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
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
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  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
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  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GRoups of Organic Molecules in ACtion for Science
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #ifndef _idef_h
  40 #define _idef_h
  41
  42 #include "simple.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48
  49 /* check kernel/toppush.c when you change these numbers */
  50 #define MAXATOMLIST     6
  51 #define MAXFORCEPARAM   12
  52 #define NR_RBDIHS       6
  53 #define NR_FOURDIHS     4
  54
  55 typedef atom_id t_iatom;
  56
  57 /* this MUST correspond to the
  58    t_interaction_function[F_NRE] in gmxlib/ifunc.c */
  59 enum {
  60   F_BONDS,
  61   F_G96BONDS,
  62   F_MORSE,
  63   F_CUBICBONDS,
  64   F_CONNBONDS,
  65   F_HARMONIC,
  66   F_FENEBONDS,
  67   F_TABBONDS,
  68   F_TABBONDSNC,
  69   F_RESTRBONDS,
  70   F_ANGLES,
  71   F_G96ANGLES,
  72   F_CROSS_BOND_BONDS,
  73   F_CROSS_BOND_ANGLES,
  74   F_UREY_BRADLEY,
  75   F_QUARTIC_ANGLES,
  76   F_TABANGLES,
  77   F_PDIHS,
  78   F_RBDIHS,
  79   F_FOURDIHS,
  80   F_IDIHS,
  81   F_PIDIHS,
  82   F_TABDIHS,
  83   F_CMAP,
  84   F_GB12,
  85   F_GB13,
  86   F_GB14,
  87   F_GBPOL,
  88   F_NPSOLVATION,
  89   F_LJ14,
  90   F_COUL14,
  91   F_LJC14_Q,
  92   F_LJC_PAIRS_NB,
  93   F_LJ,
  94   F_BHAM,
  95   F_LJ_LR,
  96   F_BHAM_LR,
  97   F_DISPCORR,
  98   F_COUL_SR,
  99   F_COUL_LR,
 100   F_RF_EXCL,
 101   F_COUL_RECIP,
 102   F_DPD,
 103   F_POLARIZATION,
 104   F_WATER_POL,
 105   F_THOLE_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_DVDL,
 137   F_DKDL,
 138   F_DHDL_CON,
 139   F_NRE         /* This number is for the total number of energies      */
 140 };
 141
 142 typedef union
 143 {
 144   /* Some parameters have A and B values for free energy calculations.
 145    * The B values are not used for regular simulations of course.
 146    * Free Energy for nonbondeds can be computed by changing the atom type.
 147    * The harmonic type is used for all harmonic potentials:
 148    * bonds, angles and improper dihedrals
 149    */
 150   struct {real a,b,c;                                      } bham;
 151   struct {real rA,krA,rB,krB;                              } harmonic;
 152   struct {real lowA,up1A,up2A,kA,lowB,up1B,up2B,kB;        } restraint;
 153   /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
 154   struct {real b0,kb,kcub;                                 } cubic;
 155   struct {real bm,kb;                                      } fene;
 156   struct {real r1e,r2e,krr;                                } cross_bb;
 157   struct {real r1e,r2e,r3e,krt;                            } cross_ba;
 158   struct {real theta,ktheta,r13,kUB;                       } u_b;
 159   struct {real theta,c[5];                                 } qangle;
 160   struct {real alpha;                                      } polarize;
 161   struct {real al_x,al_y,al_z,rOH,rHH,rOD;                 } wpol;
 162   struct {real a,alpha1,alpha2,rfac;                       } thole;
 163   struct {real c6,c12;                                     } lj;
 164   struct {real c6A,c12A,c6B,c12B;                          } lj14;
 165   struct {real fqq,qi,qj,c6,c12;                           } ljc14;
 166   struct {real qi,qj,c6,c12;                               } ljcnb;
 167   /* Proper dihedrals can not have different multiplicity when
 168    * doing free energy calculations, because the potential would not
 169    * be periodic anymore.
 170    */
 171   struct {real phiA,cpA;int mult;real phiB,cpB;            } pdihs;
 172   struct {real dA,dB;                                      } constr;
 173   /* Settle can not be used for Free energy calculations of water bond geometry.
 174    * Use shake (or lincs) instead if you have to change the water bonds.
