| /dports/science/gromacs/gromacs-2021.4/src/gromacs/topology/ |
| H A D | mtop_util.cpp | 85 int gmx_mtop_num_molecules(const gmx_mtop_t& mtop) in gmx_mtop_num_molecules()
95 int gmx_mtop_nres(const gmx_mtop_t* mtop) in gmx_mtop_nres()
197 const gmx_mtop_t* mtop; member
251 const gmx_mtop_t* mtop; member
303 const gmx_mtop_t* mtop; member
309 int gmx_mtop_ftype_count(const gmx_mtop_t* mtop, int ftype) in gmx_mtop_ftype_count()
489 t_atoms gmx_mtop_global_atoms(const gmx_mtop_t* mtop) in gmx_mtop_global_atoms()
877 static void gen_local_top(const gmx_mtop_t& mtop, in gen_local_top()
1015 std::vector<int> get_atom_index(const gmx_mtop_t* mtop) in get_atom_index()
1070 bool haveFepPerturbedMasses(const gmx_mtop_t& mtop) in haveFepPerturbedMasses()
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| H A D | mtop_lookup.h | 72 static inline void mtopGetMolblockIndex(const gmx_mtop_t* mtop, in mtopGetMolblockIndex()
135 static inline int mtopGetMoleculeIndex(const gmx_mtop_t* mtop, int globalAtomIndex, int* moleculeBl… in mtopGetMoleculeIndex()
155 static inline const t_atom& mtopGetAtomParameters(const gmx_mtop_t* mtop, int globalAtomIndex, int*… in mtopGetAtomParameters()
176 static inline real mtopGetAtomMass(const gmx_mtop_t* mtop, int globalAtomIndex, int* moleculeBlock) in mtopGetAtomMass()
201 static inline void mtopGetAtomAndResidueName(const gmx_mtop_t* mtop, in mtopGetAtomAndResidueName()
245 static inline void mtopGetAtomAndResidueName(const gmx_mtop_t& mtop, in mtopGetAtomAndResidueName()
269 static inline const t_resinfo& mtopGetResidueInfo(const gmx_mtop_t* mtop, int globalAtomIndex, int*… in mtopGetResidueInfo()
290 static inline const t_pdbinfo& mtopGetAtomPdbInfo(const gmx_mtop_t* mtop, int globalAtomIndex, int*… in mtopGetAtomPdbInfo()
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| H A D | topology.cpp | 202 void done_top_mtop(t_topology* top, gmx_mtop_t* mtop) in done_top_mtop()
222 bool gmx_mtop_has_masses(const gmx_mtop_t* mtop) in gmx_mtop_has_masses()
231 bool gmx_mtop_has_charges(const gmx_mtop_t* mtop) in gmx_mtop_has_charges()
240 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t& mtop) in gmx_mtop_has_perturbed_charges()
259 bool gmx_mtop_has_atomtypes(const gmx_mtop_t* mtop) in gmx_mtop_has_atomtypes()
268 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t* mtop) in gmx_mtop_has_pdbinfo()
389 void pr_mtop(FILE* fp, int indent, const char* title, const gmx_mtop_t* mtop, gmx_bool bShowNumbers… in pr_mtop()
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| /dports/lang/nwcc/nwcc_0.8.3/tests/ |
| H A D | ioctlstuff.c | 7 struct mtop struct
20 struct mtop mtop; in mtioctop() local
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/tests/ |
| H A D | updategroups.cpp | 150 gmx_mtop_t mtop; in TEST() local
169 gmx_mtop_t mtop; in TEST() local
187 gmx_mtop_t mtop; in TEST() local
216 gmx_mtop_t mtop; in TEST() local
230 gmx_mtop_t mtop; in TEST() local
250 gmx_mtop_t mtop; in TEST() local
267 gmx_mtop_t mtop; in TEST() local
281 gmx_mtop_t mtop; in TEST() local
310 gmx_mtop_t mtop; in TEST() local
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/topology/tests/ |
| H A D | mtop.cpp | 55 void createBasicTop(gmx_mtop_t* mtop) in createBasicTop()
82 std::vector<gmx::Range<int>> createTwoResidueTopology(gmx_mtop_t* mtop) in createTwoResidueTopology()
111 gmx_mtop_t mtop; in TEST() local
124 gmx_mtop_t mtop; in TEST() local
142 gmx_mtop_t mtop; in TEST() local
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| /dports/devel/sunpromake/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/devel/smake/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/devel/sccs/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/devel/schilybase/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/net/rscsi/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/archivers/star/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/sysutils/cdrdao/cdrdao-1.2.4/scsilib/include/ |
| H A D | mtiodefs.h | 53 struct mtop { struct
