Пример #1
0
static void upd_nbfplj(FILE *log,real *nbfp,int atnr,real f6[],real f12[],
		       int combrule)
{
  double *sigma,*epsilon,c6,c12,eps,sig,sig6;
  int n,m,k;
  
  /* Update the nonbonded force parameters */
  switch (combrule) {
  case 1:
    for(k=n=0; (n<atnr); n++) {
      for(m=0; (m<atnr); m++,k++) {
	C6 (nbfp,atnr,n,m) *= f6[k];
	C12(nbfp,atnr,n,m) *= f12[k];
      }
    }
    break;
  case 2:
  case 3:
    /* Convert to sigma and epsilon */
    snew(sigma,atnr);
    snew(epsilon,atnr);
    for(n=0; (n<atnr); n++) {
      k = n*(atnr+1);
      c6  = C6 (nbfp,atnr,n,n) * f6[k];
      c12 = C12(nbfp,atnr,n,n) * f12[k];
      if ((c6 == 0) || (c12 == 0))
	gmx_fatal(FARGS,"You can not use combination rule %d with zero C6 (%f) or C12 (%f)",combrule,c6,c12);
      sigma[n]   = pow(c12/c6,1.0/6.0);
      epsilon[n] = 0.25*(c6*c6/c12);
    }
    for(k=n=0; (n<atnr); n++) {
      for(m=0; (m<atnr); m++,k++) {
	eps  = sqrt(epsilon[n]*epsilon[m]);
	if (combrule == 2)
	  sig  = 0.5*(sigma[n]+sigma[m]);
	else
	  sig  = sqrt(sigma[n]*sigma[m]);
	sig6 = pow(sig,6.0);
    /* nbfp now includes the 6.0/12.0 derivative prefactors */
	C6 (nbfp,atnr,n,m) = 4*eps*sig6/6.0;
	C12(nbfp,atnr,n,m) = 4*eps*sig6*sig6/12.0;
      }
    }
    sfree(sigma);
    sfree(epsilon);
    break;
  default:
    gmx_fatal(FARGS,"Combination rule should be 1,2 or 3 instead of %d",
	      combrule);
  }
}
Пример #2
0
void graphics::NgoiNhaTiHon(QPainter& painter)
{
    QPoint A(150,450);
    QPoint B(350,450);
    QPoint C(350,200);
    QPoint D(250,100);
    QPoint E(150,200);

    QPolygon poly1;
    poly1 << A << B << C << D << E;
    painter.drawPolygon(poly1);
 // cai cua
    QPoint A1(250,450);
    QPoint B1(250,300);
    QPoint C1(200,300);
    QPoint D1(200,450);


    QPolygon poly11;
    poly11 << A1 << B1 << C1 << D1;
    painter.drawPolygon(poly11);
    painter.drawRect(300,250,30,30);
// ong khoi
    QPoint A12(200,150);
    QPoint B12(200,90);
    QPoint C12(175,90);
    QPoint D12(175,175);


    QPolygon poly12;
    poly12 << A12 << B12 << C12 << D12;
    painter.drawPolyline(poly12);

}
Пример #3
0
static real *mk_nbfp(t_idef *idef,bool bBHAM)
{
  real *nbfp;
  int  i,j,k,atnr;
  
  atnr=idef->atnr;
  if (bBHAM) {
    snew(nbfp,3*atnr*atnr);
    for(i=k=0; (i<atnr); i++) {
      for(j=0; (j<atnr); j++,k++) {
	BHAMA(nbfp,atnr,i,j) = idef->iparams[k].bham.a;
	BHAMB(nbfp,atnr,i,j) = idef->iparams[k].bham.b;
	BHAMC(nbfp,atnr,i,j) = idef->iparams[k].bham.c;
      }
    }
  }
  else {
    snew(nbfp,2*atnr*atnr);
    for(i=k=0; (i<atnr); i++) {
      for(j=0; (j<atnr); j++,k++) {
	C6(nbfp,atnr,i,j)   = idef->iparams[k].lj.c6;
	C12(nbfp,atnr,i,j)  = idef->iparams[k].lj.c12;
      }
    }
  }
  return nbfp;
}
Пример #4
0
static void pr_nbfp(FILE *fp,real *nbfp,bool bBHAM,int atnr)
{
  int i,j;
  
    if(fp)
    {
        for(i=0; (i<atnr); i++) {
            for(j=0; (j<atnr); j++) {
                fprintf(fp,"%2d - %2d",i,j);
                if (bBHAM)
                    fprintf(fp,"  a=%10g, b=%10g, c=%10g\n",BHAMA(nbfp,atnr,i,j),
                            BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j));
                else
                    fprintf(fp,"  c6=%10g, c12=%10g\n",C6(nbfp,atnr,i,j),
                            C12(nbfp,atnr,i,j));
            }
        }
    }
}
Пример #5
0
Файл: qmmm.c Проект: t-/adaptive
void update_QMMMrec(t_commrec *cr,
		    t_forcerec *fr,
		    rvec x[],
		    t_mdatoms *md,
		    matrix box,
		    gmx_localtop_t *top)
{
  /* updates the coordinates of both QM atoms and MM atoms and stores
   * them in the QMMMrec.
   *
   * NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
   * ns needs to be fixed!
   */
  int
    mm_max=0,mm_nr=0,mm_nr_new,i,j,is,k,shift;
  t_j_particle
    *mm_j_particles=NULL,*qm_i_particles=NULL;
  t_QMMMrec
    *qr;
  t_nblist
    QMMMlist;
  rvec
    dx,crd;
  int
    *MMatoms;
  t_QMrec
    *qm;
  t_MMrec
    *mm;
  t_pbc
    pbc;
  int
    *parallelMMarray=NULL;
  real
    c12au,c6au;

  c6au  = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,6));
  c12au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,12));

  /* every cpu has this array. On every processor we fill this array
   * with 1's and 0's. 1's indicate the atoms is a QM atom on the
   * current cpu in a later stage these arrays are all summed. indexes
   * > 0 indicate the atom is a QM atom. Every node therefore knows
   * whcih atoms are part of the QM subsystem.
   */
  /* copy some pointers */
  qr          = fr->qr;
  mm          = qr->mm;
  QMMMlist    = fr->QMMMlist;



  /*  init_pbc(box);  needs to be called first, see pbc.h */
  set_pbc_dd(&pbc,fr->ePBC,DOMAINDECOMP(cr) ? cr->dd : NULL,FALSE,box);
  /* only in standard (normal) QMMM we need the neighbouring MM
   * particles to provide a electric field of point charges for the QM
   * atoms.
   */
  if(qr->QMMMscheme==eQMMMschemenormal){ /* also implies 1 QM-layer */
    /* we NOW create/update a number of QMMMrec entries:
     *
     * 1) the shiftQM, containing the shifts of the QM atoms
     *
     * 2) the indexMM array, containing the index of the MM atoms
     *
     * 3) the shiftMM, containing the shifts of the MM atoms
     *
     * 4) the shifted coordinates of the MM atoms
     *
     * the shifts are used for computing virial of the QM/MM particles.
     */
    qm = qr->qm[0]; /* in case of normal QMMM, there is only one group */
    snew(qm_i_particles,QMMMlist.nri);
    if(QMMMlist.nri){
      qm_i_particles[0].shift = XYZ2IS(0,0,0);
      for(i=0;i<QMMMlist.nri;i++){
	qm_i_particles[i].j     = QMMMlist.iinr[i];

	if(i){
	  qm_i_particles[i].shift = pbc_dx_aiuc(&pbc,x[QMMMlist.iinr[0]],
						x[QMMMlist.iinr[i]],dx);

	}
	/* However, since nri >= nrQMatoms, we do a quicksort, and throw
	 * out double, triple, etc. entries later, as we do for the MM
	 * list too.
	 */

