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 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #ifndef _idef_h
  40 #define _idef_h
  41
  42
  43 /* check kernel/toppush.c when you change these numbers */
  44 #define MAXATOMLIST     6
  45 #define MAXFORCEPARAM   12
  46 #define NR_RBDIHS       6
  47 #define NR_FOURDIHS     4
  48
  49 typedef atom_id t_iatom;
  50
  51 /* this MUST correspond to the
  52    t_interaction_function[F_NRE] in gmxlib/ifunc.c */
  53 enum {
  54   F_BONDS,
  55   F_G96BONDS,
  56   F_MORSE,
  57   F_CUBICBONDS,
  58   F_CONNBONDS,
  59   F_HARMONIC,
  60   F_FENEBONDS,
  61   F_TABBONDS,
  62   F_TABBONDSNC,
  63   F_ANGLES,
  64   F_G96ANGLES,
  65   F_CROSS_BOND_BONDS,
  66   F_CROSS_BOND_ANGLES,
  67   F_UREY_BRADLEY,
  68   F_QUARTIC_ANGLES,
  69   F_TABANGLES,
  70   F_PDIHS,
  71   F_RBDIHS,
  72   F_FOURDIHS,
  73   F_IDIHS,
  74   F_PIDIHS,
  75   F_TABDIHS,
  76   F_CMAP,
  77   F_GB12,
  78   F_GB13,
  79   F_GB14,
  80   F_LJ14,
  81   F_COUL14,
  82   F_LJC14_Q,
  83   F_LJC_PAIRS_NB,
  84   F_LJ,
  85   F_BHAM,
  86   F_LJ_LR,
  87   F_BHAM_LR,
  88   F_DISPCORR,
  89   F_COUL_SR,
  90   F_COUL_LR,
  91   F_RF_EXCL,
  92   F_COUL_RECIP,
  93   F_DPD,
  94   F_POLARIZATION,
  95   F_WATER_POL,
  96   F_THOLE_POL,
  97   F_POSRES,
  98   F_DISRES,
  99   F_DISRESVIOL,
 100   F_ORIRES,
 101   F_ORIRESDEV,
 102   F_ANGRES,
 103   F_ANGRESZ,
 104   F_DIHRES,
 105   F_DIHRESVIOL,
 106   F_CONSTR,
 107   F_CONSTRNC,
 108   F_SETTLE,
 109   F_VSITE2,
 110   F_VSITE3,
 111   F_VSITE3FD,
 112   F_VSITE3FAD,
 113   F_VSITE3OUT,
 114   F_VSITE4FD,
 115   F_VSITE4FDN,
 116   F_VSITEN,
 117   F_COM_PULL,
 118   F_EQM,
 119   F_EPOT,
 120   F_EKIN,
 121   F_ETOT,
 122   F_ECONSERVED,
 123   F_TEMP,
 124   F_PDISPCORR,
 125   F_PRES,
 126   F_DVDL,
 127   F_DKDL,
 128   F_DHDL_CON,
 129   F_NRE         /* This number is for the total number of energies      */
 130 };
 131
 132 typedef union
 133 {
 134   /* Some parameters have A and B values for free energy calculations.
 135    * The B values are not used for regular simulations of course.
 136    * Free Energy for nonbondeds can be computed by changing the atom type.
 137    * The harmonic type is used for all harmonic potentials:
 138    * bonds, angles and improper dihedrals
 139    */
 140   struct {real a,b,c;                                      } bham;
 141   struct {real rA,krA,rB,krB;                              } harmonic;
 142   /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
 143   struct {real b0,kb,kcub;                                 } cubic;
 144   struct {real bm,kb;                                      } fene;
 145   struct {real r1e,r2e,krr;                                } cross_bb;
 146   struct {real r1e,r2e,r3e,krt;                            } cross_ba;
 147   struct {real theta,ktheta,r13,kUB;                       } u_b;
 148   struct {real theta,c[5];                                 } qangle;
 149   struct {real alpha;                                      } polarize;
 150   struct {real al_x,al_y,al_z,rOH,rHH,rOD;                 } wpol;
 151   struct {real a,alpha1,alpha2,rfac;                       } thole;
 152   struct {real c6,c12;                                     } lj;
 153   struct {real c6A,c12A,c6B,c12B;                          } lj14;
 154   struct {real fqq,qi,qj,c6,c12;                           } ljc14;
 155   struct {real qi,qj,c6,c12;                               } ljcnb;
 156   /* Proper dihedrals can not have different multiplicity when
 157    * doing free energy calculations, because the potential would not
 158    * be periodic anymore.
 159    */
 160   struct {real phiA,cpA;int mult;real phiB,cpB;            } pdihs;
 161   struct {real dA,dB;                                      } constr;
 162   /* Settle can not be used for Free energy calculations of water bond geometry.
