src/gromacs/selection/tests/toputils.cpp

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