include/types/idef.h

   1 /*
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   4  *
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   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  12  * Copyright (c) 2001-2004, The GROMACS development team,
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  14
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  35
  36
  37 #ifndef _idef_h
  38 #define _idef_h
  39
  40 #include "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_FOURDIHS     4
  52
  53 typedef atom_id t_iatom;
  54
  55 /* this MUST correspond to the
  56    t_interaction_function[F_NRE] in gmxlib/ifunc.c */
  57 enum {
  58   F_BONDS,
  59   F_G96BONDS,
  60   F_MORSE,
  61   F_CUBICBONDS,
  62   F_CONNBONDS,
  63   F_HARMONIC,
  64   F_FENEBONDS,
  65   F_TABBONDS,
  66   F_TABBONDSNC,
  67   F_RESTRBONDS,
  68   F_ANGLES,
  69   F_G96ANGLES,
  70   F_LINEAR_ANGLES,
  71   F_CROSS_BOND_BONDS,
  72   F_CROSS_BOND_ANGLES,
  73   F_UREY_BRADLEY,
  74   F_QUARTIC_ANGLES,
  75   F_TABANGLES,
  76   F_PDIHS,
  77   F_RBDIHS,
  78   F_FOURDIHS,
  79   F_IDIHS,
  80   F_PIDIHS,
  81   F_TABDIHS,
  82   F_CMAP,
  83   F_GB12,
  84   F_GB13,
  85   F_GB14,
  86   F_GBPOL,
  87   F_NPSOLVATION,
  88   F_LJ14,
  89   F_COUL14,
  90   F_LJC14_Q,
  91   F_LJC_PAIRS_NB,
  92   F_LJ,
  93   F_BHAM,
  94   F_LJ_LR,
  95   F_BHAM_LR,
  96   F_DISPCORR,
  97   F_COUL_SR,
  98   F_COUL_LR,
  99   F_RF_EXCL,
 100   F_COUL_RECIP,
 101   F_DPD,
 102   F_POLARIZATION,
 103   F_WATER_POL,
 104   F_THOLE_POL,
 105   F_ANHARM_POL,
 106   F_POSRES,
 107   F_DISRES,
 108   F_DISRESVIOL,
 109   F_ORIRES,
 110   F_ORIRESDEV,
 111   F_ANGRES,
 112   F_ANGRESZ,
 113   F_DIHRES,
 114   F_DIHRESVIOL,
 115   F_CONSTR,
 116   F_CONSTRNC,
 117   F_SETTLE,
 118   F_VSITE2,
 119   F_VSITE3,
 120   F_VSITE3FD,
 121   F_VSITE3FAD,
 122   F_VSITE3OUT,
 123   F_VSITE4FD,
 124   F_VSITE4FDN,
 125   F_VSITEN,
 126   F_COM_PULL,
 127   F_EQM,
 128   F_EPOT,
 129   F_EKIN,
 130   F_ETOT,
 131   F_ECONSERVED,
 132   F_TEMP,
 133   F_VTEMP,
 134   F_PDISPCORR,
 135   F_PRES,
 136   F_DHDL_CON,
 137   F_DVDL,
 138   F_DKDL,
 139   F_DVDL_COUL,
 140   F_DVDL_VDW,
 141   F_DVDL_BONDED,
 142   F_DVDL_RESTRAINT,
 143   F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
 144   F_NRE         /* This number is for the total number of energies      */
 145 };
 146
 147 #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)))
 148
 149 /* A macro for checking if ftype is an explicit pair-listed LJ or COULOMB
 150  * interaction type:
 151  * bonded LJ (usually 1-4), or special listed non-bonded for FEP.
 152  */
 153 #define IS_LISTED_LJ_C(ftype) ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB)
 154
 155 typedef union
 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 {real a,b,c;                                      } bham;
 164   struct {real rA,krA,rB,krB;                              } harmonic;
 165   struct {real klinA,aA,klinB,aB;                          } linangle;
 166   struct {real lowA,up1A,up2A,kA,lowB,up1B,up2B,kB;        } restraint;
 167   /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
 168   struct {real b0,kb,kcub;                                 } cubic;
 169   struct {real bm,kb;                                      } fene;
 170   struct {real r1e,r2e,krr;                                } cross_bb;
 171   struct {real r1e,r2e,r3e,krt;                            } cross_ba;
 172   struct {real thetaA,kthetaA,r13A,kUBA,thetaB,kthetaB,r13B,kUBB;} u_b;
 173   struct {real theta,c[5];                                 } qangle;
 174   struct {real alpha;                                      } polarize;
 175   struct {real alpha,drcut,khyp;                           } anharm_polarize;
 176   struct {real al_x,al_y,al_z,rOH,rHH,rOD;                 } wpol;
 177   struct {real a,alpha1,alpha2,rfac;                       } thole;
 178   struct {real c6,c12;                                     } lj;
 179   struct {real c6A,c12A,c6B,c12B;                          } lj14;
 180   struct {real fqq,qi,qj,c6,c12;                           } ljc14;
 181   struct {real qi,qj,c6,c12;                               } ljcnb;
 182   /* Proper dihedrals can not have different multiplicity when
 183    * doing free energy calculations, because the potential would not
 184    * be periodic anymore.