	/* compute the shift for the MM j-particles with respect to
	 * the QM i-particle and store them.
	 */

	crd[0] = IS2X(QMMMlist.shift[i]) + IS2X(qm_i_particles[i].shift);
	crd[1] = IS2Y(QMMMlist.shift[i]) + IS2Y(qm_i_particles[i].shift);
	crd[2] = IS2Z(QMMMlist.shift[i]) + IS2Z(qm_i_particles[i].shift);
	is = XYZ2IS(crd[0],crd[1],crd[2]);
	for(j=QMMMlist.jindex[i];
	    j<QMMMlist.jindex[i+1];
	    j++){
	  if(mm_nr >= mm_max){
	    mm_max += 1000;
	    srenew(mm_j_particles,mm_max);
	  }

	  mm_j_particles[mm_nr].j = QMMMlist.jjnr[j];
	  mm_j_particles[mm_nr].shift = is;
	  mm_nr++;
	}
      }

      /* quicksort QM and MM shift arrays and throw away multiple entries */



      qsort(qm_i_particles,QMMMlist.nri,
	    (size_t)sizeof(qm_i_particles[0]),
	    struct_comp);
      qsort(mm_j_particles,mm_nr,
	    (size_t)sizeof(mm_j_particles[0]),
	    struct_comp);
      /* remove multiples in the QM shift array, since in init_QMMM() we
       * went through the atom numbers from 0 to md.nr, the order sorted
       * here matches the one of QMindex already.
       */
      j=0;
      for(i=0;i<QMMMlist.nri;i++){
	if (i==0 || qm_i_particles[i].j!=qm_i_particles[i-1].j){
	  qm_i_particles[j++] = qm_i_particles[i];
	}
      }
      mm_nr_new = 0;
      if(qm->bTS||qm->bOPT){
	/* only remove double entries for the MM array */
	for(i=0;i<mm_nr;i++){
	  if((i==0 || mm_j_particles[i].j!=mm_j_particles[i-1].j)
	     && !md->bQM[mm_j_particles[i].j]){
	    mm_j_particles[mm_nr_new++] = mm_j_particles[i];
	  }
	}
      }
      /* we also remove mm atoms that have no charges!
      * actually this is already done in the ns.c
      */
      else{
	for(i=0;i<mm_nr;i++){
	  if((i==0 || mm_j_particles[i].j!=mm_j_particles[i-1].j)
	     && !md->bQM[mm_j_particles[i].j]
	     && (md->chargeA[mm_j_particles[i].j]
		 || (md->chargeB && md->chargeB[mm_j_particles[i].j]))) {
	    mm_j_particles[mm_nr_new++] = mm_j_particles[i];
	  }
	}
      }
      mm_nr = mm_nr_new;
      /* store the data retrieved above into the QMMMrec
       */
      k=0;
      /* Keep the compiler happy,
       * shift will always be set in the loop for i=0
       */
      shift = 0;
      for(i=0;i<qm->nrQMatoms;i++){
	/* not all qm particles might have appeared as i
	 * particles. They might have been part of the same charge
	 * group for instance.
	 */
	if (qm->indexQM[i] == qm_i_particles[k].j) {
	  shift = qm_i_particles[k++].shift;
	}
	/* use previous shift, assuming they belong the same charge
	 * group anyway,
	 */

	qm->shiftQM[i] = shift;
      }
    }
    /* parallel excecution */
    if(PAR(cr)){
      snew(parallelMMarray,2*(md->nr));
      /* only MM particles have a 1 at their atomnumber. The second part
       * of the array contains the shifts. Thus:
       * p[i]=1/0 depending on wether atomnumber i is a MM particle in the QM
       * step or not. p[i+md->nr] is the shift of atomnumber i.
       */
      for(i=0;i<2*(md->nr);i++){
	parallelMMarray[i]=0;
      }

      for(i=0;i<mm_nr;i++){
	parallelMMarray[mm_j_particles[i].j]=1;
	parallelMMarray[mm_j_particles[i].j+(md->nr)]=mm_j_particles[i].shift;
      }
      gmx_sumi(md->nr,parallelMMarray,cr);
      mm_nr=0;

      mm_max = 0;
      for(i=0;i<md->nr;i++){
	if(parallelMMarray[i]){
	  if(mm_nr >= mm_max){
	    mm_max += 1000;
	    srenew(mm->indexMM,mm_max);
	    srenew(mm->shiftMM,mm_max);
	  }
	  mm->indexMM[mm_nr]  = i;
	  mm->shiftMM[mm_nr++]= parallelMMarray[i+md->nr]/parallelMMarray[i];
	}
      }
      mm->nrMMatoms=mm_nr;
      free(parallelMMarray);
    }
    /* serial execution */
    else{
      mm->nrMMatoms = mm_nr;
      srenew(mm->shiftMM,mm_nr);
      srenew(mm->indexMM,mm_nr);
      for(i=0;i<mm_nr;i++){
	mm->indexMM[i]=mm_j_particles[i].j;
	mm->shiftMM[i]=mm_j_particles[i].shift;
      }

    }
    /* (re) allocate memory for the MM coordiate array. The QM
     * coordinate array was already allocated in init_QMMM, and is
     * only (re)filled in the update_QMMM_coordinates routine
     */
    srenew(mm->xMM,mm->nrMMatoms);
    /* now we (re) fill the array that contains the MM charges with
     * the forcefield charges. If requested, these charges will be
     * scaled by a factor
     */
    srenew(mm->MMcharges,mm->nrMMatoms);
    for(i=0;i<mm->nrMMatoms;i++){/* no free energy yet */
      mm->MMcharges[i]=md->chargeA[mm->indexMM[i]]*mm->scalefactor;
    }
    if(qm->bTS||qm->bOPT){
      /* store (copy) the c6 and c12 parameters into the MMrec struct
       */
      srenew(mm->c6,mm->nrMMatoms);
      srenew(mm->c12,mm->nrMMatoms);
      for (i=0;i<mm->nrMMatoms;i++){
	mm->c6[i]  = C6(fr->nbfp,top->idef.atnr,
			md->typeA[mm->indexMM[i]],
			md->typeA[mm->indexMM[i]])/c6au;
	mm->c12[i] =C12(fr->nbfp,top->idef.atnr,
			md->typeA[mm->indexMM[i]],
			md->typeA[mm->indexMM[i]])/c12au;
      }
      punch_QMMM_excl(qr->qm[0],mm,&(top->excls));
    }
    /* the next routine fills the coordinate fields in the QMMM rec of
     * both the qunatum atoms and the MM atoms, using the shifts
     * calculated above.
     */

    update_QMMM_coord(x,fr,qr->qm[0],qr->mm);
    free(qm_i_particles);
    free(mm_j_particles);
  }
  else { /* ONIOM */ /* ????? */
    mm->nrMMatoms=0;
    /* do for each layer */
    for (j=0;j<qr->nrQMlayers;j++){
      qm = qr->qm[j];
      qm->shiftQM[0]=XYZ2IS(0,0,0);
      for(i=1;i<qm->nrQMatoms;i++){
	qm->shiftQM[i] = pbc_dx_aiuc(&pbc,x[qm->indexQM[0]],x[qm->indexQM[i]],
				     dx);
      }
      update_QMMM_coord(x,fr,qm,mm);
    }
  }
} /* update_QMMM_rec */
Пример #6
0
Файл: qmmm.c Проект: t-/adaptive
void init_QMMMrec(t_commrec *cr,
		  matrix box,
		  gmx_mtop_t *mtop,
		  t_inputrec *ir,
		  t_forcerec *fr)
{
  /* we put the atomsnumbers of atoms that belong to the QMMM group in
   * an array that will be copied later to QMMMrec->indexQM[..]. Also
   * it will be used to create an QMMMrec->bQMMM index array that
   * simply contains true/false for QM and MM (the other) atoms.
   */

  gmx_groups_t *groups;
  atom_id   *qm_arr=NULL,vsite,ai,aj;
  int       qm_max=0,qm_nr=0,i,j,jmax,k,l,nrvsite2=0;
  t_QMMMrec *qr;
  t_MMrec   *mm;
  t_iatom   *iatoms;
  real      c12au,c6au;
  gmx_mtop_atomloop_all_t aloop;
  t_atom    *atom;
  gmx_mtop_ilistloop_all_t iloop;
  int       a_offset;
  t_ilist   *ilist_mol;

  c6au  = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,6));
  c12au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,12));
  fprintf(stderr,"there we go!\n");

  /* Make a local copy of the QMMMrec */
  qr = fr->qr;

  /* bQMMM[..] is an array containing TRUE/FALSE for atoms that are
   * QM/not QM. We first set all elemenst at false. Afterwards we use
   * the qm_arr (=MMrec->indexQM) to changes the elements
   * corresponding to the QM atoms at TRUE.  */

  qr->QMMMscheme     = ir->QMMMscheme;

