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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/smalloc.h"
47 #include "gromacs/legacyheaders/statutil.h"
48 #include "gromacs/legacyheaders/string2.h"
49 #include "gromacs/fileio/tpxio.h"
50 #include "gromacs/fileio/trxio.h"
51 #include "gromacs/legacyheaders/typedefs.h"
52 #include "gromacs/legacyheaders/vec.h"
54 #include "gromacs/utility/gmxassert.h"
56 #include "testutils/testfilemanager.h"
63 TopologyManager::TopologyManager()
64 : top_(NULL), frame_(NULL)
68 TopologyManager::~TopologyManager()
72 free_t_atoms(&top_->atoms, TRUE);
86 void TopologyManager::requestFrame()
88 GMX_RELEASE_ASSERT(top_ == NULL,
89 "Frame must be requested before initializing topology");
96 void TopologyManager::requestVelocities()
98 GMX_RELEASE_ASSERT(frame_ != NULL,
99 "Velocities requested before requesting a frame");
101 if (frame_->natoms > 0)
103 snew(frame_->v, frame_->natoms);
107 void TopologyManager::requestForces()
109 GMX_RELEASE_ASSERT(frame_ != NULL,
110 "Forces requested before requesting a frame");
112 if (frame_->natoms > 0)
114 snew(frame_->f, frame_->natoms);
118 void TopologyManager::loadTopology(const char *filename)
125 GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
127 read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
128 title, top_, &ePBC, frame_ != NULL ? &xtop : NULL,
133 frame_->flags = TRX_NEED_X;
134 frame_->natoms = top_->atoms.nr;
136 snew(frame_->x, frame_->natoms);
137 std::memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
139 copy_mat(box, frame_->box);
145 void TopologyManager::initAtoms(int count)
147 GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
149 init_t_atoms(&top_->atoms, count, FALSE);
150 for (int i = 0; i < count; ++i)
152 top_->atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
156 frame_->flags = TRX_NEED_X;
157 frame_->natoms = count;
159 snew(frame_->x, count);
162 snew(frame_->v, count);
166 snew(frame_->f, count);
171 void TopologyManager::initAtomTypes(int count, const char *const types[])
173 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
174 atomtypes_.reserve(count);
175 for (int i = 0; i < count; ++i)
177 atomtypes_.push_back(strdup(types[i]));
179 snew(top_->atoms.atomtype, top_->atoms.nr);
180 for (int i = 0, j = 0; i < top_->atoms.nr; ++i, ++j)
186 top_->atoms.atomtype[i] = &atomtypes_[j];
190 void TopologyManager::initUniformResidues(int residueSize)
192 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
193 int residueIndex = -1;
194 for (int i = 0; i < top_->atoms.nr; ++i)
196 if (i % residueSize == 0)
200 top_->atoms.atom[i].resind = residueIndex;
204 void TopologyManager::initUniformMolecules(int moleculeSize)
206 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
208 top_->mols.nalloc_index = (top_->atoms.nr + moleculeSize - 1) / moleculeSize + 1;
209 snew(top_->mols.index, top_->mols.nalloc_index);
211 while (index < top_->atoms.nr)
213 top_->mols.index[top_->mols.nr] = index;
215 index += moleculeSize;
217 top_->mols.index[top_->mols.nr] = top_->atoms.nr;