src/gromacs/topology/idef.h

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  37 #ifndef GMX_TOPOLOGY_IDEF_H
  38 #define GMX_TOPOLOGY_IDEF_H
  39
  40 #include "gromacs/legacyheaders/types/simple.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46
  47 /* check kernel/toppush.c when you change these numbers */
  48 #define MAXATOMLIST 6
  49 #define MAXFORCEPARAM   12
  50 #define NR_RBDIHS   6
  51 #define NR_CBTDIHS   6
  52 #define NR_FOURDIHS     4
  53
  54 typedef atom_id t_iatom;
  55
  56 /* this MUST correspond to the
  57    t_interaction_function[F_NRE] in gmxlib/ifunc.c */
  58 enum {
  59     F_BONDS,
  60     F_G96BONDS,
  61     F_MORSE,
  62     F_CUBICBONDS,
  63     F_CONNBONDS,
  64     F_HARMONIC,
  65     F_FENEBONDS,
  66     F_TABBONDS,
  67     F_TABBONDSNC,
  68     F_RESTRBONDS,
  69     F_ANGLES,
  70     F_G96ANGLES,
  71     F_RESTRANGLES,
  72     F_LINEAR_ANGLES,
  73     F_CROSS_BOND_BONDS,
  74     F_CROSS_BOND_ANGLES,
  75     F_UREY_BRADLEY,
  76     F_QUARTIC_ANGLES,
  77     F_TABANGLES,
  78     F_PDIHS,
  79     F_RBDIHS,
  80     F_RESTRDIHS,
  81     F_CBTDIHS,
  82     F_FOURDIHS,
  83     F_IDIHS,
  84     F_PIDIHS,
  85     F_TABDIHS,
  86     F_CMAP,
  87     F_GB12,
  88     F_GB13,
  89     F_GB14,
  90     F_GBPOL,
  91     F_NPSOLVATION,
  92     F_LJ14,
  93     F_COUL14,
  94     F_LJC14_Q,
  95     F_LJC_PAIRS_NB,
  96     F_LJ,
  97     F_BHAM,
  98     F_LJ_LR,
  99     F_BHAM_LR,
 100     F_DISPCORR,
 101     F_COUL_SR,
 102     F_COUL_LR,
 103     F_RF_EXCL,
 104     F_COUL_RECIP,
 105     F_LJ_RECIP,
 106     F_DPD,
 107     F_POLARIZATION,
 108     F_WATER_POL,
 109     F_THOLE_POL,
 110     F_ANHARM_POL,
 111     F_POSRES,
 112     F_FBPOSRES,
 113     F_DISRES,
 114     F_DISRESVIOL,
 115     F_ORIRES,
 116     F_ORIRESDEV,
 117     F_ANGRES,
 118     F_ANGRESZ,
 119     F_DIHRES,
 120     F_DIHRESVIOL,
 121     F_CONSTR,
 122     F_CONSTRNC,
 123     F_SETTLE,
 124     F_VSITE2,
 125     F_VSITE3,
 126     F_VSITE3FD,
 127     F_VSITE3FAD,
 128     F_VSITE3OUT,
 129     F_VSITE4FD,
 130     F_VSITE4FDN,
 131     F_VSITEN,
 132     F_COM_PULL,
 133     F_EQM,
 134     F_EPOT,
 135     F_EKIN,
 136     F_ETOT,
 137     F_ECONSERVED,
 138     F_TEMP,
 139     F_VTEMP_NOLONGERUSED,
 140     F_PDISPCORR,
 141     F_PRES,
 142     F_DVDL_CONSTR,
 143     F_DVDL,
 144     F_DKDL,
 145     F_DVDL_COUL,
 146     F_DVDL_VDW,
 147     F_DVDL_BONDED,
 148     F_DVDL_RESTRAINT,
 149     F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
 150     F_NRE               /* This number is for the total number of energies      */
 151 };
 152
 153 #define IS_RESTRAINT_TYPE(ifunc) (((ifunc == F_POSRES) || (ifunc == F_FBPOSRES) || (ifunc == F_DISRES) || (ifunc == F_RESTRBONDS) || (ifunc == F_DISRESVIOL) || (ifunc == F_ORIRES) || (ifunc == F_ORIRESDEV) || (ifunc == F_ANGRES) || (ifunc == F_ANGRESZ) || (ifunc == F_DIHRES)))
 154
 155 typedef union t_iparams
 156 {
 157     /* Some parameters have A and B values for free energy calculations.