  /* we take the possibility into account that a user has
   * defined more than one QM group:
   */
  /* an ugly work-around in case there is only one group In this case
   * the whole system is treated as QM. Otherwise the second group is
   * always the rest of the total system and is treated as MM.
   */

  /* small problem if there is only QM.... so no MM */

  jmax = ir->opts.ngQM;

  if(qr->QMMMscheme==eQMMMschemeoniom)
    qr->nrQMlayers = jmax;
  else
    qr->nrQMlayers = 1;

  groups = &mtop->groups;

  /* there are jmax groups of QM atoms. In case of multiple QM groups
   * I assume that the users wants to do ONIOM. However, maybe it
   * should also be possible to define more than one QM subsystem with
   * independent neighbourlists. I have to think about
   * that.. 11-11-2003
   */
  snew(qr->qm,jmax);
  for(j=0;j<jmax;j++){
    /* new layer */
    aloop = gmx_mtop_atomloop_all_init(mtop);
    while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
      if(qm_nr >= qm_max){
	qm_max += 1000;
	srenew(qm_arr,qm_max);
      }
      if (ggrpnr(groups,egcQMMM ,i) == j) {
	/* hack for tip4p */
	qm_arr[qm_nr++] = i;
      }
    }
    if(qr->QMMMscheme==eQMMMschemeoniom){
      /* add the atoms to the bQMMM array
       */

      /* I assume that users specify the QM groups from small to
       * big(ger) in the mdp file
       */
      qr->qm[j] = mk_QMrec();
      /* we need to throw out link atoms that in the previous layer
       * existed to separate this QMlayer from the previous
       * QMlayer. We use the iatoms array in the idef for that
       * purpose. If all atoms defining the current Link Atom (Dummy2)
       * are part of the current QM layer it needs to be removed from
       * qm_arr[].  */

      iloop = gmx_mtop_ilistloop_all_init(mtop);
      while (gmx_mtop_ilistloop_all_next(iloop,&ilist_mol,&a_offset)) {
	nrvsite2 = ilist_mol[F_VSITE2].nr;
	iatoms   = ilist_mol[F_VSITE2].iatoms;

	for(k=0; k<nrvsite2; k+=4) {
	  vsite = a_offset + iatoms[k+1]; /* the vsite         */
	  ai    = a_offset + iatoms[k+2]; /* constructing atom */
	  aj    = a_offset + iatoms[k+3]; /* constructing atom */
	  if (ggrpnr(groups, egcQMMM, vsite) == ggrpnr(groups, egcQMMM, ai)
	      &&
	      ggrpnr(groups, egcQMMM, vsite) == ggrpnr(groups, egcQMMM, aj)) {
	    /* this dummy link atom needs to be removed from the qm_arr
	     * before making the QMrec of this layer!
	     */
	    for(i=0;i<qm_nr;i++){
	      if(qm_arr[i]==vsite){
		/* drop the element */
		for(l=i;l<qm_nr;l++){
		  qm_arr[l]=qm_arr[l+1];
		}
		qm_nr--;
	      }
	    }
	  }
	}
      }

      /* store QM atoms in this layer in the QMrec and initialise layer
       */
      init_QMrec(j,qr->qm[j],qm_nr,qm_arr,mtop,ir);

      /* we now store the LJ C6 and C12 parameters in QM rec in case
       * we need to do an optimization
       */
      if(qr->qm[j]->bOPT || qr->qm[j]->bTS){
	for(i=0;i<qm_nr;i++){
	  qr->qm[j]->c6[i]  =  C6(fr->nbfp,mtop->ffparams.atnr,
				  atom->type,atom->type)/c6au;
	  qr->qm[j]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,
				  atom->type,atom->type)/c12au;
	}
      }
      /* now we check for frontier QM atoms. These occur in pairs that
       * construct the vsite
       */
      iloop = gmx_mtop_ilistloop_all_init(mtop);
      while (gmx_mtop_ilistloop_all_next(iloop,&ilist_mol,&a_offset)) {
	nrvsite2 = ilist_mol[F_VSITE2].nr;
	iatoms   = ilist_mol[F_VSITE2].iatoms;

	for(k=0; k<nrvsite2; k+=4){
	  vsite = a_offset + iatoms[k+1]; /* the vsite         */
	  ai    = a_offset + iatoms[k+2]; /* constructing atom */
	  aj    = a_offset + iatoms[k+3]; /* constructing atom */
	  if(ggrpnr(groups,egcQMMM,ai) < (groups->grps[egcQMMM].nr-1) &&
	     (ggrpnr(groups,egcQMMM,aj) >= (groups->grps[egcQMMM].nr-1))){
	      /* mark ai as frontier atom */
	    for(i=0;i<qm_nr;i++){
	      if( (qm_arr[i]==ai) || (qm_arr[i]==vsite) ){
		qr->qm[j]->frontatoms[i]=TRUE;
	      }
	    }
	  }
	  else if(ggrpnr(groups,egcQMMM,aj) < (groups->grps[egcQMMM].nr-1) &&
		  (ggrpnr(groups,egcQMMM,ai) >= (groups->grps[egcQMMM].nr-1))){
	    /* mark aj as frontier atom */
	    for(i=0;i<qm_nr;i++){
	      if( (qm_arr[i]==aj) || (qm_arr[i]==vsite)){
		qr->qm[j]->frontatoms[i]=TRUE;
	      }
	    }
	  }
	}
      }
    }
  }
  if(qr->QMMMscheme!=eQMMMschemeoniom){

    /* standard QMMM, all layers are merged together so there is one QM
     * subsystem and one MM subsystem.
     * Also we set the charges to zero in the md->charge arrays to prevent
     * the innerloops from doubly counting the electostatic QM MM interaction
     */
    for (k=0;k<qm_nr;k++){
      gmx_mtop_atomnr_to_atom(mtop,qm_arr[k],&atom);
      atom->q  = 0.0;
      atom->qB = 0.0;
    }
    qr->qm[0] = mk_QMrec();
    /* store QM atoms in the QMrec and initialise
     */
    init_QMrec(0,qr->qm[0],qm_nr,qm_arr,mtop,ir);
    if(qr->qm[0]->bOPT || qr->qm[0]->bTS){
      for(i=0;i<qm_nr;i++){
	gmx_mtop_atomnr_to_atom(mtop,qm_arr[i],&atom);
	qr->qm[0]->c6[i]  =  C6(fr->nbfp,mtop->ffparams.atnr,
				atom->type,atom->type)/c6au;
	qr->qm[0]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,
				atom->type,atom->type)/c12au;
      }

    }



    /* find frontier atoms and mark them true in the frontieratoms array.
     */
    for(i=0;i<qm_nr;i++) {
      gmx_mtop_atomnr_to_ilist(mtop,qm_arr[i],&ilist_mol,&a_offset);
      nrvsite2 = ilist_mol[F_VSITE2].nr;
      iatoms   = ilist_mol[F_VSITE2].iatoms;

      for(k=0;k<nrvsite2;k+=4){
	vsite = a_offset + iatoms[k+1]; /* the vsite         */
	ai    = a_offset + iatoms[k+2]; /* constructing atom */
	aj    = a_offset + iatoms[k+3]; /* constructing atom */
	if(ggrpnr(groups,egcQMMM,ai) < (groups->grps[egcQMMM].nr-1) &&
	   (ggrpnr(groups,egcQMMM,aj) >= (groups->grps[egcQMMM].nr-1))){
	/* mark ai as frontier atom */
	  if ( (qm_arr[i]==ai) || (qm_arr[i]==vsite) ){
	    qr->qm[0]->frontatoms[i]=TRUE;
	  }
	}
	else if (ggrpnr(groups,egcQMMM,aj) < (groups->grps[egcQMMM].nr-1) &&
		 (ggrpnr(groups,egcQMMM,ai) >=(groups->grps[egcQMMM].nr-1))) {
	  /* mark aj as frontier atom */
	  if ( (qm_arr[i]==aj) || (qm_arr[i]==vsite) ){
	    qr->qm[0]->frontatoms[i]=TRUE;
	  }
	}
      }
    }

