include/types/idef.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
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  34  */
  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_CROSS_BOND_BONDS,
  71   F_CROSS_BOND_ANGLES,
  72   F_UREY_BRADLEY,
  73   F_QUARTIC_ANGLES,
  74   F_TABANGLES,
  75   F_PDIHS,
  76   F_RBDIHS,
  77   F_FOURDIHS,
  78   F_IDIHS,
  79   F_PIDIHS,
  80   F_TABDIHS,
  81   F_CMAP,
  82   F_GB12,
  83   F_GB13,
  84   F_GB14,
  85   F_GBPOL,
  86   F_NPSOLVATION,
  87   F_LJ14,
  88   F_COUL14,
  89   F_LJC14_Q,
  90   F_LJC_PAIRS_NB,
  91   F_LJ,
  92   F_BHAM,
  93   F_LJ_LR,
  94   F_BHAM_LR,
  95   F_DISPCORR,
  96   F_COUL_SR,
  97   F_COUL_LR,
  98   F_RF_EXCL,
  99   F_COUL_RECIP,
 100   F_DPD,
 101   F_POLARIZATION,
 102   F_WATER_POL,
 103   F_THOLE_POL,
 104   F_POSRES,
 105   F_DISRES,
 106   F_DISRESVIOL,
 107   F_ORIRES,
 108   F_ORIRESDEV,
 109   F_ANGRES,
 110   F_ANGRESZ,
 111   F_DIHRES,
 112   F_DIHRESVIOL,
 113   F_CONSTR,
 114   F_CONSTRNC,
 115   F_SETTLE,
 116   F_VSITE2,
 117   F_VSITE3,
 118   F_VSITE3FD,
 119   F_VSITE3FAD,
 120   F_VSITE3OUT,
 121   F_VSITE4FD,
 122   F_VSITE4FDN,
 123   F_VSITEN,
 124   F_COM_PULL,
 125   F_EQM,
 126   F_EPOT,
 127   F_EKIN,
 128   F_ETOT,
 129   F_ECONSERVED,
 130   F_TEMP,
 131   F_VTEMP,
 132   F_PDISPCORR,
 133   F_PRES,
 134   F_DVDL,
 135   F_DKDL,
 136   F_DHDL_CON,
 137   F_NRE         /* This number is for the total number of energies      */
 138 };
 139
 140 typedef union
 141 {
 142   /* Some parameters have A and B values for free energy calculations.
 143    * The B values are not used for regular simulations of course.
 144    * Free Energy for nonbondeds can be computed by changing the atom type.
 145    * The harmonic type is used for all harmonic potentials:
 146    * bonds, angles and improper dihedrals
 147    */
 148   struct {real a,b,c;                                      } bham;
 149   struct {real rA,krA,rB,krB;                              } harmonic;
 150   struct {real lowA,up1A,up2A,kA,lowB,up1B,up2B,kB;        } restraint;
 151   /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
 152   struct {real b0,kb,kcub;                                 } cubic;
 153   struct {real bm,kb;                                      } fene;
 154   struct {real r1e,r2e,krr;                                } cross_bb;
 155   struct {real r1e,r2e,r3e,krt;                            } cross_ba;
 156   struct {real theta,ktheta,r13,kUB;                       } u_b;
 157   struct {real theta,c[5];                                 } qangle;
 158   struct {real alpha;                                      } polarize;
 159   struct {real al_x,al_y,al_z,rOH,rHH,rOD;                 } wpol;
 160   struct {real a,alpha1,alpha2,rfac;                       } thole;
 161   struct {real c6,c12;                                     } lj;
 162   struct {real c6A,c12A,c6B,c12B;                          } lj14;
 163   struct {real fqq,qi,qj,c6,c12;                           } ljc14;
 164   struct {real qi,qj,c6,c12;                               } ljcnb;
 165   /* Proper dihedrals can not have different multiplicity when
 166    * doing free energy calculations, because the potential would not
 167    * be periodic anymore.
 168    */
 169   struct {real phiA,cpA;int mult;real phiB,cpB;            } pdihs;
 170   struct {real dA,dB;                                      } constr;
 171   /* Settle can not be used for Free energy calculations of water bond geometry.
 172    * Use shake (or lincs) instead if you have to change the water bonds.
