src/gromacs/topology/idef.h

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  37 #ifndef GMX_TOPOLOGY_IDEF_H
  38 #define GMX_TOPOLOGY_IDEF_H
  39
  40 #include <cstdio>
  41
  42 #include <array>
  43 #include <vector>
  44
  45 #include "gromacs/math/vectypes.h"
  46 #include "gromacs/topology/ifunc.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48 #include "gromacs/utility/real.h"
  49
  50 typedef union t_iparams
  51 {
  52     /* Some parameters have A and B values for free energy calculations.
  53      * The B values are not used for regular simulations of course.
  54      * Free Energy for nonbondeds can be computed by changing the atom type.
  55      * The harmonic type is used for all harmonic potentials:
  56      * bonds, angles and improper dihedrals
  57      */
  58     struct {
  59         real a, b, c;
  60     } bham;
  61     struct {
  62         real rA, krA, rB, krB;
  63     } harmonic;
  64     struct {
  65         real klinA, aA, klinB, aB;
  66     } linangle;
  67     struct {
  68         real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
  69     } restraint;
  70     /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
  71     struct {
  72         real b0, kb, kcub;
  73     } cubic;
  74     struct {
  75         real bm, kb;
  76     } fene;
  77     struct {
  78         real r1e, r2e, krr;
  79     } cross_bb;
  80     struct {
  81         real r1e, r2e, r3e, krt;
  82     } cross_ba;
  83     struct {
  84         real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
  85     } u_b;
  86     struct {
  87         real theta, c[5];
  88     } qangle;
  89     struct {
  90         real alpha;
  91     } polarize;
  92     struct {
  93         real alpha, drcut, khyp;
  94     } anharm_polarize;
  95     struct {
  96         real al_x, al_y, al_z, rOH, rHH, rOD;
  97     } wpol;
  98     struct {
  99         real a, alpha1, alpha2, rfac;
 100     } thole;
 101     struct {
 102         real c6, c12;
 103     } lj;
 104     struct {
 105         real c6A, c12A, c6B, c12B;
 106     } lj14;
 107     struct {
 108         real fqq, qi, qj, c6, c12;
 109     } ljc14;
 110     struct {
 111         real qi, qj, c6, c12;
 112     } ljcnb;
 113     /* Proper dihedrals can not have different multiplicity when
 114      * doing free energy calculations, because the potential would not
 115      * be periodic anymore.
 116      */
 117     struct {
 118         real phiA, cpA; int mult; real phiB, cpB;
 119     } pdihs;
 120     struct {
 121         real dA, dB;
 122     } constr;
 123     /* Settle can not be used for Free energy calculations of water bond geometry.
 124      * Use shake (or lincs) instead if you have to change the water bonds.
 125      */
 126     struct {
 127         real doh, dhh;
 128     } settle;
 129     struct {
 130         real b0A, cbA, betaA, b0B, cbB, betaB;
 131     } morse;
 132     struct {
 133         real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
 134     } posres;
 135     struct {
 136         real pos0[DIM], r, k; int geom;
 137     } fbposres;
 138     struct {
 139         real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
 140     } rbdihs;
 141     struct {
 142         real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
 143     } cbtdihs;
 144     struct {
 145         real a, b, c, d, e, f;
 146     } vsite;
 147     struct {
 148         int  n; real a;
 149     } vsiten;
 150     /* NOTE: npair is only set after reading the tpx file */
 151     struct {
 152         real low, up1, up2, kfac; int type, label, npair;
 153     } disres;
 154     struct {
 155         real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
 156     } dihres;
 157     struct {
 158         int  ex, power, label; real c, obs, kfac;
 159     } orires;
 160     struct {
 161         int  table; real kA; real kB;
 162     } tab;
 163     struct {
 164         int cmapA, cmapB;
 165     } cmap;
 166     struct {
 167         real buf[MAXFORCEPARAM];
 168     } generic;                                               /* Conversion */
 169 } t_iparams;
 170
 171 typedef int t_functype;
 172
 173 /* List of listed interactions, see description further down.
 174  *
 175  * TODO: Consider storing the function type as well.
 176  * TODO: Consider providing per interaction access.
 177  */
 178 struct InteractionList
 179 {
 180     /* Returns the total number of elements in iatoms */
 181     int size() const
 182     {
 183         return gmx::ssize(iatoms);
 184     }
 185
 186     /* List of interactions, see explanation further down */
 187     std::vector<int> iatoms;
 188 };
 189
 190 /* List of interaction lists, one list for each interaction type
 191  *
 192  * TODO: Consider only including entries in use instead of all F_NRE
 193  */
 194 typedef std::array<InteractionList, F_NRE> InteractionLists;
 195
 196 /* Deprecated list of listed interactions.
 197  *
 198  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 199  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 200  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 201  * interactions.
 202  */
 203 struct t_ilist
 204 {
 205     /* Returns the total number of elements in iatoms */
 206     int size() const
 207     {
 208         return nr;
 209     }
 210
 211     int      nr;
 212     int      nr_nonperturbed;
 213     t_iatom *iatoms;
 214     int      nalloc;
 215 };
 216
 217 /* TODO: Replace t_ilist in gmx_localtop_t by InteractionList.
 218  *       The nr_nonperturbed functionality needs to be ported.
 219  *       Remove t_topology.
 220  *       Remove t_ilist and remove templating on list type
 221  *       in mshift.cpp, constr.cpp, vsite.cpp and domdec_topology.cpp.
 222  */
 223
 224 /*
 225  * The structs InteractionList and t_ilist defines a list of atoms with their interactions.
