Exemple #1
0
static void do_my_pme(FILE *fp,real tm,gmx_bool bVerbose,t_inputrec *ir,
		      rvec x[],rvec xbuf[],rvec f[],
		      real charge[],real qbuf[],real qqbuf[],
		      matrix box,gmx_bool bSort,
		      t_commrec *cr,t_nsborder *nsb,t_nrnb *nrnb,
		      t_block *excl,real qtot,
		      t_forcerec *fr,int index[],FILE *fp_xvg,
		      int ngroups,unsigned short cENER[])
{
  real   ener,vcorr,q,xx,dvdl=0,vdip,vcharge;
  tensor vir,vir_corr,vir_tot;
  rvec   mu_tot[2];
  int    i,m,ii,ig,jg;
  real   **epme,*qptr;
  
  /* Initiate local variables */  
  fr->f_el_recip = f;
  clear_mat(vir);
  clear_mat(vir_corr);
  
  if (ngroups > 1) {
    fprintf(fp,"There are %d energy groups\n",ngroups);
    snew(epme,ngroups);
    for(i=0; (i<ngroups); i++)
      snew(epme[i],ngroups);
  }
    
  /* Put x is in the box, this part needs to be parallellized properly */
  /*put_atoms_in_box(box,nsb->natoms,x);*/
  /* Here sorting of X (and q) is done.
   * Alternatively, one could just put the atoms in one of the
   * cr->nnodes slabs. That is much cheaper than sorting.
   */
  for(i=0; (i<nsb->natoms); i++)
    index[i] = i;
  if (bSort) {
    xptr = x;
    qsort(index,nsb->natoms,sizeof(index[0]),comp_xptr);
    xptr = NULL; /* To trap unintentional use of the ptr */
  }
  /* After sorting we only need the part that is to be computed on 
   * this processor. We also compute the mu_tot here (system dipole)
   */
  clear_rvec(mu_tot[0]);
  for(i=START(nsb); (i<START(nsb)+HOMENR(nsb)); i++) {
    ii      = index[i];
    q       = charge[ii];
    qbuf[i] = q;
    for(m=0; (m<DIM); m++) {
      xx         = x[ii][m];
      xbuf[i][m] = xx;
      mu_tot[0][m] += q*xx;
    }
    clear_rvec(f[ii]);
  }
  copy_rvec(mu_tot[0],mu_tot[1]);
  if (debug) {
    pr_rvec(debug,0,"qbuf",qbuf,nsb->natoms,TRUE);
    pr_rvecs(debug,0,"xbuf",xbuf,nsb->natoms);
    pr_rvecs(debug,0,"box",box,DIM);
  }
  for(ig=0; (ig<ngroups); ig++) {
    for(jg=ig; (jg<ngroups); jg++) {
      if (ngroups > 1) {
	for(i=START(nsb); (i<START(nsb)+HOMENR(nsb)); i++) {
	  if ((cENER[i] == ig) || (cENER[i] == jg))
	    qqbuf[i] = qbuf[i];
	  else
	    qqbuf[i] = 0;
	}
	qptr = qqbuf;
      }
      else
	qptr = qbuf;
      ener  = do_pme(fp,bVerbose,ir,xbuf,f,qptr,qptr,box,cr,
		     nsb,nrnb,vir,fr->ewaldcoeff,FALSE,0,&dvdl,FALSE);
      vcorr = ewald_LRcorrection(fp,nsb,cr,fr,qptr,qptr,excl,xbuf,box,mu_tot,
				 ir->ewald_geometry,ir->epsilon_surface,
				 0,&dvdl,&vdip,&vcharge);
      gmx_sum(1,&ener,cr);
      gmx_sum(1,&vcorr,cr);
      if (ngroups > 1)
	epme[ig][jg] = ener+vcorr;
    }
  }
  if (ngroups > 1) {
    if (fp_xvg) 
      fprintf(fp_xvg,"%10.3f",tm);
    for(ig=0; (ig<ngroups); ig++) {
      for(jg=ig; (jg<ngroups); jg++) {
	if (ig != jg)
	  epme[ig][jg] -= epme[ig][ig]+epme[jg][jg];
	if (fp_xvg) 
	  fprintf(fp_xvg,"  %12.5e",epme[ig][jg]);
      }
    }
    if (fp_xvg) 
      fprintf(fp_xvg,"\n");
  }
  else {
    fprintf(fp,"Time: %10.3f Energy: %12.5e  Correction: %12.5e  Total: %12.5e\n",
	    tm,ener,vcorr,ener+vcorr);
    if (fp_xvg) 
      fprintf(fp_xvg,"%10.3f %12.5e %12.5e %12.5e\n",tm,ener+vcorr,vdip,vcharge);
    if (bVerbose) {
      m_add(vir,vir_corr,vir_tot);
      gmx_sum(9,vir_tot[0],cr);
      pr_rvecs(fp,0,"virial",vir_tot,DIM); 
    }
    fflush(fp);
  }
}
Exemple #2
0
void force(FILE       *fp,     int        step,
	   t_forcerec *fr,      t_inputrec *ir,
	   t_idef     *idef,    t_nsborder *nsb,
	   t_commrec  *cr,      t_commrec *mcr,
	   t_nrnb     *nrnb,
	   t_groups   *grps,    t_mdatoms  *md,
	   int        ngener,   t_grpopts  *opts,
	   rvec       x[],      rvec       f[],
	   real       epot[],   t_fcdata   *fcd,
	   bool       bVerbose, matrix     box,
	   real       lambda,   t_graph    *graph,
	   t_block    *excl,    bool       bNBFonly,
	   matrix lr_vir,       rvec       mu_tot,
	   real       qsum,     bool       bGatherOnly)
{
  int     i,nit;
  bool    bDoEpot;
  rvec    box_size;
  real    Vlr,Vcorr=0;
  