 173    */
 174   struct {real doh,dhh;                                   } settle;
 175   /* No free energy supported for morse bonds */
 176   struct {real b0,cb,beta;                                } morse;
 177   struct {real pos0A[DIM],fcA[DIM],pos0B[DIM],fcB[DIM];   } posres;
 178   struct {real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];          } rbdihs;
 179   struct {real a,b,c,d,e,f;                               } vsite;
 180   struct {int  n; real a;                                 } vsiten;
 181   /* NOTE: npair is only set after reading the tpx file */
 182   struct {real low,up1,up2,kfac;int type,label,npair;     } disres;
 183   struct {real phi,dphi,kfac;int label,power;             } dihres;
 184   struct {int  ex,power,label; real c,obs,kfac;           } orires;
 185   struct {int  table;real kA;real kB;                     } tab;
 186   struct {real sar,st,pi,gbr,bmlt;                        } gb;
 187   struct {int cmapA,cmapB;                                } cmap;
 188   struct {real buf[MAXFORCEPARAM];                        } generic; /* Conversion */
 189 } t_iparams;
 190
 191 typedef int t_functype;
 192
 193 /*
 194  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 195  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 196  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 197  * interactions.
 198  */
 199 typedef struct
 200 {
 201   int nr;
 202   int nr_nonperturbed;
 203   t_iatom *iatoms;
 204   int nalloc;
 205 } t_ilist;
 206
 207 /*
 208  * The struct t_ilist defines a list of atoms with their interactions.
 209  * General field description:
 210  *   int nr
 211  *      the size (nr elements) of the interactions array (iatoms[]).
 212  *   t_iatom *iatoms
 213  *      specifies which atoms are involved in an interaction of a certain
 214  *       type. The layout of this array is as follows:
 215  *
 216  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 217  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 218  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 219  *
 220  *      So for interaction type type1 3 atoms are needed, and for type2 and
 221  *      type3 only 2. The type identifier is used to select the function to
 222  *      calculate the interaction and its actual parameters. This type
 223  *      identifier is an index in a params[] and functype[] array.
 224  */
 225
 226 typedef struct
 227 {
 228         real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
 229         /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 230 } cmapdata_t;
 231
 232 typedef struct
 233 {
 234         int ngrid;            /* Number of allocated cmap (cmapdata_t ) grids */
 235         int grid_spacing;     /* Grid spacing */
 236         cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
 237 } gmx_cmap_t;
 238
 239
 240 typedef struct
 241 {
 242   int        ntypes;
 243   int        atnr;
 244   t_functype *functype;
 245   t_iparams  *iparams;
 246   double     reppow;     /* The repulsion power for VdW: C12*r^-reppow   */
 247   real       fudgeQQ;    /* The scaling factor for Coulomb 1-4: f*q1*q2  */
 248   gmx_cmap_t cmap_grid;  /* The dihedral correction maps                 */
 249 } gmx_ffparams_t;
 250
 251 enum {
 252   ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
 253 };
 254
 255 typedef struct
 256 {
 257   int ntypes;
 258   int atnr;
 259   t_functype *functype;
 260   t_iparams  *iparams;
 261   real fudgeQQ;
 262   gmx_cmap_t cmap_grid;
 263   t_iparams  *iparams_posres;
 264   int iparams_posres_nalloc;
 265
 266   t_ilist il[F_NRE];
 267   int ilsort;
 268 } t_idef;
 269
 270 /*
 271  * The struct t_idef defines all the interactions for the complete
 272  * simulation. The structure is setup in such a way that the multinode
 273  * version of the program  can use it as easy as the single node version.
 274  * General field description:
 275  *   int ntypes
 276  *      defines the number of elements in functype[] and param[].
 277  *   int nodeid
 278  *      the node id (if parallel machines)
 279  *   int atnr
 280  *      the number of atomtypes
 281  *   t_functype *functype
 282  *      array of length ntypes, defines for every force type what type of
 283  *      function to use. Every "bond" with the same function but different
 284  *      force parameters is a different force type. The type identifier in the
 285  *      forceatoms[] array is an index in this array.
 286  *   t_iparams *iparams
 287  *      array of length ntypes, defines the parameters for every interaction
 288  *      type. The type identifier in the actual interaction list
 289  *      (ilist[ftype].iatoms[]) is an index in this array.
 290  *   gmx_cmap_t cmap_grid
 291  *      the grid for the dihedral pair correction maps.
 292  *   t_iparams *iparams_posres
 293  *      defines the parameters for position restraints only.
 294  *      Position restraints are the only interactions that have different
 295  *      parameters (reference positions) for different molecules
 296  *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 297  *   t_ilist il[F_NRE]
 298  *      The list of interactions for each type. Note that some,
 299  *      such as LJ and COUL will have 0 entries.
 300  */
 301
 302 typedef struct {
 303   int  n;         /* n+1 is the number of points */
 304   real scale;     /* distance between two points */
 305   real *tab;      /* the actual tables, per point there are  4 numbers */
 306 } bondedtable_t;
 307
 308 #ifdef __cplusplus
 309 }
 310 #endif
 311
 312
 313 #endif