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     /* Some parameters have A and B values for free energy calculations.
  52      * The B values are not used for regular simulations of course.
  53      * Free Energy for nonbondeds can be computed by changing the atom type.
  54      * The harmonic type is used for all harmonic potentials:
  55      * bonds, angles and improper dihedrals
  56      */
  57     struct
  58     {
  59         real a, b, c;
  60     } bham;
  61     struct
  62     {
  63         real rA, krA, rB, krB;
  64     } harmonic;
  65     struct
  66     {
  67         real klinA, aA, klinB, aB;
  68     } linangle;
  69     struct
  70     {
  71         real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
  72     } restraint;
  73     /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
  74     struct
  75     {
  76         real b0, kb, kcub;
  77     } cubic;
  78     struct
  79     {
  80         real bm, kb;
  81     } fene;
  82     struct
  83     {
  84         real r1e, r2e, krr;
  85     } cross_bb;
  86     struct
  87     {
  88         real r1e, r2e, r3e, krt;
  89     } cross_ba;
  90     struct
  91     {
  92         real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
  93     } u_b;
  94     struct
  95     {
  96         real theta, c[5];
  97     } qangle;
  98     struct
  99     {
 100         real alpha;
 101     } polarize;
 102     struct
 103     {
 104         real alpha, drcut, khyp;
 105     } anharm_polarize;
 106     struct
 107     {
 108         real al_x, al_y, al_z, rOH, rHH, rOD;
 109     } wpol;
 110     struct
 111     {
 112         real a, alpha1, alpha2, rfac;
 113     } thole;
 114     struct
 115     {
 116         real c6, c12;
 117     } lj;
 118     struct
 119     {
 120         real c6A, c12A, c6B, c12B;
 121     } lj14;
 122     struct
 123     {
 124         real fqq, qi, qj, c6, c12;
 125     } ljc14;
 126     struct
 127     {
 128         real qi, qj, c6, c12;
 129     } ljcnb;
 130     /* Proper dihedrals can not have different multiplicity when
 131      * doing free energy calculations, because the potential would not
 132      * be periodic anymore.
 133      */
 134     struct
 135     {
 136         real phiA, cpA;
 137         int  mult;
 138         real phiB, cpB;
 139     } pdihs;
 140     struct
 141     {
 142         real dA, dB;
 143     } constr;
 144     /* Settle can not be used for Free energy calculations of water bond geometry.
 145      * Use shake (or lincs) instead if you have to change the water bonds.
 146      */
 147     struct
 148     {
 149         real doh, dhh;
 150     } settle;
 151     struct
 152     {
 153         real b0A, cbA, betaA, b0B, cbB, betaB;
 154     } morse;
 155     struct
 156     {
 157         real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
 158     } posres;
 159     struct
 160     {
 161         real pos0[DIM], r, k;
 162         int  geom;
 163     } fbposres;
 164     struct
 165     {
 166         real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
 167     } rbdihs;
 168     struct
 169     {
 170         real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
 171     } cbtdihs;
 172     struct
 173     {
 174         real a, b, c, d, e, f;
 175     } vsite;
 176     struct
 177     {
 178         int  n;
 179         real a;
 180     } vsiten;
 181     /* NOTE: npair is only set after reading the tpx file */
 182     struct
 183     {
 184         real low, up1, up2, kfac;
 185         int  type, label, npair;
 186     } disres;
 187     struct
 188     {
 189         real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
 190     } dihres;
 191     struct
 192     {
 193         int  ex, power, label;
 194         real c, obs, kfac;
 195     } orires;
 196     struct
 197     {
 198         int  table;
 199         real kA;
 200         real kB;
 201     } tab;
 202     struct
 203     {
 204         int cmapA, cmapB;
 205     } cmap;
 206     struct
 207     {
 208         real buf[MAXFORCEPARAM];
 209     } generic; /* Conversion */
 210 } t_iparams;
 211
 212 typedef int t_functype;
 213
 214 /* List of listed interactions, see description further down.
 215  *
 216  * TODO: Consider storing the function type as well.
 217  * TODO: Consider providing per interaction access.
 218  */
 219 struct InteractionList
 220 {
 221     /* Returns the total number of elements in iatoms */
 222     int size() const { return gmx::ssize(iatoms); }
 223
 224     /* List of interactions, see explanation further down */
 225     std::vector<int> iatoms;
 226 };
 227
 228 /* List of interaction lists, one list for each interaction type
 229  *
 230  * TODO: Consider only including entries in use instead of all F_NRE
 231  */
 232 typedef std::array<InteractionList, F_NRE> InteractionLists;
 233
 234 /* Deprecated list of listed interactions.
 235  *
 236  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 237  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 238  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 239  * interactions.
 240  */
 241 struct t_ilist
 242 {
 243     /* Returns the total number of elements in iatoms */
 244     int size() const { return nr; }
 245
 246     int      nr;
 247     t_iatom* iatoms;
 248     int      nalloc;
 249 };
 250
 251 /* TODO: Replace t_ilist in gmx_localtop_t by InteractionList.
 252  *       The nr_nonperturbed functionality needs to be ported.
 253  *       Remove t_topology.
 254  *       Remove t_ilist and remove templating on list type
 255  *       in mshift.cpp, constr.cpp, vsite.cpp and domdec_topology.cpp.
 256  */
 257
 258 /*
 259  * The structs InteractionList and t_ilist defines a list of atoms with their interactions.
 260  * General field description:
 261  *   int nr
 262  *      the size (nr elements) of the interactions array (iatoms[]).
