include/bondf.h

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