200     }
 201     atoms.haveType = TRUE;
 202 }
 203
 204 void TopologyManager::initTopology(const int numMoleculeTypes, const int numMoleculeBlocks)
 205 {
 206     GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
 207     mtop_ = std::make_unique<gmx_mtop_t>();
 208     mtop_->moltype.resize(numMoleculeTypes);
 209     mtop_->molblock.resize(numMoleculeBlocks);
 210 }
 211
 212 void TopologyManager::setMoleculeType(const int moleculeTypeIndex, const ArrayRef<const int> residueSizes)
 213 {
 214     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 215
 216     // Make a molecule block that refers to a new molecule type
 217     auto& newMoleculeType = mtop_->moltype[moleculeTypeIndex];
 218     auto& atoms           = newMoleculeType.atoms;
 219
 220     auto numAtomsInMolecule = std::accumulate(residueSizes.begin(), residueSizes.end(), 0);
 221     init_t_atoms(&atoms, numAtomsInMolecule, FALSE);
 222     atoms.nres = residueSizes.size();
 223
 224     // Fill the residues in the molecule type
 225     int  residueIndex = 0;
 226     auto residueSize  = std::begin(residueSizes);
 227     for (int i = 0; i < atoms.nr && residueSize != std::end(residueSizes); ++residueSize, ++residueIndex)
 228     {
 229         for (int j = 0; i < atoms.nr && j < *residueSize; ++i, ++j)
 230         {
 231             atoms.atom[i].resind = residueIndex;
 232             atoms.atom[i].m      = (i % 3 == 0 ? 2.0 : 1.0);
 233         }
 234     }
 235     atoms.nres     = residueIndex;
 236     atoms.haveMass = true;
 237 }
 238
 239 void TopologyManager::setMoleculeBlock(const int moleculeBlockIndex,
 240                                        const int moleculeTypeIndex,
 241                                        const int numMoleculesToAdd)
 242 {
 243     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 244
 245     auto& newMoleculeBlock = mtop_->molblock[moleculeBlockIndex];
 246     newMoleculeBlock.type  = moleculeTypeIndex;
 247     newMoleculeBlock.nmol  = numMoleculesToAdd;
 248
 249     mtop_->natoms += numMoleculesToAdd * mtop_->moltype[moleculeTypeIndex].atoms.nr;
 250 }
 251
 252 void TopologyManager::finalizeTopology()
 253 {
 254     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 255
 256     mtop_->haveMoleculeIndices = true;
 257     mtop_->finalize();
 258 }
 259
 260 void TopologyManager::initUniformResidues(int residueSize)
 261 {
 262     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 263     t_atoms& atoms        = this->atoms();
 264     int      residueIndex = -1;
 265     for (int i = 0; i < atoms.nr; ++i)
 266     {
 267         if (i % residueSize == 0)
 268         {
 269             ++residueIndex;
 270         }
 271         atoms.atom[i].resind = residueIndex;
 272     }
 273     atoms.nres = residueIndex;
 274 }
 275
 276 void TopologyManager::initUniformMolecules(int moleculeSize)
 277 {
 278     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 279     GMX_RELEASE_ASSERT(mtop_->molblock.size() == 1,
 280                        "initUniformMolecules only implemented for a single molblock");
 281     gmx_molblock_t& molblock = mtop_->molblock[0];
 282     t_atoms&        atoms    = mtop_->moltype[molblock.type].atoms;
 283     GMX_RELEASE_ASSERT(atoms.nr % moleculeSize == 0,
 284                        "The number of atoms should be a multiple of moleculeSize");
 285     molblock.nmol  = atoms.nr / moleculeSize;
 286     atoms.nr       = moleculeSize;
 287     const int nres = atoms.atom[atoms.nr].resind;
 288     GMX_RELEASE_ASSERT(atoms.atom[atoms.nr - 1].resind != nres,
 289                        "The residues should break at molecule boundaries");
 290     atoms.nres                 = nres;
 291     mtop_->haveMoleculeIndices = true;
 292     mtop_->finalize();
 293 }
 294
 295 void TopologyManager::initFrameIndices(const ArrayRef<const int>& index)
 296 {
 297     GMX_RELEASE_ASSERT(frame_ != nullptr, "Frame not initialized");
 298     GMX_RELEASE_ASSERT(!frame_->bIndex, "Frame atom indices can only be set once");
 299
 300     frame_->bIndex = TRUE;
 301     snew(frame_->index, index.size());
 302     std::copy(index.begin(), index.end(), frame_->index);
 303
 304     frame_->natoms = index.size();
 305 }
 306
 307 t_atoms& TopologyManager::atoms()
 308 {
 309     GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
 310     GMX_RELEASE_ASSERT(mtop_->natoms == mtop_->moltype[0].atoms.nr,
 311                        "Test setup assumes all atoms in a single molecule type");
 312     return mtop_->moltype[0].atoms;
 313 }
 314
 315 } // namespace test
 316 } // namespace gmx