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37 * Implements test helper routines from toputils.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
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"
62 #include "testutils/testfilemanager.h"
69 TopologyManager::TopologyManager()
70 : mtop_(nullptr), frame_(nullptr)
74 TopologyManager::~TopologyManager()
82 if (frame_
!= nullptr)
91 for (char *atomtype
: atomtypes_
)
97 void TopologyManager::requestFrame()
99 GMX_RELEASE_ASSERT(mtop_
== NULL
,
100 "Frame must be requested before initializing topology");
107 void TopologyManager::requestVelocities()
109 GMX_RELEASE_ASSERT(frame_
!= NULL
,
110 "Velocities requested before requesting a frame");
112 if (frame_
->natoms
> 0)
114 snew(frame_
->v
, frame_
->natoms
);
118 void TopologyManager::requestForces()
120 GMX_RELEASE_ASSERT(frame_
!= NULL
,
121 "Forces requested before requesting a frame");
123 if (frame_
->natoms
> 0)
125 snew(frame_
->f
, frame_
->natoms
);
129 void TopologyManager::loadTopology(const char *filename
)
136 GMX_RELEASE_ASSERT(mtop_
== nullptr, "Topology initialized more than once");
139 gmx::test::TestFileManager::getInputFilePath(filename
).c_str(),
140 &fullTopology
, mtop_
, &ePBC
, frame_
!= NULL
? &xtop
: NULL
,
145 frame_
->natoms
= mtop_
->natoms
;
147 snew(frame_
->x
, frame_
->natoms
);
148 std::memcpy(frame_
->x
, xtop
, sizeof(*frame_
->x
) * frame_
->natoms
);
150 copy_mat(box
, frame_
->box
);
156 void TopologyManager::initAtoms(int count
)
158 GMX_RELEASE_ASSERT(mtop_
== NULL
, "Topology initialized more than once");
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
)
175 atoms
.atom
[i
].m
= (i
% 3 == 0 ? 2.0 : 1.0);
177 atoms
.haveMass
= TRUE
;
180 frame_
->natoms
= count
;
182 snew(frame_
->x
, count
);
185 snew(frame_
->v
, count
);
189 snew(frame_
->f
, count
);
194 void TopologyManager::initAtomTypes(const ConstArrayRef
<const char *> &types
)
196 GMX_RELEASE_ASSERT(mtop_
!= nullptr, "Topology not initialized");
197 atomtypes_
.reserve(types
.size());
198 for (const char *type
: types
)
200 atomtypes_
.push_back(gmx_strdup(type
));
202 t_atoms
&atoms
= this->atoms();
203 snew(atoms
.atomtype
, atoms
.nr
);
205 for (int i
= 0; i
< atoms
.nr
; ++i
, ++j
)
207 if (j
== types
.size())
211 atoms
.atomtype
[i
] = &atomtypes_
[j
];
213 atoms
.haveType
= TRUE
;
216 void TopologyManager::initUniformResidues(int residueSize
)
218 GMX_RELEASE_ASSERT(mtop_
!= NULL
, "Topology not initialized");
219 t_atoms
&atoms
= this->atoms();
220 int residueIndex
= -1;
221 for (int i
= 0; i
< atoms
.nr
; ++i
)
223 if (i
% residueSize
== 0)
227 atoms
.atom
[i
].resind
= residueIndex
;
231 void TopologyManager::initUniformMolecules(int moleculeSize
)
233 GMX_RELEASE_ASSERT(mtop_
!= NULL
, "Topology not initialized");
235 mtop_
->mols
.nalloc_index
= (mtop_
->natoms
+ moleculeSize
- 1) / moleculeSize
+ 1;
236 srenew(mtop_
->mols
.index
, mtop_
->mols
.nalloc_index
);
238 while (index
< mtop_
->natoms
)
240 mtop_
->mols
.index
[mtop_
->mols
.nr
] = index
;
242 index
+= moleculeSize
;
244 mtop_
->mols
.index
[mtop_
->mols
.nr
] = mtop_
->natoms
;
247 void TopologyManager::initFrameIndices(const ConstArrayRef
<int> &index
)
249 GMX_RELEASE_ASSERT(frame_
!= nullptr, "Frame not initialized");
250 GMX_RELEASE_ASSERT(!frame_
->bIndex
, "Frame atom indices can only be set once");
252 frame_
->bIndex
= TRUE
;
253 snew(frame_
->index
, index
.size());
254 std::copy(index
.begin(), index
.end(), frame_
->index
);
256 frame_
->natoms
= index
.size();
259 t_atoms
&TopologyManager::atoms()
261 GMX_RELEASE_ASSERT(mtop_
!= nullptr, "Topology not initialized");
262 GMX_RELEASE_ASSERT(mtop_
->natoms
== mtop_
->moltype
[0].atoms
.nr
,
263 "Test setup assumes all atoms in a single molecule type");
264 return mtop_
->moltype
[0].atoms
;