    /* MM rec creation */
    mm               = mk_MMrec();
    mm->scalefactor  = ir->scalefactor;
    mm->nrMMatoms    = (mtop->natoms)-(qr->qm[0]->nrQMatoms); /* rest of the atoms */
    qr->mm           = mm;
  } else {/* ONIOM */
    /* MM rec creation */
    mm               = mk_MMrec();
    mm->scalefactor  = ir->scalefactor;
    mm->nrMMatoms    = 0;
    qr->mm           = mm;
  }

  /* these variables get updated in the update QMMMrec */

  if(qr->nrQMlayers==1){
    /* with only one layer there is only one initialisation
     * needed. Multilayer is a bit more complicated as it requires
     * re-initialisation at every step of the simulation. This is due
     * to the use of COMMON blocks in the fortran QM subroutines.
     */
    if (qr->qm[0]->QMmethod<eQMmethodRHF)
    {
#ifdef GMX_QMMM_MOPAC
        /* semi-empiprical 1-layer ONIOM calculation requested (mopac93) */
        init_mopac(cr,qr->qm[0],qr->mm);
#else
        gmx_fatal(FARGS,"Semi-empirical QM only supported with Mopac.");
#endif
    }
    else
    {
        /* ab initio calculation requested (gamess/gaussian/ORCA) */
#ifdef GMX_QMMM_GAMESS
        init_gamess(cr,qr->qm[0],qr->mm);
#elif defined GMX_QMMM_GAUSSIAN
        init_gaussian(cr,qr->qm[0],qr->mm);
#elif defined GMX_QMMM_ORCA
        init_orca(cr,qr->qm[0],qr->mm);
#else
        gmx_fatal(FARGS,"Ab-initio calculation only supported with Gamess, Gaussian or ORCA.");
#endif
    }
  }
} /* init_QMMMrec */
Пример #7
0
inline void 
GemmNNDot
( T alpha, const DistMatrix<T>& A,
           const DistMatrix<T>& B,
  T beta,        DistMatrix<T>& C )
{
#ifndef RELEASE
    PushCallStack("internal::GemmNNDot");
    if( A.Grid() != B.Grid() || B.Grid() != C.Grid() )
        throw std::logic_error
        ("{A,B,C} must be distributed over the same grid");
    if( A.Height() != C.Height() ||
        B.Width()  != C.Width()  ||
        A.Width()  != B.Height() )
    {
        std::ostringstream msg;
        msg << "Nonconformal GemmNNDot: \n"
            << "  A ~ " << A.Height() << " x " << A.Width() << "\n"
            << "  B ~ " << B.Height() << " x " << B.Width() << "\n"
            << "  C ~ " << C.Height() << " x " << C.Width() << "\n";
        throw std::logic_error( msg.str().c_str() );
    }
#endif
    const Grid& g = A.Grid();

    if( A.Height() > B.Width() )
    {
        // Matrix views
        DistMatrix<T> AT(g), AB(g),
                      A0(g), A1(g), A2(g);         
        DistMatrix<T> BL(g),  B0(g),
                      BR(g),  B1(g),
                              B2(g);
        DistMatrix<T> CT(g), C0(g), C1L(g), C1R(g),
                      CB(g), C1(g), C10(g), C11(g), C12(g),
                             C2(g);

        // Temporary distributions
        DistMatrix<T,STAR,VC> A1_STAR_VC(g);
        DistMatrix<T,VC,STAR> B1_VC_STAR(g);
        DistMatrix<T,STAR,STAR> C11_STAR_STAR(g);

        // Star the algorithm
        Scale( beta, C );
        LockedPartitionDown
        ( A, AT,
             AB, 0 );
        PartitionDown
        ( C, CT,
             CB, 0 );
        while( AB.Height() > 0 )
        {
            LockedRepartitionDown
            ( AT,  A0,
             /**/ /**/
                   A1,
              AB,  A2 );

            RepartitionDown
            ( CT,  C0,
             /**/ /**/
                   C1,
              CB,  C2 );

            A1_STAR_VC = A1; 
            B1_VC_STAR.AlignWith( A1_STAR_VC );

            LockedPartitionRight( B, BL, BR, 0 );
            PartitionRight( C1, C1L, C1R, 0 );
            while( BR.Width() > 0 )
            {
                LockedRepartitionRight
                ( BL, /**/ BR,
                  B0, /**/ B1, B2 );

                RepartitionRight
                ( C1L, /**/ C1R,
                  C10, /**/ C11, C12 );

                Zeros( C11.Height(), C11.Width(), C11_STAR_STAR );
                //------------------------------------------------------------//
                B1_VC_STAR = B1;
                LocalGemm
                ( NORMAL, NORMAL, 
                  alpha, A1_STAR_VC, B1_VC_STAR, T(0), C11_STAR_STAR );
                C11.SumScatterUpdate( T(1), C11_STAR_STAR );
                //------------------------------------------------------------//

                SlideLockedPartitionRight
                ( BL,     /**/ BR,
                  B0, B1, /**/ B2 );

                SlidePartitionRight
                ( C1L,      /**/ C1R,
                  C10, C11, /**/ C12 );
            }
            B1_VC_STAR.FreeAlignments();

            SlideLockedPartitionDown
            ( AT,  A0,
                   A1,
             /**/ /**/
              AB,  A2 );

            SlidePartitionDown
            ( CT,  C0,
                   C1,
             /**/ /**/
              CB,  C2 );
        }
    }
    else
    {
        // Matrix views
        DistMatrix<T> AT(g), AB(g),
                      A0(g), A1(g), A2(g);         
        DistMatrix<T> BL(g),  B0(g),
                      BR(g),  B1(g),
                              B2(g);
        DistMatrix<T> 
            CL(g), CR(g),         C1T(g),  C01(g),
            C0(g), C1(g), C2(g),  C1B(g),  C11(g),
                                           C21(g);

        // Temporary distributions
        DistMatrix<T,STAR,VR> A1_STAR_VR(g);
        DistMatrix<T,VR,STAR> B1_VR_STAR(g);
        DistMatrix<T,STAR,STAR> C11_STAR_STAR(g);

        // Star the algorithm
        Scale( beta, C );
        LockedPartitionRight( B, BL, BR, 0 );
        PartitionRight( C, CL, CR, 0 );
        while( BR.Width() > 0 )
        {
            LockedRepartitionRight
            ( BL, /**/ BR,
              B0, /**/ B1, B2 );

            RepartitionRight
            ( CL, /**/ CR,
              C0, /**/ C1, C2 );

            B1_VR_STAR = B1;
            A1_STAR_VR.AlignWith( B1_VR_STAR );

            LockedPartitionDown
            ( A, AT,
                 AB, 0 );
            PartitionDown
            ( C1, C1T,
                  C1B, 0 );
            while( AB.Height() > 0 )
            {
                LockedRepartitionDown
                ( AT,  A0,
                 /**/ /**/
                       A1,
                  AB,  A2 );

                RepartitionDown
                ( C1T,  C01,
                 /***/ /***/
                        C11,
                  C1B,  C21 );

                Zeros( C11.Height(), C11.Width(), C11_STAR_STAR );
                //------------------------------------------------------------//
                A1_STAR_VR = A1;
                LocalGemm
                ( NORMAL, NORMAL, 
                  alpha, A1_STAR_VR, B1_VR_STAR, T(0), C11_STAR_STAR );
                C11.SumScatterUpdate( T(1), C11_STAR_STAR );
                //------------------------------------------------------------//

                SlideLockedPartitionDown
                ( AT,  A0,
                       A1,
                 /**/ /**/
                  AB,  A2 );

                SlidePartitionDown
                ( C1T,  C01,
                        C11,
                 /***/ /***/
                  C1B,  C21 );
            }
            A1_STAR_VR.FreeAlignments();

            SlideLockedPartitionRight
            ( BL,     /**/ BR,
              B0, B1, /**/ B2 ); 

