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37 * Implements test helper routines from toputils.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
46 #include "gromacs/legacyheaders/typedefs.h"
47 #include "gromacs/legacyheaders/vec.h"
49 #include "gromacs/fileio/tpxio.h"
50 #include "gromacs/fileio/trxio.h"
51 #include "gromacs/utility/gmxassert.h"
52 #include "gromacs/utility/smalloc.h"
54 #include "testutils/testfilemanager.h"
61 TopologyManager::TopologyManager()
62 : top_(NULL), frame_(NULL)
66 TopologyManager::~TopologyManager()
70 free_t_atoms(&top_->atoms, TRUE);
84 void TopologyManager::requestFrame()
86 GMX_RELEASE_ASSERT(top_ == NULL,
87 "Frame must be requested before initializing topology");
94 void TopologyManager::requestVelocities()
96 GMX_RELEASE_ASSERT(frame_ != NULL,
97 "Velocities requested before requesting a frame");
99 if (frame_->natoms > 0)
101 snew(frame_->v, frame_->natoms);
105 void TopologyManager::requestForces()
107 GMX_RELEASE_ASSERT(frame_ != NULL,
108 "Forces requested before requesting a frame");
110 if (frame_->natoms > 0)
112 snew(frame_->f, frame_->natoms);
116 void TopologyManager::loadTopology(const char *filename)
123 GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
125 read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
126 title, top_, &ePBC, frame_ != NULL ? &xtop : NULL,
131 frame_->flags = TRX_NEED_X;
132 frame_->natoms = top_->atoms.nr;
134 snew(frame_->x, frame_->natoms);
135 std::memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
137 copy_mat(box, frame_->box);
143 void TopologyManager::initAtoms(int count)
145 GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
147 init_t_atoms(&top_->atoms, count, FALSE);
148 for (int i = 0; i < count; ++i)
150 top_->atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
154 frame_->flags = TRX_NEED_X;
155 frame_->natoms = count;
157 snew(frame_->x, count);
160 snew(frame_->v, count);
164 snew(frame_->f, count);
169 void TopologyManager::initAtomTypes(int count, const char *const types[])
171 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
172 atomtypes_.reserve(count);
173 for (int i = 0; i < count; ++i)
175 atomtypes_.push_back(strdup(types[i]));
177 snew(top_->atoms.atomtype, top_->atoms.nr);
178 for (int i = 0, j = 0; i < top_->atoms.nr; ++i, ++j)
184 top_->atoms.atomtype[i] = &atomtypes_[j];
188 void TopologyManager::initUniformResidues(int residueSize)
190 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
191 int residueIndex = -1;
192 for (int i = 0; i < top_->atoms.nr; ++i)
194 if (i % residueSize == 0)
198 top_->atoms.atom[i].resind = residueIndex;
202 void TopologyManager::initUniformMolecules(int moleculeSize)
204 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
206 top_->mols.nalloc_index = (top_->atoms.nr + moleculeSize - 1) / moleculeSize + 1;
207 snew(top_->mols.index, top_->mols.nalloc_index);
209 while (index < top_->atoms.nr)
211 top_->mols.index[top_->mols.nr] = index;
213 index += moleculeSize;
215 top_->mols.index[top_->mols.nr] = top_->atoms.nr;