include/types/idef.h

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  38
  39
  40 #ifndef _idef_h
  41 #define _idef_h
  42
  43 #include "simple.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  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_FOURDIHS     4
  55
  56 typedef atom_id t_iatom;
  57
  58 /* this MUST correspond to the
  59    t_interaction_function[F_NRE] in gmxlib/ifunc.c */
  60 enum {
  61     F_BONDS,
  62     F_G96BONDS,
  63     F_MORSE,
  64     F_CUBICBONDS,
  65     F_CONNBONDS,
  66     F_HARMONIC,
  67     F_FENEBONDS,
  68     F_TABBONDS,
  69     F_TABBONDSNC,
  70     F_RESTRBONDS,
  71     F_ANGLES,
  72     F_G96ANGLES,
  73     F_LINEAR_ANGLES,
  74     F_CROSS_BOND_BONDS,
  75     F_CROSS_BOND_ANGLES,
  76     F_UREY_BRADLEY,
  77     F_QUARTIC_ANGLES,
  78     F_TABANGLES,
  79     F_PDIHS,
  80     F_RBDIHS,
  81     F_FOURDIHS,
  82     F_IDIHS,
  83     F_PIDIHS,
  84     F_TABDIHS,
  85     F_CMAP,
  86     F_GB12,
  87     F_GB13,
  88     F_GB14,
  89     F_GBPOL,
  90     F_NPSOLVATION,
  91     F_LJ14,
  92     F_COUL14,
  93     F_LJC14_Q,
  94     F_LJC_PAIRS_NB,
  95     F_LJ,
  96     F_BHAM,
  97     F_LJ_LR,
  98     F_BHAM_LR,
  99     F_DISPCORR,
 100     F_COUL_SR,
 101     F_COUL_LR,
 102     F_RF_EXCL,
 103     F_COUL_RECIP,
 104     F_DPD,
 105     F_POLARIZATION,
 106     F_WATER_POL,
 107     F_THOLE_POL,
 108     F_ANHARM_POL,
 109     F_POSRES,
 110     F_DISRES,
 111     F_DISRESVIOL,
 112     F_ORIRES,
 113     F_ORIRESDEV,
 114     F_ANGRES,
 115     F_ANGRESZ,
 116     F_DIHRES,
 117     F_DIHRESVIOL,
 118     F_CONSTR,
 119     F_CONSTRNC,
 120     F_SETTLE,
 121     F_VSITE2,
 122     F_VSITE3,
 123     F_VSITE3FD,
 124     F_VSITE3FAD,
 125     F_VSITE3OUT,
 126     F_VSITE4FD,
 127     F_VSITE4FDN,
 128     F_VSITEN,
 129     F_COM_PULL,
 130     F_EQM,
 131     F_EPOT,
 132     F_EKIN,
 133     F_ETOT,
 134     F_ECONSERVED,
 135     F_TEMP,
 136     F_VTEMP_NOLONGERUSED,
 137     F_PDISPCORR,
 138     F_PRES,
 139     F_DVDL_CONSTR,
 140     F_DVDL,
 141     F_DKDL,
 142     F_DVDL_COUL,
 143     F_DVDL_VDW,
 144     F_DVDL_BONDED,
 145     F_DVDL_RESTRAINT,
 146     F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
 147     F_NRE               /* This number is for the total number of energies      */
 148 };
 149
 150 #define IS_RESTRAINT_TYPE(ifunc) (((ifunc == F_POSRES) || (ifunc == F_DISRES) || (ifunc == F_RESTRBONDS) || (ifunc == F_DISRESVIOL) || (ifunc == F_ORIRES) || (ifunc == F_ORIRESDEV) || (ifunc == F_ANGRES) || (ifunc == F_ANGRESZ) || (ifunc == F_DIHRES)))
 151
 152 /* A macro for checking if ftype is an explicit pair-listed LJ or COULOMB
 153  * interaction type:
 154  * bonded LJ (usually 1-4), or special listed non-bonded for FEP.
 155  */
 156 #define IS_LISTED_LJ_C(ftype) ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB)
 157
 158 typedef union
 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 rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
 245     } rbdihs;
 246     struct {
 247         real a, b, c, d, e, f;
 248     } vsite;
 249     struct {
 250         int  n; real a;
 251     } vsiten;
 252     /* NOTE: npair is only set after reading the tpx file */
 253     struct {
 254         real low, up1, up2, kfac; int type, label, npair;
 255     } disres;
 256     struct {
 257         real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
 258     } dihres;
 259     struct {
 260         int  ex, power, label; real c, obs, kfac;
 261     } orires;
 262     struct {
 263         int  table; real kA; real kB;
 264     } tab;
 265     struct {
 266         real sar, st, pi, gbr, bmlt;
 267     } gb;
 268     struct {
 269         int cmapA, cmapB;
 270     } cmap;
 271     struct {
 272         real buf[MAXFORCEPARAM];
 273     } generic;                                               /* Conversion */
 274 } t_iparams;
 275
 276 typedef int t_functype;
 277
 278 /*
 279  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 280  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 281  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 282  * interactions.