  /* Reset box */
  for(i=0; (i<DIM); i++)
    box_size[i]=box[i][i];
    
  bDoEpot=((fr->nmol > 0) && (fr->nstcalc > 0) && (mod(step,fr->nstcalc)==0));
  /* Reset epot... */
  if (bDoEpot) 
    for(i=0; (i<fr->nmol); i++)
      fr->mol_epot[i]=0.0;
  debug_gmx();
  
  /* Call the short range functions all in one go. */
  do_fnbf(fp,cr,fr,x,f,md,
	  fr->bBHAM ? grps->estat.ee[egBHAM] : grps->estat.ee[egLJ],
	  grps->estat.ee[egCOUL],box_size,nrnb,
	  lambda,&epot[F_DVDL],FALSE,-1);
  debug_gmx();

  if (debug) 
    pr_rvecs(debug,0,"fshift after SR",fr->fshift,SHIFTS);
  
  /* Shift the coordinates. Must be done before bonded forces and PPPM, 
   * but is also necessary for SHAKE and update, therefore it can NOT 
   * go when no bonded forces have to be evaluated.
   */
  if (debug && 0)
    p_graph(debug,"DeBUGGGG",graph);
  
  /* Check whether we need to do bondeds */
  if (!bNBFonly) {
    shift_self(graph,box,x);
    if (debug && 0) {
      fprintf(debug,"BBBBBBBBBBBBBBBB\n");
      fprintf(debug,"%5d\n",graph->nnodes);
      for(i=graph->start; (i<=graph->end); i++)
	fprintf(debug,"%5d%5s%5s%5d%8.3f%8.3f%8.3f\n",
		i,"A","B",i,x[i][XX],x[i][YY],x[i][ZZ]);
      fprintf(debug,"%10.5f%10.5f%10.5f\n",
	      box[XX][XX],box[YY][YY],box[ZZ][ZZ]);
    }
    if (TRICLINIC(box))
	inc_nrnb(nrnb,eNR_SHIFTX,2*graph->nnodes);
    else
	inc_nrnb(nrnb,eNR_SHIFTX,graph->nnodes);
    debug_gmx();
  }
  
  if (EEL_LR(fr->eeltype)) {
    switch (fr->eeltype) {
    case eelPPPM:
      Vlr = do_pppm(fp,FALSE,x,fr->f_pme,md->chargeT,
		    box_size,fr->phi,cr,nsb,nrnb);
      break;
    case eelPOISSON:
      Vlr = do_poisson(fp,FALSE,ir,md->nr,x,fr->f_pme,md->chargeT,
		       box_size,fr->phi,cr,nrnb,&nit,TRUE);
      break;
    case eelPME:
      Vlr = do_pme(fp,FALSE,ir,x,fr->f_pme,md->chargeT,
		   box,cr,nsb,nrnb,lr_vir,fr->ewaldcoeff,bGatherOnly);
      break;
    case eelEWALD:
      Vlr = do_ewald(fp,FALSE,ir,x,fr->f_pme,md->chargeT,
		     box_size,cr,nsb,lr_vir,fr->ewaldcoeff);
      break;
    default:
      Vlr = 0;
      fatal_error(0,"No such electrostatics method implemented %s",
		  eel_names[fr->eeltype]);
    }
    if(fr->bEwald)
      Vcorr =
	ewald_LRcorrection(fp,nsb,cr,fr,md->chargeT,excl,x,box,mu_tot,qsum,
			   ir->ewald_geometry,ir->epsilon_surface,lr_vir);
    else
      Vcorr = shift_LRcorrection(fp,nsb,cr,fr,md->chargeT,excl,x,TRUE,box,lr_vir);
    epot[F_LR] = Vlr + Vcorr;
    if (debug)
      fprintf(debug,"Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
	      Vlr,Vcorr,epot[F_LR]);
    if (debug) {
      pr_rvecs(debug,0,"lr_vir after corr",lr_vir,DIM);
      pr_rvecs(debug,0,"fshift after LR Corrections",fr->fshift,SHIFTS);
    }
  }
  debug_gmx();
  
  if (debug)    
    print_nrnb(debug,nrnb); 
  debug_gmx();
  
  if (!bNBFonly) {
    calc_bonds(fp,cr,mcr,
	       idef,x,f,fr,graph,epot,nrnb,box,lambda,md,
	       opts->ngener,grps->estat.ee[egLJ14],grps->estat.ee[egCOUL14],
	       fcd,step,fr->bSepDVDL && do_per_step(step,ir->nstlog));    
    debug_gmx();
  }
  if (debug) 
    pr_rvecs(debug,0,"fshift after bondeds",fr->fshift,SHIFTS);
  
  for(i=0; (i<F_EPOT); i++)
    if (i != F_DISRES)
      epot[F_EPOT]+=epot[i];
}