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37 * Implements test helper routines from toputils.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
51 #include "gromacs/fileio/confio.h"
52 #include "gromacs/fileio/trxio.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/topology/atoms.h"
55 #include "gromacs/topology/mtop_util.h"
56 #include "gromacs/topology/topology.h"
57 #include "gromacs/trajectory/trajectoryframe.h"
58 #include "gromacs/utility/arrayref.h"
59 #include "gromacs/utility/cstringutil.h"
60 #include "gromacs/utility/gmxassert.h"
61 #include "gromacs/utility/smalloc.h"
63 #include "testutils/testfilemanager.h"
70 TopologyManager::TopologyManager()
75 TopologyManager::~TopologyManager()
77 if (frame_ != nullptr)
86 for (char *atomtype : atomtypes_)
92 void TopologyManager::requestFrame()
94 GMX_RELEASE_ASSERT(mtop_ == nullptr,
95 "Frame must be requested before initializing topology");
96 if (frame_ == nullptr)
102 void TopologyManager::requestVelocities()
104 GMX_RELEASE_ASSERT(frame_ != nullptr,
105 "Velocities requested before requesting a frame");
107 if (frame_->natoms > 0)
109 snew(frame_->v, frame_->natoms);
113 void TopologyManager::requestForces()
115 GMX_RELEASE_ASSERT(frame_ != nullptr,
116 "Forces requested before requesting a frame");
118 if (frame_->natoms > 0)
120 snew(frame_->f, frame_->natoms);
124 void TopologyManager::loadTopology(const char *filename)
128 rvec *xtop = nullptr;
131 GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
132 mtop_ = std::make_unique<gmx_mtop_t>();
134 gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
135 &fullTopology, mtop_.get(), &ePBC, frame_ != nullptr ? &xtop : nullptr,
138 if (frame_ != nullptr)
140 GMX_ASSERT(xtop != nullptr, "Keep the static analyzer happy");
141 frame_->natoms = mtop_->natoms;
143 snew(frame_->x, frame_->natoms);
144 std::memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
146 copy_mat(box, frame_->box);
152 void TopologyManager::initAtoms(int count)
154 GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
155 mtop_ = std::make_unique<gmx_mtop_t>();
156 mtop_->moltype.resize(1);
157 init_t_atoms(&mtop_->moltype[0].atoms, count, FALSE);
158 mtop_->molblock.resize(1);
159 mtop_->molblock[0].type = 0;
160 mtop_->molblock[0].nmol = 1;
161 mtop_->natoms = count;
162 mtop_->maxres_renum = 0;
163 gmx_mtop_finalize(mtop_.get());
164 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");
165 t_atoms &atoms = this->atoms();
166 for (int i = 0; i < count; ++i)
168 atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
170 atoms.haveMass = TRUE;
171 if (frame_ != nullptr)
173 frame_->natoms = count;
175 snew(frame_->x, count);
178 snew(frame_->v, count);
182 snew(frame_->f, count);
187 void TopologyManager::initAtomTypes(const ArrayRef<const char *const> &types)
189 GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
190 atomtypes_.reserve(types.size());
191 for (const char *type : types)
193 atomtypes_.push_back(gmx_strdup(type));
195 t_atoms &atoms = this->atoms();
196 snew(atoms.atomtype, atoms.nr);
198 for (int i = 0; i < atoms.nr; ++i, ++j)
200 if (j == types.size())
204 atoms.atomtype[i] = &atomtypes_[j];
206 atoms.haveType = TRUE;
209 void TopologyManager::initUniformResidues(int residueSize)
211 GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
212 t_atoms &atoms = this->atoms();
213 int residueIndex = -1;
214 for (int i = 0; i < atoms.nr; ++i)
216 if (i % residueSize == 0)
220 atoms.atom[i].resind = residueIndex;
222 atoms.nres = residueIndex;
225 void TopologyManager::initUniformMolecules(int moleculeSize)
227 GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
228 GMX_RELEASE_ASSERT(mtop_->molblock.size() == 1, "initUniformMolecules only implemented for a single molblock");
229 gmx_molblock_t &molblock = mtop_->molblock[0];
230 t_atoms &atoms = mtop_->moltype[molblock.type].atoms;
231 GMX_RELEASE_ASSERT(atoms.nr % moleculeSize == 0,
232 "The number of atoms should be a multiple of moleculeSize");
233 molblock.nmol = atoms.nr/moleculeSize;
234 atoms.nr = moleculeSize;
235 const int nres = atoms.atom[atoms.nr].resind;
236 GMX_RELEASE_ASSERT(atoms.atom[atoms.nr-1].resind != nres,
237 "The residues should break at molecule boundaries");
239 mtop_->haveMoleculeIndices = true;
240 gmx_mtop_finalize(mtop_.get());
243 void TopologyManager::initFrameIndices(const ArrayRef<const int> &index)
245 GMX_RELEASE_ASSERT(frame_ != nullptr, "Frame not initialized");
246 GMX_RELEASE_ASSERT(!frame_->bIndex, "Frame atom indices can only be set once");
248 frame_->bIndex = TRUE;
249 snew(frame_->index, index.size());
250 std::copy(index.begin(), index.end(), frame_->index);
252 frame_->natoms = index.size();
255 t_atoms &TopologyManager::atoms()
257 GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
258 GMX_RELEASE_ASSERT(mtop_->natoms == mtop_->moltype[0].atoms.nr,
259 "Test setup assumes all atoms in a single molecule type");
260 return mtop_->moltype[0].atoms;