Ejemplo n.º 1
0
void init_md(FILE *fplog,
			 t_commrec *cr,t_inputrec *ir,real *t,real *t0,
			 real *lambda,real *lam0,
			 t_nrnb *nrnb,gmx_mtop_t *mtop,
			 gmx_stochd_t *sd,
			 int nfile,t_filenm fnm[],
			 int *fp_trn,int *fp_xtc,int *fp_ene,char **fn_cpt,
			 FILE **fp_dgdl,FILE **fp_field,
			 t_mdebin **mdebin,
			 tensor force_vir,tensor shake_vir,rvec mu_tot,
			 bool *bNEMD,bool *bSimAnn,t_vcm **vcm, unsigned long Flags)
{
  int  i,j,n;
  real tmpt,mod;
  char filemode[2];

  sprintf(filemode, (Flags & MD_APPENDFILES) ? "a" : "w");
	
  /* Initial values */
  *t = *t0       = ir->init_t;
  if (ir->efep != efepNO) {
    *lam0 = ir->init_lambda;
    *lambda = *lam0 + ir->init_step*ir->delta_lambda;
  }
  else {
    *lambda = *lam0   = 0.0;
  } 
 
  *bSimAnn=FALSE;
  for(i=0;i<ir->opts.ngtc;i++) {
    /* set bSimAnn if any group is being annealed */
    if(ir->opts.annealing[i]!=eannNO)
      *bSimAnn = TRUE;
  }
  if (*bSimAnn) {
    update_annealing_target_temp(&(ir->opts),ir->init_t);
  }

  *bNEMD = (ir->opts.ngacc > 1) || (norm(ir->opts.acc[0]) > 0);
  
  if (sd && (ir->eI == eiBD || EI_SD(ir->eI) || ir->etc == etcVRESCALE)) {
    *sd = init_stochd(fplog,ir);
  }

  if (vcm) {
    *vcm = init_vcm(fplog,&mtop->groups,ir);
  }
   
  if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES)) {
    if (ir->etc == etcBERENDSEN) {
      please_cite(fplog,"Berendsen84a");
    }
    if (ir->etc == etcVRESCALE) {
      please_cite(fplog,"Bussi2007a");
    }
  }
 
  init_nrnb(nrnb);

  if (nfile != -1)
  {
	  *fp_trn = -1;
	  *fp_ene = -1;
	  *fp_xtc = -1;
	  
	  if (MASTER(cr)) 
	  {
		  *fp_trn = open_trn(ftp2fn(efTRN,nfile,fnm), filemode);
		  if (ir->nstxtcout > 0)
		  {
			  *fp_xtc = open_xtc(ftp2fn(efXTC,nfile,fnm), filemode);
		  }
		  *fp_ene = open_enx(ftp2fn(efENX,nfile,fnm), filemode);
		  *fn_cpt = opt2fn("-cpo",nfile,fnm);
		  
		  if ((fp_dgdl != NULL) && ir->efep!=efepNO)
		  {
			  if(Flags & MD_APPENDFILES)
			  {
				  *fp_dgdl= gmx_fio_fopen(opt2fn("-dgdl",nfile,fnm),filemode);
			  }
			  else
			  {
				  *fp_dgdl = xvgropen(opt2fn("-dgdl",nfile,fnm),
									  "dG/d\\8l\\4","Time (ps)",
									  "dG/d\\8l\\4 (kJ mol\\S-1\\N [\\8l\\4]\\S-1\\N)");
			  }
		  }
		  
		  if ((fp_field != NULL) && (ir->ex[XX].n || ir->ex[YY].n ||ir->ex[ZZ].n))
		  {
			  if(Flags & MD_APPENDFILES)
			  {
				  *fp_field = gmx_fio_fopen(opt2fn("-field",nfile,fnm),filemode);
			  }
			  else
			  {				  
				  *fp_field = xvgropen(opt2fn("-field",nfile,fnm),
									   "Applied electric field","Time (ps)",
									   "E (V/nm)");
			  }
		  }
	  }
	  *mdebin = init_mdebin( (Flags & MD_APPENDFILES) ? -1 : *fp_ene,mtop,ir);
  }