            SlidePartitionRight
            ( CL,     /**/ CR,
              C0, C1, /**/ C2 );
        }
    }
#ifndef RELEASE
    PopCallStack();
#endif
}
Пример #8
0
void do_coupling(FILE *log,int nfile,t_filenm fnm[],
		 t_coupl_rec *tcr,real t,int step,real ener[],
		 t_forcerec *fr,t_inputrec *ir,bool bMaster,
		 t_mdatoms *md,t_idef *idef,real mu_aver,int nmols,
		 t_commrec *cr,matrix box,tensor virial,
		 tensor pres,rvec mu_tot,
		 rvec x[],rvec f[],bool bDoIt)
{
#define enm2Debye 48.0321
#define d2e(x) (x)/enm2Debye
#define enm2kjmol(x) (x)*0.0143952 /* = 2.0*4.0*M_PI*EPSILON0 */

  static real *f6,*f12,*fa,*fb,*fc,*fq;
  static bool bFirst = TRUE;
  
  int         i,j,ati,atj,atnr2,type,ftype;
  real        deviation[eoObsNR],prdev[eoObsNR],epot0,dist,rmsf;
  real        ff6,ff12,ffa,ffb,ffc,ffq,factor,dt,mu_ind;
  real        Epol,Eintern,Virial,muabs,xiH=-1,xiS=-1,xi6,xi12;
  rvec        fmol[2];
  bool        bTest,bPrint;
  t_coupl_LJ  *tclj;
  t_coupl_BU  *tcbu;
  t_coupl_Q   *tcq;
  t_coupl_iparams *tip;
  
  atnr2 = idef->atnr * idef->atnr;
  if (bFirst) {
    if (PAR(cr))
      fprintf(log,"GCT: this is parallel\n");
    else
      fprintf(log,"GCT: this is not parallel\n");
    fflush(log);
    snew(f6, atnr2);
    snew(f12,atnr2);
    snew(fa, atnr2);
    snew(fb, atnr2);
    snew(fc, atnr2);
    snew(fq, idef->atnr);
    
    if (tcr->bVirial) {
      int  nrdf = 0;
      real TTT  = 0;
      real Vol  = det(box);
      
      for(i=0; (i<ir->opts.ngtc); i++) {
	nrdf += ir->opts.nrdf[i];
	TTT  += ir->opts.nrdf[i]*ir->opts.ref_t[i];
      }
      TTT /= nrdf;
      
      /* Calculate reference virial from reference temperature and pressure */
      tcr->ref_value[eoVir] = 0.5*BOLTZ*nrdf*TTT - (3.0/2.0)*
	Vol*tcr->ref_value[eoPres];
      
      fprintf(log,"GCT: TTT = %g, nrdf = %d, vir0 = %g,  Vol = %g\n",
	      TTT,nrdf,tcr->ref_value[eoVir],Vol);
      fflush(log);
    }
    bFirst = FALSE;
  }
  
  bPrint = MASTER(cr) && do_per_step(step,ir->nstlog);
  dt     = ir->delta_t;

  /* Initiate coupling to the reference pressure and temperature to start
   * coupling slowly.
   */
  if (step == 0) {
    for(i=0; (i<eoObsNR); i++)
      tcr->av_value[i] = tcr->ref_value[i];
    if ((tcr->ref_value[eoDipole]) != 0.0) {
      mu_ind = mu_aver - d2e(tcr->ref_value[eoDipole]); /* in e nm */
      Epol   = mu_ind*mu_ind/(enm2kjmol(tcr->ref_value[eoPolarizability]));
      tcr->av_value[eoEpot] -= Epol;
      fprintf(log,"GCT: mu_aver = %g(D), mu_ind = %g(D), Epol = %g (kJ/mol)\n",
	      mu_aver*enm2Debye,mu_ind*enm2Debye,Epol);
    }
  }

  /* We want to optimize the LJ params, usually to the Vaporization energy 
   * therefore we only count intermolecular degrees of freedom.
   * Note that this is now optional. switch UseEinter to yes in your gct file
   * if you want this.
   */
  dist      = calc_dist(log,x);
  muabs     = norm(mu_tot);
  Eintern   = Ecouple(tcr,ener)/nmols;
  Virial    = virial[XX][XX]+virial[YY][YY]+virial[ZZ][ZZ];

  /*calc_force(md->nr,f,fmol);*/
  clear_rvec(fmol[0]);
  
  /* Use a memory of tcr->nmemory steps, so we actually couple to the
   * average observable over the last tcr->nmemory steps. This may help
   * in avoiding local minima in parameter space.
   */
  set_act_value(tcr,eoPres, ener[F_PRES],step);
  set_act_value(tcr,eoEpot, Eintern,     step);
  set_act_value(tcr,eoVir,  Virial,      step);
  set_act_value(tcr,eoDist, dist,        step);
  set_act_value(tcr,eoMu,   muabs,       step);
  set_act_value(tcr,eoFx,   fmol[0][XX], step);
  set_act_value(tcr,eoFy,   fmol[0][YY], step);
  set_act_value(tcr,eoFz,   fmol[0][ZZ], step);
  set_act_value(tcr,eoPx,   pres[XX][XX],step);
  set_act_value(tcr,eoPy,   pres[YY][YY],step);
  set_act_value(tcr,eoPz,   pres[ZZ][ZZ],step);
  
  epot0 = tcr->ref_value[eoEpot];
  /* If dipole != 0.0 assume we want to use polarization corrected coupling */
  if ((tcr->ref_value[eoDipole]) != 0.0) {
    mu_ind = mu_aver - d2e(tcr->ref_value[eoDipole]); /* in e nm */
    
    Epol = mu_ind*mu_ind/(enm2kjmol(tcr->ref_value[eoPolarizability]));
    
    epot0 -= Epol;
    if (debug) {
      fprintf(debug,"mu_ind: %g (%g D) mu_aver: %g (%g D)\n",
	      mu_ind,mu_ind*enm2Debye,mu_aver,mu_aver*enm2Debye);
      fprintf(debug,"Eref %g Epol %g Erunav %g Eact %g\n",
	      tcr->ref_value[eoEpot],Epol,tcr->av_value[eoEpot],
	      tcr->act_value[eoEpot]);
    }
  }

  if (bPrint) {
    pr_ff(tcr,t,idef,cr,nfile,fnm);
  }
  /* Calculate the deviation of average value from the target value */
  for(i=0; (i<eoObsNR); i++) {
    deviation[i] = calc_deviation(tcr->av_value[i],tcr->act_value[i],
				  tcr->ref_value[i]);
    prdev[i]     = tcr->ref_value[i] - tcr->act_value[i];
  }
  deviation[eoEpot] = calc_deviation(tcr->av_value[eoEpot],tcr->act_value[eoEpot],
				     epot0);
  prdev[eoEpot]     = epot0 - tcr->act_value[eoEpot];
  
  if (bPrint)
    pr_dev(tcr,t,prdev,cr,nfile,fnm);
  
  /* First set all factors to 1 */
  for(i=0; (i<atnr2); i++) {
    f6[i] = f12[i] = fa[i] = fb[i] = fc[i] = 1.0;
  }
  for(i=0; (i<idef->atnr); i++) 
    fq[i] = 1.0;

  /* Now compute the actual coupling compononents */   
  if (!fr->bBHAM) {
    if (bDoIt) {
      for(i=0; (i<tcr->nLJ); i++) {
	tclj=&(tcr->tcLJ[i]);
	
	ati=tclj->at_i;
	atj=tclj->at_j;
	
	ff6 = ff12 = 1.0;	
	
	if (tclj->eObs == eoForce) {
	  gmx_fatal(FARGS,"Hack code for this to work again ");
	  if (debug)
	    fprintf(debug,"Have computed derivatives: xiH = %g, xiS = %g\n",xiH,xiS);
	  if (ati == 1) {
	    /* Hydrogen */
	    ff12 += xiH; 
	  }
	  else if (ati == 2) {
	    /* Shell */
	    ff12 += xiS; 
	  }
	  else
	    gmx_fatal(FARGS,"No H, no Shell, edit code at %s, line %d\n",
			__FILE__,__LINE__);
	  if (ff6 > 0)
	    set_factor_matrix(idef->atnr,f6, sqrt(ff6), ati,atj);
	  if (ff12 > 0)
	    set_factor_matrix(idef->atnr,f12,sqrt(ff12),ati,atj);
	}
	else {
	  if (debug)
	    fprintf(debug,"tcr->tcLJ[%d].xi_6 = %g, xi_12 = %g deviation = %g\n",i,
		    tclj->xi_6,tclj->xi_12,deviation[tclj->eObs]);
	  factor=deviation[tclj->eObs];
	  
	  upd_f_value(log,idef->atnr,tclj->xi_6, dt,factor,f6, ati,atj);
	  upd_f_value(log,idef->atnr,tclj->xi_12,dt,factor,f12,ati,atj);
	}
      }
    }
    if (PAR(cr)) {
      gprod(cr,atnr2,f6);
      gprod(cr,atnr2,f12);
#ifdef DEBUGGCT
      dump_fm(log,idef->atnr,f6,"f6");
      dump_fm(log,idef->atnr,f12,"f12");
#endif
    }
    upd_nbfplj(log,fr->nbfp,idef->atnr,f6,f12,tcr->combrule);
    
