src/kernel/xmdrun.h

   1 /*
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  36
  37 #ifndef _xmdrun_h
  38 #define _xmdrun_h
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #include <stdio.h>
  45 #include "typedefs.h"
  46 #include "network.h"
  47 #include "tgroup.h"
  48 #include "filenm.h"
  49 #include "nsb.h"
  50 #include "mshift.h"
  51 #include "force.h"
  52 #include "time.h"
  53 #include "edsam.h"
  54 #include "mdebin.h"
  55 #include "vcm.h"
  56 #include "dummies.h"
  57
  58 /* This file contains XMDRUN datatypes and function prototypes, grouped
  59  * neatly according to parts of the functionalisty
  60  */
  61
  62 /* SHELL MD STUFF */
  63 typedef struct {
  64   int     nnucl;
  65   atom_id shell;                /* The shell id                         */
  66   atom_id nucl1,nucl2,nucl3;    /* The nuclei connected to the shell    */
  67   real    k;                    /* force constant                       */
  68   real    k_1;                  /* 1 over force constant                */
  69 } t_shell;
  70
  71 /* Initialization function */
  72 extern t_shell *init_shells(FILE *log,int start,int homenr,
  73                             t_idef *idef,t_mdatoms *md,int *nshell);
  74
  75 /* Optimize shell positions */
  76 extern int relax_shells(FILE *log,t_commrec *cr,t_commrec *mcr,bool bVerbose,
  77                         int mdstep,t_parm *parm,bool bDoNS,bool bStopCM,
  78                         t_topology *top,real ener[],t_fcdata *fcd,
  79                         t_state *state,rvec vold[],rvec vt[],rvec f[],
  80                         rvec buf[],t_mdatoms *md,t_nsborder *nsb,t_nrnb *nrnb,
  81                         t_graph *graph,t_groups *grps,tensor vir_part,
  82                         tensor pme_vir_part,bool bShell,
  83                         int nshell,t_shell shells[],t_forcerec *fr,
  84                         char *traj,real t,rvec mu_tot,
  85                         int natoms,bool *bConverged,
  86                         bool bDummies,t_comm_dummies *dummycomm);
  87
  88 /* GENERAL COUPLING THEORY (GCT) STUFF */
  89 enum { eoPres, eoEpot, eoVir, eoDist, eoMu, eoForce, eoFx, eoFy, eoFz,
  90        eoPx, eoPy, eoPz,
  91        eoPolarizability, eoDipole, eoObsNR,
  92        eoMemory=eoObsNR, eoInter, eoUseVirial,  eoNR };
  93 extern char *eoNames[eoNR];
  94
  95 typedef struct {
  96   int  at_i,at_j;       /* Atom type # for i and j                      */
  97   int  eObs;            /* Observable to couple to                      */
  98   bool bPrint;          /* Does this struct have to be printed          */
  99   real c6,c12;          /* Actual value of params                       */
 100   real xi_6,xi_12;      /* Constants for coupling C6 and C12            */
 101 } t_coupl_LJ;
 102
 103 typedef struct {
 104   int  at_i,at_j;       /* Atom type # for i and j                      */
 105   int  eObs;            /* Observable to couple to                      */
 106   bool bPrint;          /* Does this struct have to be printed          */
 107   real a,b,c;           /* Actual value of params                       */
 108   real xi_a,xi_b,xi_c;  /* Constants for coupling A, B and C            */
 109 } t_coupl_BU;
 110
 111 typedef struct {
 112   int  at_i;            /* Atom type                                    */
 113   int  eObs;            /* Observable to couple to                      */
 114   bool bPrint;          /* Does this struct have to be printed          */
 115   real Q;               /* Actual value of charge                       */
 116   real xi_Q;            /* Constant for coupling Q                      */
