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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.
57 void calc_bonds(FILE *fplog,const gmx_multisim_t *ms,
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,
64 t_fcdata *fcd,int *ddgatindex,
65 t_atomtypes *atype, gmx_genborn_t *born,
66 gmx_bool bPrintSepPot,gmx_large_int_t step);
68 * The function calc_bonds() calculates all bonded force interactions.
69 * The "bonds" are specified as follows:
71 * the total number of bonded interactions.
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
82 * total potential energy split up over the function types.
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.
88 * used with bPrintSepPot
90 * the total potential energy (sum over epot).
93 void calc_bonds_lambda(FILE *fplog,
97 const t_pbc *pbc,const t_graph *g,
98 gmx_enerdata_t *enerd,t_nrnb *nrnb,
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.
107 real posres(int nbonds,
108 const t_iatom forceatoms[],const t_iparams forceparams[],
109 const rvec x[],rvec f[],rvec vir_diag,
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 */
115 real bond_angle(const rvec xi,const rvec xj,const rvec xk,
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) */
121 real dih_angle(const rvec xi,const rvec xj,const rvec xk,const rvec xl,
123 rvec r_ij,rvec r_kj,rvec r_kl,rvec m,rvec n, /* out */
125 int *t1,int *t2,int *t3);
126 /* Calculate dihedral-angle. No PBC is taken into account (use mol-shift) */
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 */
135 /*************************************************************************
137 * Bonded force functions
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;
150 #endif /* _bondf_h */