    /* Copy for printing */
    for(i=0; (i<tcr->nLJ); i++) {
      tclj=&(tcr->tcLJ[i]);
      ati = tclj->at_i;
      atj = tclj->at_j;
      if (atj == -1) 
	atj = ati;
      tclj->c6  =  C6(fr->nbfp,fr->ntype,ati,atj);
      tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj);
    }
  }
  else {
    if (bDoIt) {
      for(i=0; (i<tcr->nBU); i++) {
	tcbu   = &(tcr->tcBU[i]);
	factor = deviation[tcbu->eObs];
	ati    = tcbu->at_i;
	atj    = tcbu->at_j;
	
	upd_f_value(log,idef->atnr,tcbu->xi_a,dt,factor,fa,ati,atj);
	upd_f_value(log,idef->atnr,tcbu->xi_b,dt,factor,fb,ati,atj);
	upd_f_value(log,idef->atnr,tcbu->xi_c,dt,factor,fc,ati,atj);
      }
    }
    if (PAR(cr)) {
      gprod(cr,atnr2,fa);
      gprod(cr,atnr2,fb);
      gprod(cr,atnr2,fc);
    }
    upd_nbfpbu(log,fr->nbfp,idef->atnr,fa,fb,fc);
    /* Copy for printing */
    for(i=0; (i<tcr->nBU); i++) {
      tcbu=&(tcr->tcBU[i]);
      ati = tcbu->at_i;
      atj = tcbu->at_j;
      if (atj == -1) 
	atj = ati;
      tcbu->a = BHAMA(fr->nbfp,fr->ntype,ati,atj);
      tcbu->b = BHAMB(fr->nbfp,fr->ntype,ati,atj);
      tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj);
      if (debug)
	fprintf(debug,"buck (type=%d) = %e, %e, %e\n",
		tcbu->at_i,tcbu->a,tcbu->b,tcbu->c);
    }
  }
  if (bDoIt) {
    for(i=0; (i<tcr->nQ); i++) {
      tcq=&(tcr->tcQ[i]);
      if (tcq->xi_Q)     
	ffq = 1.0 + (dt/tcq->xi_Q) * deviation[tcq->eObs];
      else
	ffq = 1.0;
      fq[tcq->at_i] *= ffq;
    }
  }
  if (PAR(cr))
    gprod(cr,idef->atnr,fq);
  
  for(j=0; (j<md->nr); j++) {
    md->chargeA[j] *= fq[md->typeA[j]];
  }
  for(i=0; (i<tcr->nQ); i++) {
    tcq=&(tcr->tcQ[i]);
    for(j=0; (j<md->nr); j++) {
      if (md->typeA[j] == tcq->at_i) {
	tcq->Q = md->chargeA[j];
	break;
      }
    }
    if (j == md->nr)
      gmx_fatal(FARGS,"Coupling type %d not found",tcq->at_i);
  }  
  for(i=0; (i<tcr->nIP); i++) {
    tip    = &(tcr->tIP[i]);
    type   = tip->type;
    ftype  = idef->functype[type];
    factor = dt*deviation[tip->eObs];
      
    switch(ftype) {
    case F_BONDS:
      if (tip->xi.harmonic.krA) idef->iparams[type].harmonic.krA *= (1+factor/tip->xi.harmonic.krA);
      if (tip->xi.harmonic.rA) idef->iparams[type].harmonic.rA *= (1+factor/tip->xi.harmonic.rA);
	break;
    default:
      break;
    }
    tip->iprint=idef->iparams[type];
  }
}
Пример #9
0
void sirius_v500(std::vector<Element>& the_ring) {

	int  harmonic_number = 864;

	//double energy = 3e9;

	// AC10_5
	double qaf_strength       =  2.536876;
	double qad_strength       = -2.730416;
	double qbd2_strength      = -3.961194;
	double qbf_strength       =  3.902838;
	double qbd1_strength      = -2.966239;
	double qf1_strength       =  2.367821;
	double qf2_strength       =  3.354286;
	double qf3_strength       =  3.080632;
	double qf4_strength       =  2.707639;
	double sa1_strength       = -115.7829759411277/2;
	double sa2_strength       =   49.50386128829739/2;
	double sb1_strength       = -214.5386552515188/2;
	double sb2_strength       =  133.1252391065637/2;
	double sd1_strength       = -302.6188062085843/2;
	double sf1_strength       =  369.5045185071228/2;
	double sd2_strength       = -164.3042864671946/2;
	double sd3_strength       = -289.9270429064217/2;
	double sf2_strength       =  333.7039740852999/2;


    //""" --- drift spaces --- """

    double id_length = 2.0; // [m]

    Element dia1     = Element::drift("dia", id_length/2);
    Element dia2     = Element::drift("dia", 3.26920 + 3.65e-3 - id_length/2);
    Element dib1     = Element::drift("dib", id_length/2);
    Element dib2     = Element::drift("dib", 2.909200 + 3.65e-3 - id_length/2);
    Element d10      = Element::drift("d10", 0.100000);
    Element d11      = Element::drift("d11", 0.110000);
    Element d12      = Element::drift("d12", 0.120000);
    Element d13      = Element::drift("d13", 0.130000);
    Element d15      = Element::drift("d15", 0.150000);
    Element d17      = Element::drift("d17", 0.170000);
    Element d18      = Element::drift("d18", 0.180000);
    Element d20      = Element::drift("d20", 0.200000);
    Element d22      = Element::drift("d22", 0.220000);
    Element d23      = Element::drift("d23", 0.230000);
    Element d26      = Element::drift("d26", 0.260000);
    Element d32      = Element::drift("d32", 0.320000);
    Element d44      = Element::drift("d44", 0.440000);

    //""" --- markers --- """
    Element mc     = Element::marker("mc");
	Element mia    = Element::marker("mia");
	Element mib    = Element::marker("mib");
	Element mb1    = Element::marker("mb1");
	Element mb2    = Element::marker("mb2");
	Element mb3    = Element::marker("mb3");
	Element inicio = Element::marker("inicio");
	Element fim    = Element::marker("fim");
	Element mida   = Element::marker("id_enda");
	Element midb   = Element::marker("id_endb");

    //""" --- beam position monitors --- """
	Element mon    = Element::marker("BPM");

    //""" --- quadrupoles --- """
    Element qaf      = Element::quadrupole("qaf",  0.340000, qaf_strength);
	Element qad      = Element::quadrupole("qad",  0.140000, qad_strength);
	Element qbd2     = Element::quadrupole("qbd2", 0.140000, qbd2_strength);
	Element qbf      = Element::quadrupole("qbf",  0.340000, qbf_strength);
	Element qbd1     = Element::quadrupole("qbd1", 0.140000, qbd1_strength);
	Element qf1      = Element::quadrupole("qf1",  0.250000, qf1_strength);
	Element qf2      = Element::quadrupole("qf2",  0.250000, qf2_strength);
	Element qf3      = Element::quadrupole("qf3",  0.250000, qf3_strength);
	Element qf4      = Element::quadrupole("qf4",  0.250000, qf4_strength);

    //""" --- bending magnets --- """

    double deg_2_rad = (M_PI/180.0);

    std::string dip_nam;
	double      dip_len, dip_ang, dip_K, dip_S;
    Element     h1, h2;

    //""" -- b1 -- """
    dip_nam =  "b1";
    dip_len =  0.828080;
    dip_ang =  2.766540 * deg_2_rad;
    dip_K   = -0.78;
    dip_S   =  0;
    h1      = Element::rbend(dip_nam, dip_len/2, dip_ang/2, 1*dip_ang/2, 0*dip_ang/2, dip_K, dip_S);
    h2      = Element::rbend(dip_nam, dip_len/2, dip_ang/2, 0*dip_ang/2, 1*dip_ang/2, dip_K, dip_S);
    std::vector<Element> B1 = {h1, mb1, h2};

