src/gromacs/legacyheaders/bondf.h

   1 /*
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  37
  38 #ifndef _bondf_h
  39 #define _bondf_h
  40
  41 #include <stdio.h>
  42
  43 #include "typedefs.h"
  44 #include "nrnb.h"
  45 #include "genborn.h"
  46
  47 #ifdef __cplusplus
  48 extern "C" {
  49 #endif
  50
  51 struct t_graph;
  52 struct t_pbc;
  53
  54 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 void calc_bonds(const gmx_multisim_t *ms,
  62                 const t_idef *idef,
  63                 rvec x[], history_t *hist,
  64                 rvec f[], t_forcerec *fr,
  65                 const struct t_pbc *pbc, const struct 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,
  70                 int force_flags);
  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  *   return value:
  90  *          the total potential energy (sum over epot).
  91  */
  92
  93 void calc_bonds_lambda(const t_idef *idef,
  94                        rvec x[],
  95                        t_forcerec *fr,
  96                        const struct t_pbc *pbc, const struct t_graph *g,
  97                        gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
  98                        real *lambda,
  99                        const t_mdatoms *md,
 100                        t_fcdata *fcd, int *global_atom_index);
 101 /* As calc_bonds, but only determines the potential energy
 102  * for the perturbed interactions.
 103  * The shift forces in fr are not affected.
 104  */
 105
 106 real posres(int nbonds,
 107             const t_iatom forceatoms[], const t_iparams forceparams[],
 108             const rvec x[], rvec f[], rvec vir_diag,
 109             struct t_pbc *pbc,
 110             real lambda, real *dvdlambda,
 111             int refcoord_scaling, int ePBC, rvec comA, rvec comB);
 112 /* Position restraints require a different pbc treatment from other bondeds */
 113
 114 real fbposres(int nbonds,
 115               const t_iatom forceatoms[], const t_iparams forceparams[],
 116               const rvec x[], rvec f[], rvec vir_diag,
 117               struct t_pbc *pbc, int refcoord_scaling, int ePBC, rvec com);
 118 /* Flat-bottom posres. Same PBC treatment as in normal position restraints */
 119
 120 real bond_angle(const rvec xi, const rvec xj, const rvec xk,
 121                 const struct t_pbc *pbc,
 122                 rvec r_ij, rvec r_kj, real *costh,
 123                 int *t1, int *t2);  /* out */
 124 /* Calculate bond-angle. No PBC is taken into account (use mol-shift) */
 125
 126 real dih_angle(const rvec xi, const rvec xj, const rvec xk, const rvec xl,
 127                const struct t_pbc *pbc,
 128                rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, /* out */
 129                real *sign,
 130                int *t1, int *t2, int *t3);
 131 /* Calculate dihedral-angle. No PBC is taken into account (use mol-shift) */
 132
 133 void do_dih_fup(int i, int j, int k, int l, real ddphi,
 134                 rvec r_ij, rvec r_kj, rvec r_kl,
 135                 rvec m, rvec n, rvec f[], rvec fshift[],
 136                 const struct t_pbc *pbc, const struct t_graph *g,
 137                 const rvec *x, int t1, int t2, int t3);
 138 /* Do an update of the forces for dihedral potentials */
 139
 140 void make_dp_periodic(real *dp);
 141 /* make a dihedral fall in the range (-pi,pi) */
 142
 143 /*************************************************************************
 144  *
 145  *  Bonded force functions
 146  *
 147  *************************************************************************/
 148 t_ifunc bonds, g96bonds, morse_bonds, cubic_bonds, FENE_bonds, restraint_bonds;
 149 t_ifunc angles, g96angles, cross_bond_bond, cross_bond_angle, urey_bradley, quartic_angles, linear_angles;
 150 t_ifunc restrangles;
 151 t_ifunc pdihs, idihs, rbdihs;
 152 t_ifunc restrdihs, cbtdihs;
 153 t_ifunc tab_bonds, tab_angles, tab_dihs;
 154 t_ifunc polarize, anharm_polarize, water_pol, thole_pol, angres, angresz, dihres, unimplemented;
 155
 156
 157 /* Divided the bonded interactions over the threads, count=fr->nthreads
 158  * and set up the bonded thread-force buffer reduction.
 159  * This should be called each time the bonded setup changes;
 160  * i.e. at start-up without domain decomposition and at DD.
 161  */
 162 void setup_bonded_threading(t_forcerec *fr, t_idef *idef);
 163
 164 #ifdef __cplusplus
 165 }
 166 #endif
 167
 168 #endif  /* _bondf_h */