 163    * Use shake (or lincs) instead if you have to change the water bonds.
 164    */
 165   struct {real doh,dhh;                                   } settle;
 166   /* No free energy supported for morse bonds */
 167   struct {real b0,cb,beta;                                } morse;
 168   struct {real pos0A[DIM],fcA[DIM],pos0B[DIM],fcB[DIM];   } posres;
 169   struct {real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];          } rbdihs;
 170   struct {real a,b,c,d,e,f;                               } vsite;
 171   struct {int  n; real a;                                 } vsiten;
 172   struct {real low,up1,up2,kfac;int type,label;           } disres;
 173   struct {real phi,dphi,kfac;int label,power;             } dihres;
 174   struct {int  ex,power,label; real c,obs,kfac;           } orires;
 175   struct {int  table;real kA;real kB;                     } tab;
 176   struct {real sar,st,pi,gbr,bmlt;                        } gb;
 177   struct {int cmapA,cmapB;                                } cmap;
 178   struct {real buf[MAXFORCEPARAM];                        } generic; /* Conversion */
 179 } t_iparams;
 180
 181 typedef int t_functype;
 182
 183 /*
 184  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 185  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 186  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 187  * interactions.
 188  */
 189 typedef struct
 190 {
 191   int nr;
 192   int nr_nonperturbed;
 193   t_iatom *iatoms;
 194   int nalloc;
 195 } t_ilist;
 196
 197 /*
 198  * The struct t_ilist defines a list of atoms with their interactions.
 199  * General field description:
 200  *   int nr
 201  *      the size (nr elements) of the interactions array (iatoms[]).
 202  *   t_iatom *iatoms
 203  *      specifies which atoms are involved in an interaction of a certain
 204  *       type. The layout of this array is as follows:
 205  *
 206  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 207  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 208  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 209  *
 210  *      So for interaction type type1 3 atoms are needed, and for type2 and
 211  *      type3 only 2. The type identifier is used to select the function to
 212  *      calculate the interaction and its actual parameters. This type
 213  *      identifier is an index in a params[] and functype[] array.
 214  */
 215
 216 typedef struct
 217 {
 218         real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
 219         /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 220 } cmapdata_t;
 221
 222 typedef struct
 223 {
 224         int ngrid;            /* Number of allocated cmap (cmapdata_t ) grids */
 225         int grid_spacing;     /* Grid spacing */
 226         cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
 227 } gmx_cmap_t;
 228
 229
 230 typedef struct
 231 {
 232   int        ntypes;
 233   int        atnr;
 234   t_functype *functype;
 235   t_iparams  *iparams;
 236   double     reppow;     /* The repulsion power for VdW: C12*r^-reppow   */
 237   real       fudgeQQ;    /* The scaling factor for Coulomb 1-4: f*q1*q2  */
 238 } gmx_ffparams_t;
 239
 240 enum {
 241   ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
 242 };
 243
 244 typedef struct
 245 {
 246   int ntypes;
 247   int atnr;
 248   t_functype *functype;
 249   t_iparams  *iparams;
 250   real fudgeQQ;
 251   t_iparams  *iparams_posres;
 252   int iparams_posres_nalloc;
 253
 254   t_ilist il[F_NRE];
 255   int ilsort;
 256 } t_idef;
 257
 258 /*
 259  * The struct t_idef defines all the interactions for the complete
 260  * simulation. The structure is setup in such a way that the multinode
 261  * version of the program  can use it as easy as the single node version.
 262  * General field description:
 263  *   int ntypes
 264  *      defines the number of elements in functype[] and param[].
 265  *   int nodeid
 266  *      the node id (if parallel machines)
 267  *   int atnr
 268  *      the number of atomtypes
 269  *   t_functype *functype
 270  *      array of length ntypes, defines for every force type what type of
 271  *      function to use. Every "bond" with the same function but different
 272  *      force parameters is a different force type. The type identifier in the
 273  *      forceatoms[] array is an index in this array.
 274      t_iparams *iparams;
 275  *      array of length ntypes, defines the parameters for every interaction
 276  *      type. The type identifier in the actual interaction list
 277  *      (bondeds.iatoms[] or shakes.iatoms[]) is an index in this array.
 278  *   t_ilist il[F_NRE]
 279  *      The list of interactions for each type. Note that some,
 280  *      such as LJ and COUL will have 0 entries.
 281  */
 282
 283 typedef struct {
 284   int  n;         /* n+1 is the number of points */
 285   real scale;     /* distance between two points */
 286   real *tab;      /* the actual tables, per point there are  4 numbers */
 287 } bondedtable_t;
 288
 289 #endif