libgromacs-dev 2018.1-1 / usr / include / gromacs / topology / idef.h

/*
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 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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#ifndef GMX_TOPOLOGY_IDEF_H
#define GMX_TOPOLOGY_IDEF_H

#include <stdio.h>

#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

#ifdef __cplusplus
extern "C" {
#endif

/* check kernel/toppush.c when you change these numbers */
#define MAXATOMLIST 6
#define MAXFORCEPARAM   12
#define NR_RBDIHS   6
#define NR_CBTDIHS   6
#define NR_FOURDIHS     4

typedef int t_iatom;

/* this MUST correspond to the
   t_interaction_function[F_NRE] in gmxlib/ifunc.c */
enum {
    F_BONDS,
    F_G96BONDS,
    F_MORSE,
    F_CUBICBONDS,
    F_CONNBONDS,
    F_HARMONIC,
    F_FENEBONDS,
    F_TABBONDS,
    F_TABBONDSNC,
    F_RESTRBONDS,
    F_ANGLES,
    F_G96ANGLES,
    F_RESTRANGLES,
    F_LINEAR_ANGLES,
    F_CROSS_BOND_BONDS,
    F_CROSS_BOND_ANGLES,
    F_UREY_BRADLEY,
    F_QUARTIC_ANGLES,
    F_TABANGLES,
    F_PDIHS,
    F_RBDIHS,
    F_RESTRDIHS,
    F_CBTDIHS,
    F_FOURDIHS,
    F_IDIHS,
    F_PIDIHS,
    F_TABDIHS,
    F_CMAP,
    F_GB12,
    F_GB13,
    F_GB14,
    F_GBPOL,
    F_NPSOLVATION,
    F_LJ14,
    F_COUL14,
    F_LJC14_Q,
    F_LJC_PAIRS_NB,
    F_LJ,
    F_BHAM,
    F_LJ_LR_NOLONGERUSED,
    F_BHAM_LR_NOLONGERUSED,
    F_DISPCORR,
    F_COUL_SR,
    F_COUL_LR_NOLONGERUSED,
    F_RF_EXCL,
    F_COUL_RECIP,
    F_LJ_RECIP,
    F_DPD,
    F_POLARIZATION,
    F_WATER_POL,
    F_THOLE_POL,
    F_ANHARM_POL,
    F_POSRES,
    F_FBPOSRES,
    F_DISRES,
    F_DISRESVIOL,
    F_ORIRES,
    F_ORIRESDEV,
    F_ANGRES,
    F_ANGRESZ,
    F_DIHRES,
    F_DIHRESVIOL,
    F_CONSTR,
    F_CONSTRNC,
    F_SETTLE,
    F_VSITE2,
    F_VSITE3,
    F_VSITE3FD,
    F_VSITE3FAD,
    F_VSITE3OUT,
    F_VSITE4FD,
    F_VSITE4FDN,
    F_VSITEN,
    F_COM_PULL,
    F_EQM,
    F_EPOT,
    F_EKIN,
    F_ETOT,
    F_ECONSERVED,
    F_TEMP,
    F_VTEMP_NOLONGERUSED,
    F_PDISPCORR,
    F_PRES,
    F_DVDL_CONSTR,
    F_DVDL,
    F_DKDL,
    F_DVDL_COUL,
    F_DVDL_VDW,
    F_DVDL_BONDED,
    F_DVDL_RESTRAINT,
    F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
    F_NRE               /* This number is for the total number of energies      */
};

#define IS_RESTRAINT_TYPE(ifunc) (((ifunc == F_POSRES) || (ifunc == F_FBPOSRES) || (ifunc == F_DISRES) || (ifunc == F_RESTRBONDS) || (ifunc == F_DISRESVIOL) || (ifunc == F_ORIRES) || (ifunc == F_ORIRESDEV) || (ifunc == F_ANGRES) || (ifunc == F_ANGRESZ) || (ifunc == F_DIHRES)))

typedef union t_iparams
{
    /* Some parameters have A and B values for free energy calculations.
     * The B values are not used for regular simulations of course.
     * Free Energy for nonbondeds can be computed by changing the atom type.
     * The harmonic type is used for all harmonic potentials:
     * bonds, angles and improper dihedrals
     */
    struct {
        real a, b, c;
    } bham;
    struct {
        real rA, krA, rB, krB;
    } harmonic;
    struct {
        real klinA, aA, klinB, aB;
    } linangle;
    struct {
        real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
    } restraint;
    /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
    struct {
        real b0, kb, kcub;
    } cubic;
    struct {
        real bm, kb;
    } fene;
    struct {
        real r1e, r2e, krr;
    } cross_bb;
    struct {
        real r1e, r2e, r3e, krt;
    } cross_ba;
    struct {
        real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
    } u_b;
    struct {
        real theta, c[5];
    } qangle;
    struct {
        real alpha;
    } polarize;
    struct {
        real alpha, drcut, khyp;
    } anharm_polarize;
    struct {
        real al_x, al_y, al_z, rOH, rHH, rOD;
    } wpol;
    struct {
        real a, alpha1, alpha2, rfac;
    } thole;
    struct {
        real c6, c12;
    } lj;
    struct {
        real c6A, c12A, c6B, c12B;
    } lj14;
    struct {
        real fqq, qi, qj, c6, c12;
    } ljc14;
    struct {
        real qi, qj, c6, c12;
    } ljcnb;
    /* Proper dihedrals can not have different multiplicity when
     * doing free energy calculations, because the potential would not
     * be periodic anymore.
     */
    struct {
        real phiA, cpA; int mult; real phiB, cpB;
    } pdihs;
    struct {
        real dA, dB;
    } constr;
    /* Settle can not be used for Free energy calculations of water bond geometry.
     * Use shake (or lincs) instead if you have to change the water bonds.
     */
    struct {
        real doh, dhh;
    } settle;
    struct {
        real b0A, cbA, betaA, b0B, cbB, betaB;
    } morse;
    struct {
        real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
    } posres;
    struct {
        real pos0[DIM], r, k; int geom;
    } fbposres;
    struct {
        real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
    } rbdihs;
    struct {
        real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
    } cbtdihs;
    struct {
        real a, b, c, d, e, f;
    } vsite;
    struct {
        int  n; real a;
    } vsiten;
    /* NOTE: npair is only set after reading the tpx file */
    struct {
        real low, up1, up2, kfac; int type, label, npair;
    } disres;
    struct {
        real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
    } dihres;
    struct {
        int  ex, power, label; real c, obs, kfac;
    } orires;
    struct {
        int  table; real kA; real kB;
    } tab;
    struct {
        real sar, st, pi, gbr, bmlt;
    } gb;
    struct {
        int cmapA, cmapB;
    } cmap;
    struct {
        real buf[MAXFORCEPARAM];
    } generic;                                               /* Conversion */
} t_iparams;