  /* Initiate variables */  
  clear_mat(force_vir);
  clear_mat(shake_vir);
  clear_rvec(mu_tot);

  debug_gmx();
}
Ejemplo n.º 2
0
void init_md(t_commrec *cr,t_inputrec *ir,tensor box,real *t,real *t0,
	     real *lambda,real *lam0,real *SAfactor,
	     t_nrnb *mynrnb,bool *bTYZ,t_topology *top,
	     int nfile,t_filenm fnm[],char **traj,
	     char **xtc_traj,int *fp_ene,
	     FILE **fp_dgdl,t_mdebin **mdebin,t_groups *grps,
	     tensor force_vir,tensor pme_vir,
	     tensor shake_vir,t_mdatoms *mdatoms,rvec mu_tot,
	     bool *bNEMD,t_vcm **vcm,t_nsborder *nsb)
{
  bool bBHAM,b14,bLR,bLJLR;
  int  i;
  
  /* Initial values */
  *t = *t0       = ir->init_t;
  if (ir->efep != efepNO) {
    *lambda = *lam0 = ir->init_lambda;
  }
  else {
    *lambda = *lam0   = 0.0;
  } 
  if (ir->bSimAnn) {
    *SAfactor = 1.0 - *t0/ir->zero_temp_time;
    if (*SAfactor < 0) 
      *SAfactor = 0;
  } else
    *SAfactor     = 1.0;
    
  init_nrnb(mynrnb);
  
  /* Check Environment variables & other booleans */
#ifdef SPEC_CPU
  *bTYZ = FALSE;
#else
  *bTYZ=getenv("TYZ") != NULL;
#endif
  set_pot_bools(ir,top,&bLR,&bLJLR,&bBHAM,&b14);
  
  if (nfile != -1) {
    /* Filenames */
    *traj     = ftp2fn(efTRN,nfile,fnm);
    *xtc_traj = ftp2fn(efXTC,nfile,fnm);
    
#ifndef SPEC_CPU
    if (MASTER(cr)) {
      *fp_ene = open_enx(ftp2fn(efENX,nfile,fnm),"w");
      if ((fp_dgdl != NULL) && ir->efep!=efepNO)
	*fp_dgdl =
	  xvgropen(opt2fn("-dgdl",nfile,fnm),
		   "dG/d\\8l\\4","Time (ps)",
		   "dG/d\\8l\\4 (kJ mol\\S-1\\N nm\\S-2\\N \\8l\\4\\S-1\\N)");
    } else
#endif
      *fp_ene = -1;

    *mdebin = init_mdebin(*fp_ene,grps,&(top->atoms),&(top->idef),
			  bLR,bLJLR,bBHAM,b14,ir->efep!=efepNO,ir->epc,
			  ir->eDispCorr,(TRICLINIC(ir->compress) || TRICLINIC(box)),
			  (ir->etc==etcNOSEHOOVER),cr);
  }
  
  /* Initiate variables */  
  clear_mat(force_vir);
  clear_mat(pme_vir);
  clear_mat(shake_vir);
  clear_rvec(mu_tot);
  
  /* Set initial values for invmass etc. */
  init_mdatoms(mdatoms,*lambda,TRUE);

  *vcm = init_vcm(stdlog,top,cr,mdatoms,START(nsb),HOMENR(nsb),ir->nstcomm);
    
  debug_gmx();

  *bNEMD = (ir->opts.ngacc > 1) || (norm(ir->opts.acc[0]) > 0);

  if (ir->eI == eiSD)
    init_sd_consts(ir->opts.ngtc,ir->opts.tau_t,ir->delta_t);

}