 117 } t_coupl_Q;
 118
 119 typedef struct {
 120   int       type;       /* Type number in the iparams struct    */
 121   int       eObs;       /* Observable to couple to              */
 122   t_iparams xi;         /* Parameters that need to be changed   */
 123   t_iparams iprint;
 124 } t_coupl_iparams;
 125
 126 typedef struct {
 127   real       act_value[eoObsNR];
 128   real       av_value [eoObsNR];
 129   real       ref_value[eoObsNR];
 130   bool       bObsUsed[eoObsNR];
 131   int        nLJ,nBU,nQ,nIP;
 132   t_coupl_LJ *tcLJ;
 133   t_coupl_BU *tcBU;
 134   t_coupl_Q  *tcQ;
 135   t_coupl_iparams *tIP;
 136   int        nmemory;
 137   bool       bInter;
 138   bool       bVirial;
 139 } t_coupl_rec;
 140
 141 extern void write_gct(char *fn,t_coupl_rec *tcr,t_idef *idef);
 142
 143 extern void read_gct(char *fn,t_coupl_rec *tcr);
 144
 145 extern void comm_tcr(FILE *log,t_commrec *cr,t_coupl_rec **tcr);
 146
 147 extern void copy_ff(t_coupl_rec *tcr,t_forcerec *fr,t_mdatoms *md,
 148                     t_idef *idef);
 149
 150 extern t_coupl_rec *init_coupling(FILE *log,int nfile,t_filenm fnm[],
 151                                   t_commrec *cr,t_forcerec *fr,t_mdatoms *md,
 152                                   t_idef *idef);
 153
 154 extern void calc_force(int natom,rvec f[],rvec fff[]);
 155
 156 extern void calc_f_dev(int natoms,real charge[],rvec x[],rvec f[],
 157                        t_idef *idef,real *xiH,real *xiS);
 158
 159 extern void do_coupling(FILE *log,int nfile,t_filenm fnm[],
 160                         t_coupl_rec *tcr,real t,int step,real ener[],
 161                         t_forcerec *fr,t_inputrec *ir,bool bMaster,
 162                         t_mdatoms *md,t_idef *idef,real mu_aver,int nmols,
 163                         t_commrec *cr,matrix box,tensor virial,
 164                         tensor pres,rvec mu_tot,
 165                         rvec x[],rvec f[],bool bDoIt);
 166
 167 /* IONIZATION STUFF. */
 168 extern void ionize(FILE *log,t_mdatoms *md,char **atomname[],
 169                    real t,t_inputrec *ir,rvec x[],rvec v[],
 170                    int start,int end,matrix box,t_commrec *cr);
 171
 172 /* CODE TO ADD SPECIAL 2-DIMENSIONAL LENNARD-JONES CORRECTION TO FORCES AND ENERGY */
 173 extern void do_glas(FILE *log,int start,int homenr,rvec x[],rvec f[],
 174                     t_forcerec *fr,t_mdatoms *md,int atnr,t_inputrec *ir,
 175                     real ener[]);
 176
 177 extern real mol_dipole(int k0,int k1,atom_id ma[],rvec x[],real q[]);
 178 /* Calculate total dipole for group of atoms */
 179
 180 extern real calc_mu_aver(t_commrec *cr,t_nsborder *nsb,rvec x[],real q[],rvec mu,
 181                          t_topology *top,t_mdatoms *md,int gnx,atom_id grpindex[]);
 182 /* Compute average dipole */
 183
 184 /********************************************************************/
 185 /* Force field scanning stuff */
 186 typedef struct {
 187   real tol,fmax,npow,epot,fac_epot,fac_pres,fac_msf,pres;
 188   int  molsize,nmol;
 189   bool bComb,bVerbose,bLogEps;
 190 } t_ffscan;
 191
 192
 193 extern void update_forcefield(int nfile,t_filenm fnm[],t_forcerec *fr,
 194                               int natoms,rvec x[],matrix box);
 195 /* Modify the parameters */
 196
 197 extern void print_forcefield(FILE *fp,real ener[],int natoms,rvec f[],
 198                              rvec fshake[],rvec x[],t_block *mols,real mass[],
 199                              tensor pres);
 200 /* Print results */
 201
 202 extern void set_ffvars(t_ffscan *ff);
 203 /* Set variables for force scanning */
 204
 205 #endif  /* _xmdrun_h */