include/bondf.h

   1 /*
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  35
  36 #ifndef _bondf_h
  37 #define _bondf_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 #include <stdio.h>
  49 #include "typedefs.h"
  50 #include "nrnb.h"
  51 #include "pbc.h"
  52 #include "genborn.h"
  53
  54 extern int glatnr(int *global_atom_index,int i);
  55 /* Returns the global topology atom number belonging to local atom index i.
  56  * This function is intended for writing ascii output
  57  * and returns atom numbers starting at 1.
  58  * When global_atom_index=NULL returns i+1.
  59  */
  60
  61 extern void calc_bonds(FILE *fplog,const gmx_multisim_t *ms,
  62                        const t_idef *idef,
  63                        rvec x[],history_t *hist,
  64                        rvec f[],t_forcerec *fr,
  65                        const t_pbc *pbc,const t_graph *g,
  66                        gmx_enerdata_t *enerd,t_nrnb *nrnb,real lambda,
  67                        const t_mdatoms *md,
  68                        t_fcdata *fcd,int *ddgatindex,
  69                        t_atomtypes *atype, gmx_genborn_t *born,gmx_cmap_t *cmap,
  70                        bool bPrintSepPot,gmx_step_t step);
  71 /*
  72  * The function calc_bonds() calculates all bonded force interactions.
  73  * The "bonds" are specified as follows:
  74  *   int nbonds
  75  *          the total number of bonded interactions.
  76  *   t_iatom *forceatoms
  77  *     specifies which atoms are involved in a bond of a certain
  78  *     type, see also struct t_idef.
  79  *   t_functype *functype
  80  *          defines for every bonded force type what type of function to
  81  *     use, see also struct t_idef.
  82  *   t_iparams *forceparams
  83  *          defines the parameters for every bond type, see also struct
  84  *     t_idef.
  85  *   real epot[NR_F]
  86  *     total potential energy split up over the function types.
  87  *   int *ddgatindex
  88  *     global atom number indices, should be NULL when not using DD.
  89  *   bool bPrintSepPot
  90  *     if TRUE print local potential and dVdlambda for each bonded type.
  91  *   int step
  92  *     used with bPrintSepPot
  93  *   return value:
  94  *          the total potential energy (sum over epot).
  95  */
  96
  97 extern void calc_bonds_lambda(FILE *fplog,
  98                               const t_idef *idef,
  99                               rvec x[],
 100                               t_forcerec *fr,
 101                               const t_pbc *pbc,const t_graph *g,
 102                               gmx_enerdata_t *enerd,t_nrnb *nrnb,
 103                               real lambda,
 104                               const t_mdatoms *md,
 105                               t_fcdata *fcd,int *global_atom_index);
 106 /* As calc_bonds, but only determines the potential energy
 107  * for the perturbed interactions.
 108  * The shift forces in fr are not affected.
 109  */
 110
 111 extern real posres(int nbonds,
 112                    const t_iatom forceatoms[],const t_iparams forceparams[],
 113                    const rvec x[],rvec f[],rvec vir_diag,
 114                    t_pbc *pbc,
 115                    real lambda,real *dvdlambda,
 116                    int refcoord_scaling,int ePBC,rvec comA,rvec comB);
 117 /* Position restraints require a different pbc treatment from other bondeds */
 118
 119 extern real bond_angle(const rvec xi,const rvec xj,const rvec xk,
 120                        const t_pbc *pbc,
 121                        rvec r_ij,rvec r_kj,real *costh,
 122                        int *t1,int *t2);        /* out */
 123 /* Calculate bond-angle. No PBC is taken into account (use mol-shift) */
 124
 125 extern real dih_angle(const rvec xi,const rvec xj,const rvec xk,const rvec xl,
 126                       const t_pbc *pbc,
 127                       rvec r_ij,rvec r_kj,rvec r_kl,rvec m,rvec n, /* out */
 128                       real *cos_phi,real *sign,
 129                       int *t1,int *t2,int *t3);
 130 /* Calculate dihedral-angle. No PBC is taken into account (use mol-shift) */
 131
 132 extern void do_dih_fup(int i,int j,int k,int l,real ddphi,
 133                        rvec r_ij,rvec r_kj,rvec r_kl,
 134                        rvec m,rvec n,rvec f[],rvec fshift[],
 135                        const t_pbc *pbc,const t_graph *g,
 136                        const rvec *x,int t1,int t2,int t3);
 137 /* Do an update of the forces for dihedral potentials */
 138
 139 /*************************************************************************
 140  *
 141  *  Bonded force functions
 142  *
 143  *************************************************************************/
 144   extern t_ifunc bonds,g96bonds,morse_bonds,cubic_bonds,FENE_bonds;
 145   extern t_ifunc angles,g96angles,cross_bond_bond,cross_bond_angle,urey_bradley,quartic_angles;
 146   extern t_ifunc pdihs,idihs,rbdihs;
 147   extern t_ifunc tab_bonds,tab_angles,tab_dihs;
 148   extern t_ifunc polarize,water_pol,thole_pol,angres,angresz,unimplemented;
 149
 150 #ifdef __cplusplus
 151 }
 152 #endif
 153
 154 #endif  /* _bondf_h */