src/gromacs/topology/idef.h

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  37 #ifndef GMX_TOPOLOGY_IDEF_H
  38 #define GMX_TOPOLOGY_IDEF_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44 #include "gromacs/utility/real.h"
  45
  46 #ifdef __cplusplus
  47 extern "C" {
  48 #endif
  49
  50 /* check kernel/toppush.c when you change these numbers */
  51 #define MAXATOMLIST 6
  52 #define MAXFORCEPARAM   12
  53 #define NR_RBDIHS   6
  54 #define NR_CBTDIHS   6
  55 #define NR_FOURDIHS     4
  56
  57 typedef int t_iatom;
  58
  59 /* this MUST correspond to the
  60    t_interaction_function[F_NRE] in gmxlib/ifunc.c */
  61 enum {
  62     F_BONDS,
  63     F_G96BONDS,
  64     F_MORSE,
  65     F_CUBICBONDS,
  66     F_CONNBONDS,
  67     F_HARMONIC,
  68     F_FENEBONDS,
  69     F_TABBONDS,
  70     F_TABBONDSNC,
  71     F_RESTRBONDS,
  72     F_ANGLES,
  73     F_G96ANGLES,
  74     F_RESTRANGLES,
  75     F_LINEAR_ANGLES,
  76     F_CROSS_BOND_BONDS,
  77     F_CROSS_BOND_ANGLES,
  78     F_UREY_BRADLEY,
  79     F_QUARTIC_ANGLES,
  80     F_TABANGLES,
  81     F_PDIHS,
  82     F_RBDIHS,
  83     F_RESTRDIHS,
  84     F_CBTDIHS,
  85     F_FOURDIHS,
  86     F_IDIHS,
  87     F_PIDIHS,
  88     F_TABDIHS,
  89     F_CMAP,
  90     F_GB12,
  91     F_GB13,
  92     F_GB14,
  93     F_GBPOL,
  94     F_NPSOLVATION,
  95     F_LJ14,
  96     F_COUL14,
  97     F_LJC14_Q,
  98     F_LJC_PAIRS_NB,
  99     F_LJ,
 100     F_BHAM,
 101     F_LJ_LR_NOLONGERUSED,
 102     F_BHAM_LR_NOLONGERUSED,
 103     F_DISPCORR,
 104     F_COUL_SR,
 105     F_COUL_LR_NOLONGERUSED,
 106     F_RF_EXCL,
 107     F_COUL_RECIP,
 108     F_LJ_RECIP,
 109     F_DPD,
 110     F_POLARIZATION,
 111     F_WATER_POL,
 112     F_THOLE_POL,
 113     F_ANHARM_POL,
 114     F_POSRES,
 115     F_FBPOSRES,
 116     F_DISRES,
 117     F_DISRESVIOL,
 118     F_ORIRES,
 119     F_ORIRESDEV,
 120     F_ANGRES,
 121     F_ANGRESZ,
 122     F_DIHRES,
 123     F_DIHRESVIOL,
 124     F_CONSTR,
 125     F_CONSTRNC,
 126     F_SETTLE,
 127     F_VSITE2,
 128     F_VSITE3,
 129     F_VSITE3FD,
 130     F_VSITE3FAD,
 131     F_VSITE3OUT,
 132     F_VSITE4FD,
 133     F_VSITE4FDN,
 134     F_VSITEN,
 135     F_COM_PULL,
 136     F_EQM,
 137     F_EPOT,
 138     F_EKIN,
 139     F_ETOT,
 140     F_ECONSERVED,
 141     F_TEMP,
 142     F_VTEMP_NOLONGERUSED,
 143     F_PDISPCORR,
 144     F_PRES,
 145     F_DVDL_CONSTR,
 146     F_DVDL,
 147     F_DKDL,
 148     F_DVDL_COUL,
 149     F_DVDL_VDW,
 150     F_DVDL_BONDED,
 151     F_DVDL_RESTRAINT,
 152     F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
 153     F_NRE               /* This number is for the total number of energies      */
 154 };
 155
 156 #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)))
 157
 158 typedef union t_iparams
 159 {
 160     /* Some parameters have A and B values for free energy calculations.
 161      * The B values are not used for regular simulations of course.
 162      * Free Energy for nonbondeds can be computed by changing the atom type.