    //""" -- b2 -- """
    dip_nam =  "b2";
    dip_len =  1.228262;
    dip_ang =  4.103510 * deg_2_rad;
    dip_K   = -0.78;
    dip_S   =  0.00;
    h1      = Element::rbend(dip_nam, dip_len/2, dip_ang/2, 1*dip_ang/2, 0*dip_ang/2, dip_K, dip_S);
    h2      = Element::rbend(dip_nam, dip_len/2, dip_ang/2, 0*dip_ang/2, 1*dip_ang/2, dip_K, dip_S);
    std::vector<Element> B2 = {h1, mb2, h2};

    //""" -- b3 -- """
    dip_nam =  "b3";
    dip_len =  0.428011;
    dip_ang =  1.429950 * deg_2_rad;
    dip_K   = -0.78;
    dip_S   =  0.00;
    h1      = Element::rbend(dip_nam, dip_len/2, dip_ang/2, 1*dip_ang/2, 0*dip_ang/2, dip_K, dip_S);
    h2      = Element::rbend(dip_nam, dip_len/2, dip_ang/2, 0*dip_ang/2, 1*dip_ang/2, dip_K, dip_S);
    std::vector<Element> B3 = {h1, mb3, h2};

    //""" -- bc -- """
    dip_nam =  "bc";
    dip_len =  0.125394;
    dip_ang =  1.4 * deg_2_rad;
    dip_K   =  0.00;
    dip_S   = -18.93;
    Element bce      = Element::rbend(dip_nam, dip_len/2, dip_ang/2, 1*dip_ang/2, 0*dip_ang/2, dip_K, dip_S);
    Element bcs      = Element::rbend(dip_nam, dip_len/2, dip_ang/2, 0*dip_ang/2, 1*dip_ang/2, dip_K, dip_S);
    std::vector<Element> BC = {bce, mc, bcs};

    //""" --- correctors --- """
    Element ch     = Element::hcorrector("hcm",  0, 0);
    Element cv     = Element::vcorrector("vcm",  0, 0);
    Element crhv   = Element::corrector ("crhv", 0, 0, 0);

    //""" --- sextupoles --- """
    Element sa1      = Element::sextupole("sa1", 0.150000, sa1_strength);
    Element sa2      = Element::sextupole("sa2", 0.150000, sa2_strength);
    Element sb1      = Element::sextupole("sb1", 0.150000, sb1_strength);
    Element sb2      = Element::sextupole("sb2", 0.150000, sb2_strength);
    Element sd1      = Element::sextupole("sd1", 0.150000, sd1_strength);
    Element sf1      = Element::sextupole("sf1", 0.150000, sf1_strength);
    Element sd2      = Element::sextupole("sd2", 0.150000, sd2_strength);
    Element sd3      = Element::sextupole("sd3", 0.150000, sd3_strength);
    Element sf2      = Element::sextupole("sf2", 0.150000, sf2_strength);

    //""" --- rf cavity --- """
    Element cav = Element::rfcavity("cav", 0, 500e6, 2.5e6);

    //""" lines """
    std::vector<Element> insa   = { dia1, mida, dia2, crhv, cv, d12, ch, d12, sa2, d12, mon, d12, qaf, d23, qad, d17, sa1, d17};
    std::vector<Element> insb   = { dib1, midb, dib2, d10, crhv, qbd2, d12, cv, d12, ch, d12, sb2, d12, mon, d12, qbf, d23, qbd1, d17, sb1, d17};
    std::vector<Element> cline1 = { d32, cv,  d12, ch,  d15, sd1, d17, qf1, d12, mon, d11, sf1, d20, qf2, d17, sd2, d12, ch, d10, mon, d10};
    std::vector<Element> cline2 = { d18, cv,  d26, sd3, d17, qf3, d12, mon, d11, sf2, d20, qf4, d15, ch,  crhv, d12, mon, d44};
    std::vector<Element> cline3 = { d44, mon, d12, ch,  d15, qf4, d20, sf2, d11, mon, d12, qf3, d17, sd3, d26, cv, crhv, d18};
    std::vector<Element> cline4 = { d20, ch,  d12, sd2, d17, qf2, d20, sf1, d11, mon, d12, qf1, d17, sd1, d15, ch,  d12, cv, d22, mon, d10};

    //""" Injection Section """
    Element dmiainj  = Element::drift("dmiainj", 0.3);
	Element dinjk3   = Element::drift("dinjk3" , 0.3);
	Element dk3k4    = Element::drift("dk3k4"  , 0.6);
	Element dk4pmm   = Element::drift("dk4pmm" , 0.2);
	Element dpmmcv   = Element::drift("dpmmcv" , (3.2692 + 3.65e-3 - 0.3 - 0.3 - 0.6 - 0.2 - 3*0.6));
	Element dcvk1    = Element::drift("dcvk1"  , (3.2692 + 3.65e-3 - 0.6 - 1.4 - 2*0.6));

	Element dk1k2    = Element::drift("dk1k2"  , 0.6);
	Element sef      = Element::sextupole("sef", 0.6, 0.0, 5);
	Element dk2sef   = Element::drift("dk2mia" , 0.8);

	Element kick     = Element::corrector("kick", 0.6, 0, 0);
	Element pmm      = Element::sextupole("pmm", 0.6, 0.0, 5);
	Element inj      = Element::marker("inj");

	std::vector<Element> insaend  = {cv, d12, ch, d12, sa2, d12, mon, d12, qaf, d23, qad, d17, sa1, d17};
    std::vector<Element> insainj  = latt_join({{dmiainj, inj, dinjk3, kick, dk3k4, kick, dk4pmm, pmm, dpmmcv}, insaend});
    std::vector<Element> injinsa  = latt_join({latt_reverse(insaend), {dcvk1, kick, dk1k2, kick, dk2sef, sef}});

    std::vector<Element> B3BCB3   = latt_join({B3,{d13},BC,{d13},B3});
    std::vector<Element> R01 = latt_join({injinsa, {fim, inicio, mia}, insainj});   //#% injection sector, marker of the lattice model starting element
    std::vector<Element> R03 = latt_join({latt_reverse(insa), {mia, cav}, insa});   //#% sector with cavities
    std::vector<Element> R05 = latt_join({latt_reverse(insa), {mia}, insa});
    std::vector<Element> R07(R05);
    std::vector<Element> R09(R05);
    std::vector<Element> R11(R05);
    std::vector<Element> R13(R05);
    std::vector<Element> R15(R05);
    std::vector<Element> R17(R05);
    std::vector<Element> R19(R05);
    std::vector<Element> R02 = latt_join({latt_reverse(insb), {mib}, insb});
    std::vector<Element> R04(R02);
    std::vector<Element> R06(R02);
    std::vector<Element> R08(R02);
    std::vector<Element> R10(R02);
    std::vector<Element> R12(R02);
    std::vector<Element> R14(R02);
    std::vector<Element> R16(R02);
    std::vector<Element> R18(R02);
    std::vector<Element> R20(R02);


    std::vector<Element> C01 = latt_join({B1, cline1, B2, cline2, B3BCB3, cline3, B2, cline4, B1});
    std::vector<Element> C02(C01);
    std::vector<Element> C03(C01);
    std::vector<Element> C04(C01);
    std::vector<Element> C05(C01);
    std::vector<Element> C06(C01);
    std::vector<Element> C07(C01);
    std::vector<Element> C08(C01);
    std::vector<Element> C09(C01);
    std::vector<Element> C10(C01);
    std::vector<Element> C11(C01);
    std::vector<Element> C12(C01);
    std::vector<Element> C13(C01);
    std::vector<Element> C14(C01);
    std::vector<Element> C15(C01);
    std::vector<Element> C16(C01);
    std::vector<Element> C17(C01);
    std::vector<Element> C18(C01);
    std::vector<Element> C19(C01);
    std::vector<Element> C20(C01);


    the_ring = latt_join({
        R01, C01, R02, C02, R03, C03, R04, C04, R05, C05,
        R06, C06, R07, C07, R08, C08, R09, C09, R10, C10,
        R11, C11, R12, C12, R13, C13, R14, C14, R15, C15,
        R16, C16, R17, C17, R18, C18, R19, C19, R20, C20,
    });