 283  */
 284 typedef struct
 285 {
 286     int      nr;
 287     int      nr_nonperturbed;
 288     t_iatom *iatoms;
 289     int      nalloc;
 290 } t_ilist;
 291
 292 /*
 293  * The struct t_ilist defines a list of atoms with their interactions.
 294  * General field description:
 295  *   int nr
 296  *      the size (nr elements) of the interactions array (iatoms[]).
 297  *   t_iatom *iatoms
 298  *  specifies which atoms are involved in an interaction of a certain
 299  *       type. The layout of this array is as follows:
 300  *
 301  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 302  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 303  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 304  *
 305  *  So for interaction type type1 3 atoms are needed, and for type2 and
 306  *      type3 only 2. The type identifier is used to select the function to
 307  *      calculate the interaction and its actual parameters. This type
 308  *      identifier is an index in a params[] and functype[] array.
 309  */
 310
 311 typedef struct
 312 {
 313     real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
 314     /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 315 } cmapdata_t;
 316
 317 typedef struct
 318 {
 319     int         ngrid;        /* Number of allocated cmap (cmapdata_t ) grids */
 320     int         grid_spacing; /* Grid spacing */
 321     cmapdata_t *cmapdata;     /* Pointer to grid with actual, pre-interpolated data */
 322 } gmx_cmap_t;
 323
 324
 325 typedef struct
 326 {
 327     int         ntypes;
 328     int         atnr;
 329     t_functype *functype;
 330     t_iparams  *iparams;
 331     double      reppow;    /* The repulsion power for VdW: C12*r^-reppow   */
 332     real        fudgeQQ;   /* The scaling factor for Coulomb 1-4: f*q1*q2  */
 333     gmx_cmap_t  cmap_grid; /* The dihedral correction maps                 */
 334 } gmx_ffparams_t;
 335
 336 enum {
 337     ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
 338 };
 339
 340 typedef struct
 341 {
 342     int         ntypes;
 343     int         atnr;
 344     t_functype *functype;
 345     t_iparams  *iparams;
 346     real        fudgeQQ;
 347     gmx_cmap_t  cmap_grid;
 348     t_iparams  *iparams_posres;
 349     int         iparams_posres_nalloc;
 350
 351     t_ilist     il[F_NRE];
 352     int         ilsort;
 353 } t_idef;
 354
 355 /*
 356  * The struct t_idef defines all the interactions for the complete
 357  * simulation. The structure is setup in such a way that the multinode
 358  * version of the program  can use it as easy as the single node version.
 359  * General field description:
 360  *   int ntypes
 361  *      defines the number of elements in functype[] and param[].
 362  *   int nodeid
 363  *      the node id (if parallel machines)
 364  *   int atnr
 365  *      the number of atomtypes
 366  *   t_functype *functype
 367  *      array of length ntypes, defines for every force type what type of
 368  *      function to use. Every "bond" with the same function but different
 369  *      force parameters is a different force type. The type identifier in the
 370  *      forceatoms[] array is an index in this array.
 371  *   t_iparams *iparams
 372  *      array of length ntypes, defines the parameters for every interaction
 373  *      type. The type identifier in the actual interaction list
 374  *      (ilist[ftype].iatoms[]) is an index in this array.
 375  *   gmx_cmap_t cmap_grid
 376  *      the grid for the dihedral pair correction maps.
 377  *   t_iparams *iparams_posres
 378  *      defines the parameters for position restraints only.
 379  *      Position restraints are the only interactions that have different
 380  *      parameters (reference positions) for different molecules
 381  *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 382  *   t_ilist il[F_NRE]
 383  *      The list of interactions for each type. Note that some,
 384  *      such as LJ and COUL will have 0 entries.
 385  */
 386
 387 typedef struct {
 388     int   n;      /* n+1 is the number of points */
 389     real  scale;  /* distance between two points */
 390     real *data;   /* the actual table data, per point there are 4 numbers */
 391 } bondedtable_t;
 392
 393 #ifdef __cplusplus
 394 }
 395 #endif
 396
 397
 398 #endif