 163      * The harmonic type is used for all harmonic potentials:
 164      * bonds, angles and improper dihedrals
 165      */
 166     struct {
 167         real a, b, c;
 168     } bham;
 169     struct {
 170         real rA, krA, rB, krB;
 171     } harmonic;
 172     struct {
 173         real klinA, aA, klinB, aB;
 174     } linangle;
 175     struct {
 176         real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
 177     } restraint;
 178     /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
 179     struct {
 180         real b0, kb, kcub;
 181     } cubic;
 182     struct {
 183         real bm, kb;
 184     } fene;
 185     struct {
 186         real r1e, r2e, krr;
 187     } cross_bb;
 188     struct {
 189         real r1e, r2e, r3e, krt;
 190     } cross_ba;
 191     struct {
 192         real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
 193     } u_b;
 194     struct {
 195         real theta, c[5];
 196     } qangle;
 197     struct {
 198         real alpha;
 199     } polarize;
 200     struct {
 201         real alpha, drcut, khyp;
 202     } anharm_polarize;
 203     struct {
 204         real al_x, al_y, al_z, rOH, rHH, rOD;
 205     } wpol;
 206     struct {
 207         real a, alpha1, alpha2, rfac;
 208     } thole;
 209     struct {
 210         real c6, c12;
 211     } lj;
 212     struct {
 213         real c6A, c12A, c6B, c12B;
 214     } lj14;
 215     struct {
 216         real fqq, qi, qj, c6, c12;
 217     } ljc14;
 218     struct {
 219         real qi, qj, c6, c12;
 220     } ljcnb;
 221     /* Proper dihedrals can not have different multiplicity when
 222      * doing free energy calculations, because the potential would not
 223      * be periodic anymore.
 224      */
 225     struct {
 226         real phiA, cpA; int mult; real phiB, cpB;
 227     } pdihs;
 228     struct {
 229         real dA, dB;
 230     } constr;
 231     /* Settle can not be used for Free energy calculations of water bond geometry.
 232      * Use shake (or lincs) instead if you have to change the water bonds.
 233      */
 234     struct {
 235         real doh, dhh;
 236     } settle;
 237     struct {
 238         real b0A, cbA, betaA, b0B, cbB, betaB;
 239     } morse;
 240     struct {
 241         real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
 242     } posres;
 243     struct {
 244         real pos0[DIM], r, k; int geom;
 245     } fbposres;
 246     struct {
 247         real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
 248     } rbdihs;
 249     struct {
 250         real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
 251     } cbtdihs;
 252     struct {
 253         real a, b, c, d, e, f;
 254     } vsite;
 255     struct {
 256         int  n; real a;
 257     } vsiten;
 258     /* NOTE: npair is only set after reading the tpx file */
 259     struct {
 260         real low, up1, up2, kfac; int type, label, npair;
 261     } disres;
 262     struct {
 263         real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
 264     } dihres;
 265     struct {
 266         int  ex, power, label; real c, obs, kfac;
 267     } orires;
 268     struct {
 269         int  table; real kA; real kB;
 270     } tab;
 271     struct {
 272         real sar, st, pi, gbr, bmlt;
 273     } gb;
 274     struct {
 275         int cmapA, cmapB;
 276     } cmap;
 277     struct {
 278         real buf[MAXFORCEPARAM];
 279     } generic;                                               /* Conversion */
 280 } t_iparams;
 281
 282 typedef int t_functype;
 283
 284 /*
 285  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 286  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 287  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 288  * interactions.
 289  */
 290 typedef struct t_ilist
 291 {
 292     int      nr;
 293     int      nr_nonperturbed;
 294     t_iatom *iatoms;
 295     int      nalloc;
 296 } t_ilist;
 297
 298 /*
 299  * The struct t_ilist defines a list of atoms with their interactions.
 300  * General field description:
 301  *   int nr
 302  *      the size (nr elements) of the interactions array (iatoms[]).
 303  *   t_iatom *iatoms
 304  *  specifies which atoms are involved in an interaction of a certain
 305  *       type. The layout of this array is as follows:
 306  *
 307  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 308  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 309  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 310  *
 311  *  So for interaction type type1 3 atoms are needed, and for type2 and
 312  *      type3 only 2. The type identifier is used to select the function to
 313  *      calculate the interaction and its actual parameters. This type
 314  *      identifier is an index in a params[] and functype[] array.