 226  * General field description:
 227  *   int nr
 228  *      the size (nr elements) of the interactions array (iatoms[]).
 229  *   t_iatom *iatoms
 230  *  specifies which atoms are involved in an interaction of a certain
 231  *       type. The layout of this array is as follows:
 232  *
 233  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 234  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 235  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 236  *
 237  *  So for interaction type type1 3 atoms are needed, and for type2 and
 238  *      type3 only 2. The type identifier is used to select the function to
 239  *      calculate the interaction and its actual parameters. This type
 240  *      identifier is an index in a params[] and functype[] array.
 241  */
 242
 243 /*! \brief Type for returning a list of InteractionList references
 244  *
 245  * TODO: Remove when the function type is made part of InteractionList
 246  */
 247 struct InteractionListHandle
 248 {
 249     const int               functionType; //!< The function type
 250     const std::vector<int> &iatoms;       //!< Reference to interaction list
 251 };
 252
 253 /*! \brief Returns a list of all non-empty InteractionList entries with any of the interaction flags in \p flags set
 254  *
 255  * \param[in] ilists  Set of interaction lists
 256  * \param[in] flags   Bit mask with one or more IF_... bits set
 257  */
 258 static inline const std::vector<InteractionListHandle>
 259 extractILists(const InteractionLists &ilists,
 260               int                     flags)
 261 {
 262     std::vector<InteractionListHandle> handles;
 263     for (size_t ftype = 0; ftype < ilists.size(); ftype++)
 264     {
 265         if ((interaction_function[ftype].flags & flags) && ilists[ftype].size() > 0)
 266         {
 267             handles.push_back({ static_cast<int>(ftype), ilists[ftype].iatoms });
 268         }
 269     }
 270     return handles;
 271 }
 272
 273 /*! \brief Returns the stride for the iatoms array in \p ilistHandle
 274  *
 275  * \param[in] ilistHandle  The ilist to return the stride for
 276  */
 277 static inline int ilistStride(const InteractionListHandle &ilistHandle)
 278 {
 279     return 1 + NRAL(ilistHandle.functionType);
 280 }
 281
 282 struct gmx_cmapdata_t
 283 {
 284     std::vector<real> cmap; /* Has length 4*grid_spacing*grid_spacing, */
 285     /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 286 };
 287
 288 struct gmx_cmap_t
 289 {
 290     int                         grid_spacing = 0; /* Grid spacing */
 291     std::vector<gmx_cmapdata_t> cmapdata;         /* Lists of grids with actual, pre-interpolated data */
 292 };
 293
 294
 295 enum {
 296     ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
 297 };
 298
 299 typedef struct t_idef
 300 {
 301     int         ntypes;
 302     int         atnr;
 303     t_functype *functype;
 304     t_iparams  *iparams;
 305     real        fudgeQQ;
 306     gmx_cmap_t *cmap_grid;
 307     t_iparams  *iparams_posres, *iparams_fbposres;
 308     int         iparams_posres_nalloc, iparams_fbposres_nalloc;
 309
 310     t_ilist     il[F_NRE];
 311     int         ilsort;
 312 } t_idef;
 313
 314 /*
 315  * The struct t_idef defines all the interactions for the complete
 316  * simulation. The structure is setup in such a way that the multinode
 317  * version of the program  can use it as easy as the single node version.
 318  * General field description:
 319  *   int ntypes
 320  *      defines the number of elements in functype[] and param[].
 321  *   int nodeid
 322  *      the node id (if parallel machines)
 323  *   int atnr
 324  *      the number of atomtypes
 325  *   t_functype *functype
 326  *      array of length ntypes, defines for every force type what type of
 327  *      function to use. Every "bond" with the same function but different
 328  *      force parameters is a different force type. The type identifier in the
 329  *      forceatoms[] array is an index in this array.
 330  *   t_iparams *iparams
 331  *      array of length ntypes, defines the parameters for every interaction
 332  *      type. The type identifier in the actual interaction list
 333  *      (ilist[ftype].iatoms[]) is an index in this array.
 334  *   gmx_cmap_t cmap_grid
 335  *      the grid for the dihedral pair correction maps.
 336  *   t_iparams *iparams_posres, *iparams_fbposres
 337  *      defines the parameters for position restraints only.
 338  *      Position restraints are the only interactions that have different
 339  *      parameters (reference positions) for different molecules
 340  *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 341  *   t_ilist il[F_NRE]
 342  *      The list of interactions for each type. Note that some,
 343  *      such as LJ and COUL will have 0 entries.
 344  *   int ilsort
 345  *      The state of the sorting of il, values are provided above.
 346  */
 347
 348 void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams);
 349 void pr_ilist(FILE *fp, int indent, const char *title,
 350               const t_functype *functype, const InteractionList &ilist,
 351               gmx_bool bShowNumbers,
 352               gmx_bool bShowParameters, const t_iparams *iparams);
 353 void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
 354              gmx_bool bShowNumbers, gmx_bool bShowParameters);
 355
 356 /*! \brief
 357  * Properly initialize idef struct.
 358  *
 359  * \param[in] idef Pointer to idef struct to initialize.
 360  */
 361 void init_idef(t_idef *idef);
 362
 363 /*! \brief
 364  * Properly clean up idef struct.
 365  *
 366  * \param[in] idef Pointer to idef struct to clean up.
 367  */
 368 void done_idef(t_idef *idef);
 369
 370 void copy_ilist(const t_ilist *src, t_ilist *dst);
 371
 372 #endif