 158      * The B values are not used for regular simulations of course.
 159      * Free Energy for nonbondeds can be computed by changing the atom type.
 160      * The harmonic type is used for all harmonic potentials:
 161      * bonds, angles and improper dihedrals
 162      */
 163     struct {
 164         real a, b, c;
 165     } bham;
 166     struct {
 167         real rA, krA, rB, krB;
 168     } harmonic;
 169     struct {
 170         real klinA, aA, klinB, aB;
 171     } linangle;
 172     struct {
 173         real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
 174     } restraint;
 175     /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
 176     struct {
 177         real b0, kb, kcub;
 178     } cubic;
 179     struct {
 180         real bm, kb;
 181     } fene;
 182     struct {
 183         real r1e, r2e, krr;
 184     } cross_bb;
 185     struct {
 186         real r1e, r2e, r3e, krt;
 187     } cross_ba;
 188     struct {
 189         real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
 190     } u_b;
 191     struct {
 192         real theta, c[5];
 193     } qangle;
 194     struct {
 195         real alpha;
 196     } polarize;
 197     struct {
 198         real alpha, drcut, khyp;
 199     } anharm_polarize;
 200     struct {
 201         real al_x, al_y, al_z, rOH, rHH, rOD;
 202     } wpol;
 203     struct {
 204         real a, alpha1, alpha2, rfac;
 205     } thole;
 206     struct {
 207         real c6, c12;
 208     } lj;
 209     struct {
 210         real c6A, c12A, c6B, c12B;
 211     } lj14;
 212     struct {
 213         real fqq, qi, qj, c6, c12;
 214     } ljc14;
 215     struct {
 216         real qi, qj, c6, c12;
 217     } ljcnb;
 218     /* Proper dihedrals can not have different multiplicity when
 219      * doing free energy calculations, because the potential would not
 220      * be periodic anymore.
 221      */
 222     struct {
 223         real phiA, cpA; int mult; real phiB, cpB;
 224     } pdihs;
 225     struct {
 226         real dA, dB;
 227     } constr;
 228     /* Settle can not be used for Free energy calculations of water bond geometry.
 229      * Use shake (or lincs) instead if you have to change the water bonds.
 230      */
 231     struct {
 232         real doh, dhh;
 233     } settle;
 234     struct {
 235         real b0A, cbA, betaA, b0B, cbB, betaB;
 236     } morse;
 237     struct {
 238         real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
 239     } posres;
 240     struct {
 241         real pos0[DIM], r, k; int geom;
 242     } fbposres;
 243     struct {
 244         real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
 245     } rbdihs;
 246     struct {
 247         real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
 248     } cbtdihs;
 249     struct {
 250         real a, b, c, d, e, f;
 251     } vsite;
 252     struct {
 253         int  n; real a;
 254     } vsiten;
 255     /* NOTE: npair is only set after reading the tpx file */
 256     struct {
 257         real low, up1, up2, kfac; int type, label, npair;
 258     } disres;
 259     struct {
 260         real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
 261     } dihres;
 262     struct {
 263         int  ex, power, label; real c, obs, kfac;
 264     } orires;
 265     struct {
 266         int  table; real kA; real kB;
 267     } tab;
 268     struct {
 269         real sar, st, pi, gbr, bmlt;
 270     } gb;
 271     struct {
 272         int cmapA, cmapB;
 273     } cmap;
 274     struct {
 275         real buf[MAXFORCEPARAM];
 276     } generic;                                               /* Conversion */
 277 } t_iparams;
 278
 279 typedef int t_functype;
 280
 281 /*
 282  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 283  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 284  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 285  * interactions.
 286  */
 287 typedef struct t_ilist
 288 {
 289     int      nr;
 290     int      nr_nonperturbed;
 291     t_iatom *iatoms;
 292     int      nalloc;
 293 } t_ilist;
 294
 295 /*
 296  * The struct t_ilist defines a list of atoms with their interactions.
 297  * General field description:
 298  *   int nr
 299  *      the size (nr elements) of the interactions array (iatoms[]).