 315  */
 316
 317 typedef struct
 318 {
 319     real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
 320     /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 321 } gmx_cmapdata_t;
 322
 323 typedef struct gmx_cmap_t
 324 {
 325     int             ngrid;        /* Number of allocated cmap (cmapdata_t ) grids */
 326     int             grid_spacing; /* Grid spacing */
 327     gmx_cmapdata_t *cmapdata;     /* Pointer to grid with actual, pre-interpolated data */
 328 } gmx_cmap_t;
 329
 330
 331 typedef struct gmx_ffparams_t
 332 {
 333     int         ntypes;
 334     int         atnr;
 335     t_functype *functype;
 336     t_iparams  *iparams;
 337     double      reppow;    /* The repulsion power for VdW: C12*r^-reppow   */
 338     real        fudgeQQ;   /* The scaling factor for Coulomb 1-4: f*q1*q2  */
 339     gmx_cmap_t  cmap_grid; /* The dihedral correction maps                 */
 340 } gmx_ffparams_t;
 341
 342 enum {
 343     ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
 344 };
 345
 346 typedef struct t_idef
 347 {
 348     int         ntypes;
 349     int         atnr;
 350     t_functype *functype;
 351     t_iparams  *iparams;
 352     real        fudgeQQ;
 353     gmx_cmap_t  cmap_grid;
 354     t_iparams  *iparams_posres, *iparams_fbposres;
 355     int         iparams_posres_nalloc, iparams_fbposres_nalloc;
 356
 357     t_ilist     il[F_NRE];
 358     int         ilsort;
 359     int         nthreads;
 360     int        *il_thread_division;
 361     int         il_thread_division_nalloc;
 362 } t_idef;
 363
 364 /*
 365  * The struct t_idef defines all the interactions for the complete
 366  * simulation. The structure is setup in such a way that the multinode
 367  * version of the program  can use it as easy as the single node version.
 368  * General field description:
 369  *   int ntypes
 370  *      defines the number of elements in functype[] and param[].
 371  *   int nodeid
 372  *      the node id (if parallel machines)
 373  *   int atnr
 374  *      the number of atomtypes
 375  *   t_functype *functype
 376  *      array of length ntypes, defines for every force type what type of
 377  *      function to use. Every "bond" with the same function but different
 378  *      force parameters is a different force type. The type identifier in the
 379  *      forceatoms[] array is an index in this array.
 380  *   t_iparams *iparams
 381  *      array of length ntypes, defines the parameters for every interaction
 382  *      type. The type identifier in the actual interaction list
 383  *      (ilist[ftype].iatoms[]) is an index in this array.
 384  *   gmx_cmap_t cmap_grid
 385  *      the grid for the dihedral pair correction maps.
 386  *   t_iparams *iparams_posres, *iparams_fbposres
 387  *      defines the parameters for position restraints only.
 388  *      Position restraints are the only interactions that have different
 389  *      parameters (reference positions) for different molecules
 390  *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 391  *   t_ilist il[F_NRE]
 392  *      The list of interactions for each type. Note that some,
 393  *      such as LJ and COUL will have 0 entries.
 394  *   int ilsort
 395  *      The state of the sorting of il, values are provided above.
 396  *   int nthreads
 397  *      The number of threads used to set il_thread_division.
 398  *   int *il_thread_division
 399  *      The division of the normal bonded interactions of threads.
 400  *      il_thread_division[ftype*(nthreads+1)+t] contains an index
 401  *      into il[ftype].iatoms; thread th operates on t=th to t=th+1.
 402  *   int il_thread_division_nalloc
 403  *      The allocated size of il_thread_division,
 404  *      should be at least F_NRE*(nthreads+1).
 405  */
 406
 407 void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams);
 408 void pr_ilist(FILE *fp, int indent, const char *title,
 409               const t_functype *functype, const t_ilist *ilist,
 410               gmx_bool bShowNumbers,
 411               gmx_bool bShowParameters, const t_iparams *iparams);
 412 void pr_ffparams(FILE *fp, int indent, const char *title,
 413                  const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers);
 414 void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
 415              gmx_bool bShowNumbers, gmx_bool bShowParameters);
 416
 417 #ifdef __cplusplus
 418 }
 419 #endif
 420
 421 #endif