 263  *   t_iatom *iatoms
 264  *  specifies which atoms are involved in an interaction of a certain
 265  *       type. The layout of this array is as follows:
 266  *
 267  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 268  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 269  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 270  *
 271  *  So for interaction type type1 3 atoms are needed, and for type2 and
 272  *      type3 only 2. The type identifier is used to select the function to
 273  *      calculate the interaction and its actual parameters. This type
 274  *      identifier is an index in a params[] and functype[] array.
 275  */
 276
 277 /*! \brief Type for returning a list of InteractionList references
 278  *
 279  * TODO: Remove when the function type is made part of InteractionList
 280  */
 281 struct InteractionListHandle
 282 {
 283     const int               functionType; //!< The function type
 284     const std::vector<int>& iatoms;       //!< Reference to interaction list
 285 };
 286
 287 /*! \brief Returns a list of all non-empty InteractionList entries with any of the interaction flags in \p flags set
 288  *
 289  * \param[in] ilists  Set of interaction lists
 290  * \param[in] flags   Bit mask with one or more IF_... bits set
 291  */
 292 static inline std::vector<InteractionListHandle> extractILists(const InteractionLists& ilists, int flags)
 293 {
 294     std::vector<InteractionListHandle> handles;
 295     for (size_t ftype = 0; ftype < ilists.size(); ftype++)
 296     {
 297         if ((interaction_function[ftype].flags & flags) && ilists[ftype].size() > 0)
 298         {
 299             handles.push_back({ static_cast<int>(ftype), ilists[ftype].iatoms });
 300         }
 301     }
 302     return handles;
 303 }
 304
 305 /*! \brief Returns the stride for the iatoms array in \p ilistHandle
 306  *
 307  * \param[in] ilistHandle  The ilist to return the stride for
 308  */
 309 static inline int ilistStride(const InteractionListHandle& ilistHandle)
 310 {
 311     return 1 + NRAL(ilistHandle.functionType);
 312 }
 313
 314 struct gmx_cmapdata_t
 315 {
 316     std::vector<real> cmap; /* Has length 4*grid_spacing*grid_spacing, */
 317     /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 318 };
 319
 320 struct gmx_cmap_t
 321 {
 322     int                         grid_spacing = 0; /* Grid spacing */
 323     std::vector<gmx_cmapdata_t> cmapdata; /* Lists of grids with actual, pre-interpolated data */
 324 };
 325
 326
 327 enum
 328 {
 329     ilsortUNKNOWN,
 330     ilsortNO_FE,
 331     ilsortFE_UNSORTED,
 332     ilsortFE_SORTED
 333 };
 334
 335 typedef struct t_idef
 336 {
 337     int         ntypes;
 338     int         atnr;
 339     t_functype* functype;
 340     t_iparams*  iparams;
 341     real        fudgeQQ;
 342     gmx_cmap_t* cmap_grid;
 343     t_iparams * iparams_posres, *iparams_fbposres;
 344     int         iparams_posres_nalloc, iparams_fbposres_nalloc;
 345
 346     t_ilist il[F_NRE];
 347     /* The number of non-perturbed interactions at the start of each entry in il */
 348     int numNonperturbedInteractions[F_NRE];
 349     int ilsort;
 350 } t_idef;
 351
 352 /*
 353  * The struct t_idef defines all the interactions for the complete
 354  * simulation. The structure is setup in such a way that the multinode
 355  * version of the program  can use it as easy as the single node version.
 356  * General field description:
 357  *   int ntypes
 358  *      defines the number of elements in functype[] and param[].
 359  *   int nodeid
 360  *      the node id (if parallel machines)
 361  *   int atnr
 362  *      the number of atomtypes
 363  *   t_functype *functype
 364  *      array of length ntypes, defines for every force type what type of
 365  *      function to use. Every "bond" with the same function but different
 366  *      force parameters is a different force type. The type identifier in the
 367  *      forceatoms[] array is an index in this array.
 368  *   t_iparams *iparams
 369  *      array of length ntypes, defines the parameters for every interaction
 370  *      type. The type identifier in the actual interaction list
 371  *      (ilist[ftype].iatoms[]) is an index in this array.
 372  *   gmx_cmap_t cmap_grid
 373  *      the grid for the dihedral pair correction maps.
 374  *   t_iparams *iparams_posres, *iparams_fbposres
 375  *      defines the parameters for position restraints only.
 376  *      Position restraints are the only interactions that have different
 377  *      parameters (reference positions) for different molecules
 378  *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 379  *   t_ilist il[F_NRE]
 380  *      The list of interactions for each type. Note that some,
 381  *      such as LJ and COUL will have 0 entries.
 382  *   int ilsort
 383  *      The state of the sorting of il, values are provided above.
 384  */
 385
 386 namespace gmx
 387 {
 388 class TextWriter;
 389 } // namespace gmx
 390
 391 void printInteractionParameters(gmx::TextWriter* writer, t_functype ftype, const t_iparams& iparams);
 392 void pr_iparams(FILE* fp, t_functype ftype, const t_iparams& iparams);
 393 void pr_ilist(FILE*                  fp,
 394               int                    indent,
 395               const char*            title,
 396               const t_functype*      functype,
 397               const InteractionList& ilist,
 398               gmx_bool               bShowNumbers,
 399               gmx_bool               bShowParameters,
 400               const t_iparams*       iparams);
 401 void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters);
 402
 403 /*! \brief
 404  * Properly initialize idef struct.
 405  *
 406  * \param[in] idef Pointer to idef struct to initialize.
 407  */
 408 void init_idef(t_idef* idef);
 409
 410 /*! \brief
 411  * Properly clean up idef struct.
 412  *
 413  * \param[in] idef Pointer to idef struct to clean up.
 414  */
 415 void done_idef(t_idef* idef);
 416
 417 void copy_ilist(const t_ilist* src, t_ilist* dst);
 418
 419 #endif