 175    */
 176   struct {real doh,dhh;                                   } settle;
 177   /* No free energy supported for morse bonds */
 178   struct {real b0,cb,beta;                                } morse;
 179   struct {real pos0A[DIM],fcA[DIM],pos0B[DIM],fcB[DIM];   } posres;
 180   struct {real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];          } rbdihs;
 181   struct {real a,b,c,d,e,f;                               } vsite;
 182   struct {int  n; real a;                                 } vsiten;
 183   /* NOTE: npair is only set after reading the tpx file */
 184   struct {real low,up1,up2,kfac;int type,label,npair;     } disres;
 185   struct {real phi,dphi,kfac;int label,power;             } dihres;
 186   struct {int  ex,power,label; real c,obs,kfac;           } orires;
 187   struct {int  table;real kA;real kB;                     } tab;
 188   struct {real sar,st,pi,gbr,bmlt;                        } gb;
 189   struct {int cmapA,cmapB;                                } cmap;
 190   struct {real buf[MAXFORCEPARAM];                        } generic; /* Conversion */
 191 } t_iparams;
 192
 193 typedef int t_functype;
 194
 195 /*
 196  * The nonperturbed/perturbed interactions are now separated (sorted) in the
 197  * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 198  * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 199  * interactions.
 200  */
 201 typedef struct
 202 {
 203   int nr;
 204   int nr_nonperturbed;
 205   t_iatom *iatoms;
 206   int nalloc;
 207 } t_ilist;
 208
 209 /*
 210  * The struct t_ilist defines a list of atoms with their interactions.
 211  * General field description:
 212  *   int nr
 213  *      the size (nr elements) of the interactions array (iatoms[]).
 214  *   t_iatom *iatoms
 215  *      specifies which atoms are involved in an interaction of a certain
 216  *       type. The layout of this array is as follows:
 217  *
 218  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 219  *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 220  *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 221  *
 222  *      So for interaction type type1 3 atoms are needed, and for type2 and
 223  *      type3 only 2. The type identifier is used to select the function to
 224  *      calculate the interaction and its actual parameters. This type
 225  *      identifier is an index in a params[] and functype[] array.
 226  */
 227
 228 typedef struct
 229 {
 230         real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
 231         /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
 232 } cmapdata_t;
 233
 234 typedef struct
 235 {
 236         int ngrid;            /* Number of allocated cmap (cmapdata_t ) grids */
 237         int grid_spacing;     /* Grid spacing */
 238         cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
 239 } gmx_cmap_t;
 240
 241
 242 typedef struct
 243 {
 244   int        ntypes;
 245   int        atnr;
 246   t_functype *functype;
 247   t_iparams  *iparams;
 248   double     reppow;     /* The repulsion power for VdW: C12*r^-reppow   */
 249   real       fudgeQQ;    /* The scaling factor for Coulomb 1-4: f*q1*q2  */
 250   gmx_cmap_t cmap_grid;  /* The dihedral correction maps                 */
 251 } gmx_ffparams_t;
 252
 253 enum {
 254   ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
 255 };
 256
 257 typedef struct
 258 {
 259   int ntypes;
 260   int atnr;
 261   t_functype *functype;
 262   t_iparams  *iparams;
 263   real fudgeQQ;
 264   gmx_cmap_t cmap_grid;
 265   t_iparams  *iparams_posres;
 266   int iparams_posres_nalloc;
 267
 268   t_ilist il[F_NRE];
 269   int ilsort;
 270 } t_idef;
 271
 272 /*
 273  * The struct t_idef defines all the interactions for the complete
 274  * simulation. The structure is setup in such a way that the multinode
 275  * version of the program  can use it as easy as the single node version.
 276  * General field description:
 277  *   int ntypes
 278  *      defines the number of elements in functype[] and param[].
 279  *   int nodeid
 280  *      the node id (if parallel machines)
 281  *   int atnr
 282  *      the number of atomtypes
 283  *   t_functype *functype
 284  *      array of length ntypes, defines for every force type what type of
 285  *      function to use. Every "bond" with the same function but different
 286  *      force parameters is a different force type. The type identifier in the
 287  *      forceatoms[] array is an index in this array.
 288  *   t_iparams *iparams
 289  *      array of length ntypes, defines the parameters for every interaction
 290  *      type. The type identifier in the actual interaction list
 291  *      (ilist[ftype].iatoms[]) is an index in this array.
 292  *   gmx_cmap_t cmap_grid
 293  *      the grid for the dihedral pair correction maps.
 294  *   t_iparams *iparams_posres
 295  *      defines the parameters for position restraints only.
 296  *      Position restraints are the only interactions that have different
 297  *      parameters (reference positions) for different molecules
 298  *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 299  *   t_ilist il[F_NRE]
 300  *      The list of interactions for each type. Note that some,
 301  *      such as LJ and COUL will have 0 entries.
 302  */
 303
 304 typedef struct {
 305   int  n;         /* n+1 is the number of points */
 306   real scale;     /* distance between two points */
 307   real *tab;      /* the actual tables, per point there are  4 numbers */
 308 } bondedtable_t;
 309
 310 #ifdef __cplusplus
 311 }
 312 #endif
 313
 314
 315 #endif