include/bondf.h

   1 /*
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  38
  39 #ifndef _bondf_h
  40 #define _bondf_h
  41
  42
  43 #include <stdio.h>
  44 #include "visibility.h"
  45 #include "typedefs.h"
  46 #include "nrnb.h"
  47 #include "pbc.h"
  48 #include "genborn.h"
  49
  50 #ifdef __cplusplus
  51 extern "C" {
  52 #endif
  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 GMX_LIBGMX_EXPORT
  62 void calc_bonds(FILE *fplog, const gmx_multisim_t *ms,
  63                 const t_idef *idef,
  64                 rvec x[], history_t *hist,
  65                 rvec f[], t_forcerec *fr,
  66                 const t_pbc *pbc, const t_graph *g,
  67                 gmx_enerdata_t *enerd, t_nrnb *nrnb, real *lambda,
  68                 const t_mdatoms *md,
  69                 t_fcdata *fcd, int *ddgatindex,
  70                 t_atomtypes *atype, gmx_genborn_t *born,
  71                 int force_flags,
  72                 gmx_bool bPrintSepPot, gmx_large_int_t step);
  73 /*
  74  * The function calc_bonds() calculates all bonded force interactions.
  75  * The "bonds" are specified as follows:
  76  *   int nbonds
  77  *          the total number of bonded interactions.
  78  *   t_iatom *forceatoms
  79  *     specifies which atoms are involved in a bond of a certain
  80  *     type, see also struct t_idef.
  81  *   t_functype *functype
  82  *          defines for every bonded force type what type of function to
  83  *     use, see also struct t_idef.
  84  *   t_iparams *forceparams
  85  *          defines the parameters for every bond type, see also struct
  86  *     t_idef.
  87  *   real epot[NR_F]
  88  *     total potential energy split up over the function types.
  89  *   int *ddgatindex
  90  *     global atom number indices, should be NULL when not using DD.
  91  *   gmx_bool bPrintSepPot
  92  *     if TRUE print local potential and dVdlambda for each bonded type.
  93  *   int step
  94  *     used with bPrintSepPot
  95  *   return value:
  96  *          the total potential energy (sum over epot).
  97  */
  98
  99 GMX_LIBGMX_EXPORT
 100 void calc_bonds_lambda(FILE *fplog,
 101                        const t_idef *idef,
 102                        rvec x[],
 103                        t_forcerec *fr,
 104                        const t_pbc *pbc, const t_graph *g,
 105                        gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
 106                        real *lambda,
 107                        const t_mdatoms *md,
 108                        t_fcdata *fcd, int *global_atom_index);
 109 /* As calc_bonds, but only determines the potential energy
 110  * for the perturbed interactions.
 111  * The shift forces in fr are not affected.
 112  */
 113
 114 GMX_LIBGMX_EXPORT
 115 real posres(int nbonds,
 116             const t_iatom forceatoms[], const t_iparams forceparams[],
 117             const rvec x[], rvec f[], rvec vir_diag,
 118             t_pbc *pbc,
 119             real lambda, real *dvdlambda,
 120             int refcoord_scaling, int ePBC, rvec comA, rvec comB);
 121 /* Position restraints require a different pbc treatment from other bondeds */
 122
 123 GMX_LIBGMX_EXPORT
 124 real bond_angle(const rvec xi, const rvec xj, const rvec xk,
 125                 const t_pbc *pbc,
 126                 rvec r_ij, rvec r_kj, real *costh,
 127                 int *t1, int *t2);  /* out */
 128 /* Calculate bond-angle. No PBC is taken into account (use mol-shift) */
 129
 130 GMX_LIBGMX_EXPORT
 131 real dih_angle(const rvec xi, const rvec xj, const rvec xk, const rvec xl,
 132                const t_pbc *pbc,
 133                rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, /* out */
 134                real *sign,
 135                int *t1, int *t2, int *t3);
 136 /* Calculate dihedral-angle. No PBC is taken into account (use mol-shift) */
 137
 138 void do_dih_fup(int i, int j, int k, int l, real ddphi,
 139                 rvec r_ij, rvec r_kj, rvec r_kl,
 140                 rvec m, rvec n, rvec f[], rvec fshift[],
 141                 const t_pbc *pbc, const t_graph *g,
 142                 const rvec *x, int t1, int t2, int t3);
 143 /* Do an update of the forces for dihedral potentials */
 144
 145 void make_dp_periodic(real *dp);
 146 /* make a dihedral fall in the range (-pi,pi) */
 147
 148 /*************************************************************************
 149  *
 150  *  Bonded force functions
 151  *
 152  *************************************************************************/
 153 t_ifunc bonds, g96bonds, morse_bonds, cubic_bonds, FENE_bonds, restraint_bonds;
 154 t_ifunc angles, g96angles, cross_bond_bond, cross_bond_angle, urey_bradley, quartic_angles, linear_angles;
 155 t_ifunc pdihs, idihs, rbdihs;
 156 t_ifunc tab_bonds, tab_angles, tab_dihs;
 157 t_ifunc polarize, anharm_polarize, water_pol, thole_pol, angres, angresz, dihres, unimplemented;
 158
 159
 160 /* Divided the bonded interactions over the threads, count=fr->nthreads
 161  * and set up the bonded thread-force buffer reduction.
 162  * This should be called each time the bonded setup changes;
 163  * i.e. at start-up without domain decomposition and at DD.
 164  */
 165 GMX_LIBGMX_EXPORT
 166 void setup_bonded_threading(t_forcerec *fr, t_idef *idef);
 167
 168 #ifdef __cplusplus
 169 }
 170 #endif
 171
 172 #endif  /* _bondf_h */