src/gromacs/gmxpreprocess/gpp_atomtype.h

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  37
  38 #ifndef GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
  39 #define GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
  40
  41 #include <stdio.h>
  42
  43 #include "gromacs/gmxpreprocess/grompp-impl.h"
  44
  45 struct gmx_mtop_t;
  46
  47 typedef struct gpp_atomtype *gpp_atomtype_t;
  48
  49 int get_atomtype_type(const char *str, gpp_atomtype_t at);
  50 /* Return atomtype corresponding to case-insensitive str
  51    or NOTSET if not found */
  52
  53 int get_atomtype_ntypes(gpp_atomtype_t at);
  54 /* Return number of atomtypes */
  55
  56 char *get_atomtype_name(int nt, gpp_atomtype_t at);
  57 /* Return name corresponding to atomtype nt, or NULL if not found */
  58
  59 real get_atomtype_massA(int nt, gpp_atomtype_t at);
  60 real get_atomtype_massB(int nt, gpp_atomtype_t at);
  61 real get_atomtype_qA(int nt, gpp_atomtype_t at);
  62 real get_atomtype_qB(int nt, gpp_atomtype_t at);
  63 real get_atomtype_radius(int nt, gpp_atomtype_t at);
  64 real get_atomtype_vol(int nt, gpp_atomtype_t at);
  65 real get_atomtype_surftens(int nt, gpp_atomtype_t at);
  66 real get_atomtype_gb_radius(int nt, gpp_atomtype_t at);
  67 real get_atomtype_S_hct(int nt, gpp_atomtype_t at);
  68 int get_atomtype_ptype(int nt, gpp_atomtype_t at);
  69 int get_atomtype_batype(int nt, gpp_atomtype_t at);
  70 int get_atomtype_atomnumber(int nt, gpp_atomtype_t at);
  71
  72 /* Return the above variable for atomtype nt, or NOTSET if not found */
  73
  74 real get_atomtype_nbparam(int nt, int param, gpp_atomtype_t at);
  75 /* Similar to the previous but returns the paramth parameter or NOTSET */
  76
  77 gpp_atomtype_t init_atomtype(void);
  78 /* Return a new atomtype structure */
  79
  80 void done_atomtype(gpp_atomtype_t at);
  81 /* Free the memory in the structure */
  82
  83 int set_atomtype(int nt, gpp_atomtype_t at, struct t_symtab *tab,
  84                  t_atom *a, const char *name, t_param *nb,
  85                  int bondatomtype,
  86                  real radius, real vol, real surftens, int atomnumber,
  87                  real gb_radius, real S_hct);
  88 /* Set the values of an existing atom type nt. Returns nt on success or
  89    NOTSET on error. */
  90
  91 int
  92 set_atomtype_gbparam(gpp_atomtype_t at, int i,
  93                      real radius, real vol, real surftens,
  94                      real gb_radius, real S_hct);
  95
  96 int add_atomtype(gpp_atomtype_t at, struct t_symtab *tab,
  97                  t_atom *a, const char *name, t_param *nb,
  98                  int bondatomtype,
  99                  real radius, real vol, real surftens, int atomnumber,
 100                  real gb_radius, real S_hct);
 101 /* Add a complete new atom type to an existing atomtype structure. Returns
 102    the number of the atom type. */
 103
 104 void print_at (FILE * out, gpp_atomtype_t at);
 105 /* Print an atomtype record to a text file */
 106
 107 void renum_atype(t_params plist[], gmx_mtop_t *mtop,
 108                  int *wall_atomtype,
 109                  gpp_atomtype_t at, gmx_bool bVerbose);
 110
 111 void copy_atomtype_atomtypes(gpp_atomtype_t atype, t_atomtypes *atypes);
 112 /* Copy from one structure to another */
 113
 114 #endif