/usr/include/gromacs/bondf.h

/*
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 * check out http://www.gromacs.org for more information.
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#ifndef _bondf_h
#define _bondf_h


#include <stdio.h>
#include "visibility.h"
#include "typedefs.h"
#include "nrnb.h"
#include "pbc.h"
#include "genborn.h"

#ifdef __cplusplus
extern "C" {
#endif

int glatnr(int *global_atom_index, int i);
/* Returns the global topology atom number belonging to local atom index i.
 * This function is intended for writing ascii output
 * and returns atom numbers starting at 1.
 * When global_atom_index=NULL returns i+1.
 */

GMX_LIBGMX_EXPORT
void calc_bonds(FILE *fplog, const gmx_multisim_t *ms,
                const t_idef *idef,
                rvec x[], history_t *hist,
                rvec f[], t_forcerec *fr,
                const t_pbc *pbc, const t_graph *g,
                gmx_enerdata_t *enerd, t_nrnb *nrnb, real *lambda,
                const t_mdatoms *md,
                t_fcdata *fcd, int *ddgatindex,
                t_atomtypes *atype, gmx_genborn_t *born,
                int force_flags,
                gmx_bool bPrintSepPot, gmx_large_int_t step);
/*
 * The function calc_bonds() calculates all bonded force interactions.
 * The "bonds" are specified as follows:
 *   int nbonds
 *	    the total number of bonded interactions.
 *   t_iatom *forceatoms
 *     specifies which atoms are involved in a bond of a certain
 *     type, see also struct t_idef.
 *   t_functype *functype
 *	    defines for every bonded force type what type of function to
 *     use, see also struct t_idef.
 *   t_iparams *forceparams
 *	    defines the parameters for every bond type, see also struct
 *     t_idef.
 *   real epot[NR_F]
 *     total potential energy split up over the function types.
 *   int *ddgatindex
 *     global atom number indices, should be NULL when not using DD.
 *   gmx_bool bPrintSepPot
 *     if TRUE print local potential and dVdlambda for each bonded type.
 *   int step
 *     used with bPrintSepPot
 *   return value:
 *	    the total potential energy (sum over epot).
 */

GMX_LIBGMX_EXPORT
void calc_bonds_lambda(FILE *fplog,
                       const t_idef *idef,
                       rvec x[],
                       t_forcerec *fr,
                       const t_pbc *pbc, const t_graph *g,
                       gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
                       real *lambda,
                       const t_mdatoms *md,
                       t_fcdata *fcd, int *global_atom_index);
/* As calc_bonds, but only determines the potential energy
 * for the perturbed interactions.
 * The shift forces in fr are not affected.
 */

GMX_LIBGMX_EXPORT
real posres(int nbonds,
            const t_iatom forceatoms[], const t_iparams forceparams[],
            const rvec x[], rvec f[], rvec vir_diag,
            t_pbc *pbc,
            real lambda, real *dvdlambda,
            int refcoord_scaling, int ePBC, rvec comA, rvec comB);
/* Position restraints require a different pbc treatment from other bondeds */

GMX_LIBGMX_EXPORT
real bond_angle(const rvec xi, const rvec xj, const rvec xk,
                const t_pbc *pbc,
                rvec r_ij, rvec r_kj, real *costh,
                int *t1, int *t2);  /* out */
/* Calculate bond-angle. No PBC is taken into account (use mol-shift) */

GMX_LIBGMX_EXPORT
real dih_angle(const rvec xi, const rvec xj, const rvec xk, const rvec xl,
               const t_pbc *pbc,
               rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, /* out */
               real *sign,
               int *t1, int *t2, int *t3);
/* Calculate dihedral-angle. No PBC is taken into account (use mol-shift) */

void do_dih_fup(int i, int j, int k, int l, real ddphi,
                rvec r_ij, rvec r_kj, rvec r_kl,
                rvec m, rvec n, rvec f[], rvec fshift[],
                const t_pbc *pbc, const t_graph *g,
                const rvec *x, int t1, int t2, int t3);
/* Do an update of the forces for dihedral potentials */

void make_dp_periodic(real *dp);
/* make a dihedral fall in the range (-pi,pi) */

/*************************************************************************
 *
 *  Bonded force functions
 *
 *************************************************************************/
t_ifunc bonds, g96bonds, morse_bonds, cubic_bonds, FENE_bonds, restraint_bonds;
t_ifunc angles, g96angles, cross_bond_bond, cross_bond_angle, urey_bradley, quartic_angles, linear_angles;
t_ifunc pdihs, idihs, rbdihs;
t_ifunc tab_bonds, tab_angles, tab_dihs;
t_ifunc polarize, anharm_polarize, water_pol, thole_pol, angres, angresz, dihres, unimplemented;


/* Divided the bonded interactions over the threads, count=fr->nthreads
 * and set up the bonded thread-force buffer reduction.
 * This should be called each time the bonded setup changes;
 * i.e. at start-up without domain decomposition and at DD.
 */
GMX_LIBGMX_EXPORT
void setup_bonded_threading(t_forcerec *fr, t_idef *idef);

#ifdef __cplusplus
}
#endif

#endif  /* _bondf_h */
gromacs-dev 4.6.5-1build1 / usr / include / gromacs / bondf.h