54 short mt_op; /* op code (see below) */
55 daddr_t mt_count; /* repeat count or param */
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| /dports/sysutils/cdrtools/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/editors/ved/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/sysutils/schilyutils/schily-2021-09-18/include/schily/ |
| H A D | mtio.h | 51 struct mtop { struct
52 short mt_op; /* op code (see below) */
53 daddr_t mt_count; /* repeat count or param */
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/coordinateio/ |
| H A D | coordinatefile.h | 111 …ryFileOpener(const std::string& name, int filetype, const Selection& sel, const gmx_mtop_t* mtop) : in TrajectoryFileOpener()
202 const gmx_mtop_t* mtop, in TrajectoryFrameWriter()
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| /dports/science/afni/afni-AFNI_21.3.16/src/ |
| H A D | plug_maskave.c | 223 short mbot , mtop ; in MASKAVE_main() local
241 byte mbot , mtop ; in MASKAVE_main() local
264 float mbot , mtop ; in MASKAVE_main() local
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| H A D | mri_to_byte.c | 226 byte mbot, mtop; in mri_to_bytemask() local
244 short mbot, mtop; in mri_to_bytemask() local
262 int mbot, mtop; in mri_to_bytemask() local
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/fileio/ |
| H A D | tpxio.cpp | 2516 static void set_disres_npair(gmx_mtop_t* mtop) in set_disres_npair()
2545 static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version) in do_mtop()
2860 static void do_tpx_mtop(gmx::ISerializer* serializer, TpxFileHeader* tpx, gmx_mtop_t* mtop) in do_tpx_mtop()
3036 static void do_tpx_finalize(TpxFileHeader* tpx, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop) in do_tpx_finalize()
3092 gmx_mtop_t* mtop) in do_tpx_body()
3145 …TpxFileHeader populateTpxHeader(const t_state& state, const t_inputrec* ir, const gmx_mtop_t* mtop) in populateTpxHeader()
3215 gmx_mtop_t* mtop) in readTpxBody()
3267 …write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t* mtop) in write_tpx_state()
3304 gmx_mtop_t* mtop) in completeTprDeserialization()
3319 gmx_mtop_t* mtop) in completeTprDeserialization()
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| H A D | confio.cpp | 177 const gmx_mtop_t* mtop, in write_sto_conf_mtop()
406 gmx_mtop_t mtop; in readConfAndAtoms() local
450 gmx_mtop_t* mtop, in readConfAndTopology()
501 gmx_mtop_t mtop; in read_tps_conf() local
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/mimic/ |
| H A D | utilities.cpp | 42 std::vector<int> genQmmmIndices(const gmx_mtop_t& mtop) in genQmmmIndices()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/ |
| H A D | forcerec.cpp | 204 static std::vector<cginfo_mb_t> init_cginfo_mb(const gmx_mtop_t* mtop, const t_forcerec* fr) in init_cginfo_mb()
366 static bool set_chargesum(FILE* log, t_forcerec* fr, const gmx_mtop_t* mtop) in set_chargesum()
435 static real calcBuckinghamBMax(FILE* fplog, const gmx_mtop_t* mtop) in calcBuckinghamBMax()
504 static void count_tables(int ftype1, int ftype2, const gmx_mtop_t* mtop, int* ncount, int** count) in count_tables()
559 const gmx_mtop_t* mtop, in make_bonded_tables()
828 const gmx_mtop_t* mtop, in init_interaction_const()
955 const gmx_mtop_t* mtop, in init_forcerec()
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| H A D | perf_est.cpp | 157 void count_bonded_distances(const gmx_mtop_t& mtop, const t_inputrec& ir, double* ndistance_c, doub… in count_bonded_distances()
256 static void pp_verlet_load(const gmx_mtop_t& mtop, in pp_verlet_load()
368 float pme_load_estimate(const gmx_mtop_t& mtop, const t_inputrec& ir, const matrix box) in pme_load_estimate()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/nbnxm/ |
| H A D | pairlist_tuning.cpp | 128 const gmx_mtop_t* mtop, in increaseNstlist()
399 const gmx_mtop_t* mtop, in setDynamicPairlistPruningParameters()
508 const gmx_mtop_t* mtop, in setupDynamicPairlistPruning()
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