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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/tpxio.h"
49 #include "gromacs/legacyheaders/typedefs.h"
50 #include "gromacs/legacyheaders/vec.h"
52 #include "gromacs/utility/gmxassert.h"
54 #include "testutils/testfilemanager.h"
61 TopologyManager::TopologyManager()
62 : top_(NULL), frame_(NULL)
66 TopologyManager::~TopologyManager()
70 free_t_atoms(&top_->atoms, TRUE);
82 void TopologyManager::requestFrame()
84 GMX_RELEASE_ASSERT(top_ == NULL,
85 "Frame must be requested before initializing topology");
92 void TopologyManager::loadTopology(const char *filename)
99 GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
101 read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
102 title, top_, &ePBC, frame_ != NULL ? &xtop : NULL,
107 frame_->flags = TRX_NEED_X;
108 frame_->natoms = top_->atoms.nr;
110 snew(frame_->x, frame_->natoms);
111 std::memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
113 copy_mat(box, frame_->box);
119 void TopologyManager::initAtoms(int count)
121 GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
123 init_t_atoms(&top_->atoms, count, FALSE);
124 for (int i = 0; i < count; ++i)
126 top_->atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
130 frame_->flags = TRX_NEED_X;
131 frame_->natoms = count;
133 snew(frame_->x, count);
137 void TopologyManager::initUniformResidues(int residueSize)
139 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
140 int residueIndex = -1;
141 for (int i = 0; i < top_->atoms.nr; ++i)
143 if (i % residueSize == 0)
147 top_->atoms.atom[i].resind = residueIndex;
151 void TopologyManager::initUniformMolecules(int moleculeSize)
153 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
155 top_->mols.nalloc_index = (top_->atoms.nr + moleculeSize - 1) / moleculeSize + 1;
156 snew(top_->mols.index, top_->mols.nalloc_index);
158 while (index < top_->atoms.nr)
160 top_->mols.index[top_->mols.nr] = index;
162 index += moleculeSize;
164 top_->mols.index[top_->mols.nr] = top_->atoms.nr;