 185    */
 186   struct {real phiA,cpA;int mult;real phiB,cpB;            } pdihs;
 187   struct {real dA,dB;                                      } constr;
 188   /* Settle can not be used for Free energy calculations of water bond geometry.
 189    * Use shake (or lincs) instead if you have to change the water bonds.
 190    */
 191   struct {real doh,dhh;                                   } settle;
 192   struct {real b0A,cbA,betaA,b0B,cbB,betaB;               } morse;
 193   struct {real pos0A[DIM],fcA[DIM],pos0B[DIM],fcB[DIM];   } posres;
 194   struct {real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];          } rbdihs;
 195   struct {real a,b,c,d,e,f;                               } vsite;
 196   struct {int  n; real a;                                 } vsiten;
 197   /* NOTE: npair is only set after reading the tpx file */
 198   struct {real low,up1,up2,kfac;int type,label,npair;     } disres;
 199   struct {real phiA,dphiA,kfacA,phiB,dphiB,kfacB;         } dihres;
 200   struct {int  ex,power,label; real c,obs,kfac;           } orires;
 201   struct {int  table;real kA;real kB;                     } tab;
 202   struct {real sar,st,pi,gbr,bmlt;                        } gb;
 203   struct {int cmapA,cmapB;                                } cmap;
 204   struct {real buf[MAXFORCEPARAM];                        } generic; /* Conversion */
 205 } t_iparams;
 206
 207 typedef int t_functype;
 208
 209 /*
 210  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 211  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 212  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 213  * interactions.
 214  */
 215 typedef struct
 216 {
 217   int nr;
 218   int nr_nonperturbed;
 219   t_iatom *iatoms;
 220   int nalloc;
 221 } t_ilist;
 222
 223 /*
 224  * The struct t_ilist defines a list of atoms with their interactions.
 225  * General field description:
 226  *   int nr
 227  *      the size (nr elements) of the interactions array (iatoms[]).
 228  *   t_iatom *iatoms
 229  *      specifies which atoms are involved in an interaction of a certain
 230  *       type. The layout of this array is as follows:
 231  *
 232  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 233  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 234  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 235  *
 236  *      So for interaction type type1 3 atoms are needed, and for type2 and
 237  *      type3 only 2. The type identifier is used to select the function to
 238  *      calculate the interaction and its actual parameters. This type
 239  *      identifier is an index in a params[] and functype[] array.
 240  */
 241
 242 typedef struct
 243 {
 244         real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
 245         /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 246 } cmapdata_t;
 247
 248 typedef struct
 249 {
 250         int ngrid;            /* Number of allocated cmap (cmapdata_t ) grids */
 251         int grid_spacing;     /* Grid spacing */
 252         cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
 253 } gmx_cmap_t;
 254
 255
 256 typedef struct
 257 {
 258   int        ntypes;
 259   int        atnr;
 260   t_functype *functype;
 261   t_iparams  *iparams;
 262   double     reppow;     /* The repulsion power for VdW: C12*r^-reppow   */
 263   real       fudgeQQ;    /* The scaling factor for Coulomb 1-4: f*q1*q2  */
 264   gmx_cmap_t cmap_grid;  /* The dihedral correction maps                 */
 265 } gmx_ffparams_t;
 266
 267 enum {
 268   ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
 269 };
 270
 271 typedef struct
 272 {
 273   int ntypes;
 274   int atnr;
 275   t_functype *functype;
 276   t_iparams  *iparams;
 277   real fudgeQQ;
 278   gmx_cmap_t cmap_grid;
 279   t_iparams  *iparams_posres;
 280   int iparams_posres_nalloc;
 281
 282   t_ilist il[F_NRE];
 283   int ilsort;
 284 } t_idef;
 285
 286 /*
 287  * The struct t_idef defines all the interactions for the complete
 288  * simulation. The structure is setup in such a way that the multinode
 289  * version of the program  can use it as easy as the single node version.
 290  * General field description:
 291  *   int ntypes
 292  *      defines the number of elements in functype[] and param[].
 293  *   int nodeid
 294  *      the node id (if parallel machines)
 295  *   int atnr
 296  *      the number of atomtypes
 297  *   t_functype *functype
 298  *      array of length ntypes, defines for every force type what type of
 299  *      function to use. Every "bond" with the same function but different
 300  *      force parameters is a different force type. The type identifier in the
 301  *      forceatoms[] array is an index in this array.
 302  *   t_iparams *iparams
 303  *      array of length ntypes, defines the parameters for every interaction
 304  *      type. The type identifier in the actual interaction list
 305  *      (ilist[ftype].iatoms[]) is an index in this array.
 306  *   gmx_cmap_t cmap_grid
 307  *      the grid for the dihedral pair correction maps.
 308  *   t_iparams *iparams_posres
 309  *      defines the parameters for position restraints only.
 310  *      Position restraints are the only interactions that have different
 311  *      parameters (reference positions) for different molecules
 312  *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 313  *   t_ilist il[F_NRE]
 314  *      The list of interactions for each type. Note that some,
 315  *      such as LJ and COUL will have 0 entries.
 316  */
 317
 318 typedef struct {
 319   int  n;         /* n+1 is the number of points */
 320   real scale;     /* distance between two points */
 321   real *tab;      /* the actual tables, per point there are  4 numbers */
 322 } bondedtable_t;
 323
 324 #ifdef __cplusplus
 325 }
 326 #endif
 327
 328
 329 #endif