 300  *   t_iatom *iatoms
 301  *  specifies which atoms are involved in an interaction of a certain
 302  *       type. The layout of this array is as follows:
 303  *
 304  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 305  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 306  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 307  *
 308  *  So for interaction type type1 3 atoms are needed, and for type2 and
 309  *      type3 only 2. The type identifier is used to select the function to
 310  *      calculate the interaction and its actual parameters. This type
 311  *      identifier is an index in a params[] and functype[] array.
 312  */
 313
 314 typedef struct
 315 {
 316     real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
 317     /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 318 } gmx_cmapdata_t;
 319
 320 typedef struct gmx_cmap_t
 321 {
 322     int             ngrid;        /* Number of allocated cmap (cmapdata_t ) grids */
 323     int             grid_spacing; /* Grid spacing */
 324     gmx_cmapdata_t *cmapdata;     /* Pointer to grid with actual, pre-interpolated data */
 325 } gmx_cmap_t;
 326
 327
 328 typedef struct gmx_ffparams_t
 329 {
 330     int         ntypes;
 331     int         atnr;
 332     t_functype *functype;
 333     t_iparams  *iparams;
 334     double      reppow;    /* The repulsion power for VdW: C12*r^-reppow   */
 335     real        fudgeQQ;   /* The scaling factor for Coulomb 1-4: f*q1*q2  */
 336     gmx_cmap_t  cmap_grid; /* The dihedral correction maps                 */
 337 } gmx_ffparams_t;
 338
 339 enum {
 340     ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
 341 };
 342
 343 typedef struct t_idef
 344 {
 345     int         ntypes;
 346     int         atnr;
 347     t_functype *functype;
 348     t_iparams  *iparams;
 349     real        fudgeQQ;
 350     gmx_cmap_t  cmap_grid;
 351     t_iparams  *iparams_posres, *iparams_fbposres;
 352     int         iparams_posres_nalloc, iparams_fbposres_nalloc;
 353
 354     t_ilist     il[F_NRE];
 355     int         ilsort;
 356     int         nthreads;
 357     int        *il_thread_division;
 358     int         il_thread_division_nalloc;
 359 } t_idef;
 360
 361 /*
 362  * The struct t_idef defines all the interactions for the complete
 363  * simulation. The structure is setup in such a way that the multinode
 364  * version of the program  can use it as easy as the single node version.
 365  * General field description:
 366  *   int ntypes
 367  *      defines the number of elements in functype[] and param[].
 368  *   int nodeid
 369  *      the node id (if parallel machines)
 370  *   int atnr
 371  *      the number of atomtypes
 372  *   t_functype *functype
 373  *      array of length ntypes, defines for every force type what type of
 374  *      function to use. Every "bond" with the same function but different
 375  *      force parameters is a different force type. The type identifier in the
 376  *      forceatoms[] array is an index in this array.
 377  *   t_iparams *iparams
 378  *      array of length ntypes, defines the parameters for every interaction
 379  *      type. The type identifier in the actual interaction list
 380  *      (ilist[ftype].iatoms[]) is an index in this array.
 381  *   gmx_cmap_t cmap_grid
 382  *      the grid for the dihedral pair correction maps.
 383  *   t_iparams *iparams_posres, *iparams_fbposres
 384  *      defines the parameters for position restraints only.
 385  *      Position restraints are the only interactions that have different
 386  *      parameters (reference positions) for different molecules
 387  *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 388  *   t_ilist il[F_NRE]
 389  *      The list of interactions for each type. Note that some,
 390  *      such as LJ and COUL will have 0 entries.
 391  *   int ilsort
 392  *      The state of the sorting of il, values are provided above.
 393  *   int nthreads
 394  *      The number of threads used to set il_thread_division.
 395  *   int *il_thread_division
 396  *      The division of the normal bonded interactions of threads.
 397  *      il_thread_division[ftype*(nthreads+1)+t] contains an index
 398  *      into il[ftype].iatoms; thread th operates on t=th to t=th+1.
 399  *   int il_thread_division_nalloc
 400  *      The allocated size of il_thread_division,
 401  *      should be at least F_NRE*(nthreads+1).
 402  */
 403
 404 #ifdef __cplusplus
 405 }
 406 #endif
 407
 408 #endif