src/mdlib/adress.h

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  35
  36 #ifndef _adress_h_
  37 #define _adress_h_
  38
  39 /** \file adress.h
  40  *
  41  * \brief Implementation of the AdResS method
  42  *
  43  */
  44
  45 #include "types/simple.h"
  46 #include "typedefs.h"
  47
  48 /** \brief calculates the AdResS weight of a particle
  49  *
  50  * \param[in] x position of the particle
  51  * \param[in] adresstype type of address weight function
  52  *                       eAdressOff - explicit simulation
  53  *                       eAdressConst - constant weight all over the box
  54  *                       eAdressXSplit - split in x direction with ref as center
  55  *                       eAdressSphere - spherical splitting with ref as center
  56  *                       else - weight = 1 - explicit simulation
  57  * \param[in] adressr radius/size of the explicit zone
  58  * \param[in] adressw size of the hybrid zone
  59  * \param[in] ref center of the explicit zone
  60  *                for adresstype 1 - unused
  61  *                for adresstype 2 - only ref[0] is used
  62  * \param[in] pbc for calculating shortest distance to ref
  63  *
  64  * \return weight of the particle
  65  *
  66  */
  67 real
  68 adress_weight(rvec             x,
  69               int              adresstype,
  70               real             adressr,
  71               real             adressw,
  72               rvec *           ref,
  73               t_pbc *          pbc,
  74               t_forcerec *         fr);
  75
  76 /** \brief update the weight of all coarse-grained particles in several charge groups for com vsites
  77  *
  78  * \param[in,out] fplog log file in case of debug
  79  * \param[in] cg0 first charge group to update
  80  * \param[in] cg1 last+1 charge group to update
  81  * \param[in] cgs block containing the cg index
  82  * \param[in] x array with all the particle positions
  83  * \param[in] fr the forcerec containing all the parameters
  84  * \param[in,out] mdatoms the struct containing all the atoms properties
  85  * \param[in] pbc for shortest distance in adress_weight
  86  */
  87 void
  88 update_adress_weights_com(FILE *               fplog,
  89                           int                  cg0,
  90                           int                  cg1,
  91                           t_block *            cgs,
  92                           rvec                 x[],
  93                           t_forcerec *         fr,
  94                           t_mdatoms *          mdatoms,
  95                           t_pbc *              pbc);
  96
  97 /** \brief update the weight of all coarse-grained particles for cog vsites
  98  *
  99  * \param[in] ip contains interaction parameters, in this case the number of constructing atoms n for vsitesn
 100  * \param[in] ilist list of interaction types, in this case the virtual site types are what's important
 101  * \param[in] x array with all the particle positions
 102  * \param[in] fr the forcerec containing all the parameters
 103  * \param[in,out] mdatoms the struct containing all the atoms properties
 104  * \param[in] pbc for shortest distance in adress_weight
 105  */
 106 void
 107 update_adress_weights_cog(t_iparams            ip[],
 108                           t_ilist              ilist[],
 109                           rvec                 x[],
 110                           t_forcerec *         fr,
 111                           t_mdatoms *          mdatoms,
 112                           t_pbc *              pbc);
 113 /** \brief update the weight of all coarse-grained particles in several charge groups for atom vsites
 114  *
 115  * \param[in] cg0 first charge group to update
 116  * \param[in] cg1 last+1 charge group to update
 117  * \param[in] cgs block containing the cg index
 118  * \param[in] x array with all the particle positions
 119  * \param[in] fr the forcerec containing all the parameters
 120  * \param[in,out] mdatoms the struct containing all the atoms properties
 121  * \param[in] pbc for shortest distance in adress_weight
 122  */
 123 void
 124 update_adress_weights_atom(int                  cg0,
 125                            int                  cg1,
 126                            t_block *            cgs,
 127                            rvec                 x[],
 128                            t_forcerec *         fr,
 129                            t_mdatoms *          mdatoms,
 130                            t_pbc *              pbc);
 131
 132 void
 133 update_adress_weights_atom_per_atom(int                  cg0,
 134                            int                  cg1,
 135                            t_block *            cgs,
 136                            rvec                 x[],
 137                            t_forcerec *         fr,
 138                            t_mdatoms *          mdatoms,
 139                            t_pbc *              pbc);
 140
 141 /** \brief add AdResS IC thermodynamic force to f_novirsum
 142  *
 143  * \param[in] cg0 first charge group to update
 144  * \param[in] cg1 last+1 charge group to update
 145  * \param[in] cgs block containing the cg index
 146  * \param[in] x array with all the particle positions
 147  * \param[in,out] f the force array pointing at f_novirsum from sim_util.c
 148  * \param[in] fr the forcerec containing all the parameters
 149  * \param[in] mdatoms the struct containing all the atoms properties
 150  * \param[in] pbc for shortest distance to fr->adress_refs
 151  */
 152 void
 153 adress_thermo_force(int                  cg0,
 154                     int                  cg1,
 155                     t_block *            cgs,
 156                     rvec                 x[],
 157                     rvec                 f[],
 158                     t_forcerec *         fr,
 159                     t_mdatoms *          mdatoms,
 160                     t_pbc *              pbc);
 161
 162 void adress_set_kernel_flags(int n_ex, int n_hyb, int n_cg, t_mdatoms * mdatoms);
 163
 164 /* functions to look up if a energy group is explicit or coarse-grained*/
 165 gmx_bool egp_explicit(t_forcerec *   fr, int egp_nr);
 166 gmx_bool egp_coarsegrained(t_forcerec *   fr, int egp_nr);
 167 #endif