typedef int t_functype;

/*
 * The nonperturbed/perturbed interactions are now separated (sorted) in the
 * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
 * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
 * interactions.
 */
typedef struct t_ilist
{
    int      nr;
    int      nr_nonperturbed;
    t_iatom *iatoms;
    int      nalloc;
} t_ilist;

/*
 * The struct t_ilist defines a list of atoms with their interactions.
 * General field description:
 *   int nr
 *      the size (nr elements) of the interactions array (iatoms[]).
 *   t_iatom *iatoms
 *  specifies which atoms are involved in an interaction of a certain
 *       type. The layout of this array is as follows:
 *
 *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 *
 *  So for interaction type type1 3 atoms are needed, and for type2 and
 *      type3 only 2. The type identifier is used to select the function to
 *      calculate the interaction and its actual parameters. This type
 *      identifier is an index in a params[] and functype[] array.
 */

typedef struct
{
    real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
    /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
} gmx_cmapdata_t;

typedef struct gmx_cmap_t
{
    int             ngrid;        /* Number of allocated cmap (cmapdata_t ) grids */
    int             grid_spacing; /* Grid spacing */
    gmx_cmapdata_t *cmapdata;     /* Pointer to grid with actual, pre-interpolated data */
} gmx_cmap_t;


typedef struct gmx_ffparams_t
{
    int         ntypes;
    int         atnr;
    t_functype *functype;
    t_iparams  *iparams;
    double      reppow;    /* The repulsion power for VdW: C12*r^-reppow   */
    real        fudgeQQ;   /* The scaling factor for Coulomb 1-4: f*q1*q2  */
    gmx_cmap_t  cmap_grid; /* The dihedral correction maps                 */
} gmx_ffparams_t;

enum {
    ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
};

typedef struct t_idef
{
    int         ntypes;
    int         atnr;
    t_functype *functype;
    t_iparams  *iparams;
    real        fudgeQQ;
    gmx_cmap_t  cmap_grid;
    t_iparams  *iparams_posres, *iparams_fbposres;
    int         iparams_posres_nalloc, iparams_fbposres_nalloc;

    t_ilist     il[F_NRE];
    int         ilsort;
    int         nthreads;
    int        *il_thread_division;
    int         il_thread_division_nalloc;
} t_idef;

/*
 * The struct t_idef defines all the interactions for the complete
 * simulation. The structure is setup in such a way that the multinode
 * version of the program  can use it as easy as the single node version.
 * General field description:
 *   int ntypes
 *      defines the number of elements in functype[] and param[].
 *   int nodeid
 *      the node id (if parallel machines)
 *   int atnr
 *      the number of atomtypes
 *   t_functype *functype
 *      array of length ntypes, defines for every force type what type of
 *      function to use. Every "bond" with the same function but different
 *      force parameters is a different force type. The type identifier in the
 *      forceatoms[] array is an index in this array.
 *   t_iparams *iparams
 *      array of length ntypes, defines the parameters for every interaction
 *      type. The type identifier in the actual interaction list
 *      (ilist[ftype].iatoms[]) is an index in this array.
 *   gmx_cmap_t cmap_grid
 *      the grid for the dihedral pair correction maps.
 *   t_iparams *iparams_posres, *iparams_fbposres
 *      defines the parameters for position restraints only.
 *      Position restraints are the only interactions that have different
 *      parameters (reference positions) for different molecules
 *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 *   t_ilist il[F_NRE]
 *      The list of interactions for each type. Note that some,
 *      such as LJ and COUL will have 0 entries.
 *   int ilsort
 *      The state of the sorting of il, values are provided above.
 *   int nthreads
 *      The number of threads used to set il_thread_division.
 *   int *il_thread_division
 *      The division of the normal bonded interactions of threads.
 *      il_thread_division[ftype*(nthreads+1)+t] contains an index
 *      into il[ftype].iatoms; thread th operates on t=th to t=th+1.
 *   int il_thread_division_nalloc
 *      The allocated size of il_thread_division,
 *      should be at least F_NRE*(nthreads+1).
 */

void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams);
void pr_ilist(FILE *fp, int indent, const char *title,
              const t_functype *functype, const t_ilist *ilist,
              gmx_bool bShowNumbers,
              gmx_bool bShowParameters, const t_iparams *iparams);
void pr_ffparams(FILE *fp, int indent, const char *title,
                 const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers);
void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
             gmx_bool bShowNumbers, gmx_bool bShowParameters);

#ifdef __cplusplus
}
#endif

#endif