    //""" shift lattice to start at the marker "inicio" """
    std::vector<int> idx = latt_findcells_fam_name(the_ring, "inicio");
    if (idx.size() > 0) {
    	std::vector<Element>::iterator it = the_ring.begin() + idx[0];
    	std::rotate(the_ring.begin(), it, the_ring.end());
    };

    //""" check if there are elements with negative lengths """
    std::vector<double> lens = latt_getcellstruct<double>(the_ring, "length", latt_range(the_ring));
    for(unsigned int i=0; i<lens.size(); ++i) {
    	if (lens[i] < 0) {
    		std::cerr << "negative drift in lattice!" << std::endl;
    	}
    }

    //""" sets cavity frequency according to lattice length """
    double C = latt_findspos(the_ring, 1+the_ring.size());

    double rev_freq = light_speed / C;
    std::vector<int> rf_idx = latt_findcells_fam_name(the_ring, "cav");

    for(unsigned int idx = 0; idx<rf_idx.size(); ++idx) {
    	the_ring[rf_idx[idx]].frequency = rev_freq * harmonic_number;
    }
    latt_setcavity(the_ring, "on");
    //latt_setradiation(the_ring, "on", 3e9);

    //""" adjusts number of integraton steps for each element family """
    the_ring = latt_set_num_integ_steps(the_ring);

}
Пример #10
0
void do_glas(FILE *log,int start,int homenr,rvec x[],rvec f[],
	     t_forcerec *fr,t_mdatoms *md,int atnr,t_inputrec *ir,
	     real ener[])
{
  static bool   bFirst=TRUE,bGlas;
  static real   d[2],pi6,pi12,rc9,rc4,rc10,rc3,rc;
  static real   *c6,*c12;
  real wd,wdd,zi,fz,dd,d10,d4,d9,d3,r9,r3,sign,cc6,cc12;
  int  *type;
  int  i,j,ti;
  
  type=md->typeA;
  if (bFirst) {
    pi6  = ir->userreal1;
    pi12 = ir->userreal2;
    d[0] = ir->userreal3;
    d[1] = ir->userreal4;
    
    /* Check whether these constants have been set. */
    bGlas = (pi6 != 0) && (pi12 != 0) && (d[0] != 0) && (d[1] != 0);
    
    if (bGlas) {
      if (ir->eDispCorr != edispcNO) {
	gmx_fatal(FARGS,"Can not have Long Range C6 corrections and GLASMD");
      }
      rc   = max(fr->rvdw,fr->rlist);
      rc3  = rc*rc*rc;
      rc4  = rc3*rc;
      rc9  = rc3*rc3*rc3;
      rc10 = rc9*rc;
    
      fprintf(log,
	      "Constants for GLASMD: pi6 = %10g, pi12 = %10g\n"
	      "                      d1  = %10g, d2   = %10g\n"
	      "                      rc3 = %10g, rc4  = %10g\n"
	      "                      rc9 = %10g, rc10 = %10g\n",
	      pi6,pi12,d[0],d[1],rc3,rc4,rc9,rc10);
      if (d[0] > d[1])
	gmx_fatal(FARGS,"d1 > d2 for GLASMD (check log file)");
    
      snew(c6,atnr);
      snew(c12,atnr);
    
      for(i=0; (i<atnr); i++) {
	c6[i]  = C6 (fr->nbfp,atnr,i,i);
	c12[i] = C12(fr->nbfp,atnr,i,i);
      }
    }
    else
      fprintf(stderr,"No glasmd!\n");
    bFirst = FALSE;
  }
  
  if (bGlas) {
    wd=0;
    for(i=start; (i<start+homenr); i++) {
      ti   = type[i];
      if ((c6[ti] != 0) || (c12[ti] != 0)) {
	zi   = x[i][ZZ];
	cc6  = M_PI*sqrt(c6[ti]*pi6);
	cc12 = M_PI*sqrt(c12[ti]*pi12);
	
	/* Use a factor for the sign, this saves taking absolute values */
	sign = 1;
	for(j=0; (j<2); j++) {
	  dd = sign*(zi-d[j]);
	  if (dd >= rc) {
	    d3  = dd*dd*dd;
	    d9  = d3*d3*d3;
	    wdd = cc12/(45.0*d9) - cc6/(6.0*d3);
	    d4  = d3*dd;
	    d10 = d9*dd;
	    fz  = sign*(cc12/(5.0*d10) - cc6/(2.0*d4));
	  }
	  else {
	    wdd = cc12*(2.0/(9.0*rc9) - dd/(5.0*rc10)) -
	      cc6*(2.0/(3.0*rc3) - dd/(2.0*rc4));
	    fz  = sign*(cc12/(5.0*rc10)-cc6/(2.0*rc4));
	  }
	  wd       += wdd;
	  f[i][ZZ] += fz;
	  sign      = -sign;
	}
      }
    }
    ener[F_LJ_LR] = wd;
  }
}
Пример #11
0
static void update_ff(t_forcerec *fr,int nparm,t_range range[],int param_val[])
{
    static double *sigma=NULL,*eps=NULL,*c6=NULL,*cn=NULL,*bhama=NULL,*bhamb=NULL,*bhamc=NULL;
    real   val,*nbfp;
    int    i,j,atnr;

    atnr = fr->ntype;
    nbfp = fr->nbfp;

    if (fr->bBHAM) {
        if (bhama == NULL) {
            snew(bhama,atnr);
            snew(bhamb,atnr);
            snew(bhamc,atnr);
        }
    }
    else {
        if (sigma == NULL) {
            snew(sigma,atnr);
            snew(eps,atnr);
            snew(c6,atnr);
            snew(cn,atnr);
        }
    }
    /* Get current values for everything */
    for(i=0; (i<nparm); i++) {
        if (ga)
            val = range[i].rval;
        else
            val = value_range(&range[i],param_val[i]);
        if(debug)
            fprintf(debug,"val = %g\n",val);
        switch (range[i].ptype) {
        case eseSIGMA:
            sigma[range[i].atype] = val;
            break;
        case eseEPSILON:
            eps[range[i].atype] = val;
            break;
        case eseBHAMA:
            bhama[range[i].atype] = val;
            break;
        case eseBHAMB:
            bhamb[range[i].atype] = val;
            break;
        case eseBHAMC:
            bhamc[range[i].atype] = val;
            break;
        case eseCELLX:
            scale[XX] = val;
            break;
        case eseCELLY:
            scale[YY] = val;
            break;
        case eseCELLZ:
            scale[ZZ] = val;
            break;
        default:
            gmx_fatal(FARGS,"Unknown ptype");
        }
    }
    if (fr->bBHAM) {
        for(i=0; (i<atnr); i++) {
            for(j=0; (j<=i); j++) {
                BHAMA(nbfp,atnr,i,j) = BHAMA(nbfp,atnr,j,i) = sqrt(bhama[i]*bhama[j]);
                BHAMB(nbfp,atnr,i,j) = BHAMB(nbfp,atnr,j,i) = sqrt(bhamb[i]*bhamb[j]);
                BHAMC(nbfp,atnr,i,j) = BHAMC(nbfp,atnr,j,i) = sqrt(bhamc[i]*bhamc[j]);
            }
        }
    }
    else {
        /* Now build a new matrix */
        for(i=0; (i<atnr); i++) {
            c6[i] = 4*eps[i]*pow(sigma[i],6.0);
            cn[i] = 4*eps[i]*pow(sigma[i],ff.npow);
        }
        for(i=0; (i<atnr); i++) {
            for(j=0; (j<=i); j++) {
                C6(nbfp,atnr,i,j)  = C6(nbfp,atnr,j,i)  = sqrt(c6[i]*c6[j]);
                C12(nbfp,atnr,i,j) = C12(nbfp,atnr,j,i) = sqrt(cn[i]*cn[j]);
            }
        }
    }

    if (debug) {
        if (!fr->bBHAM)
            for(i=0; (i<atnr); i++)
                fprintf(debug,"atnr = %2d  sigma = %8.4f  eps = %8.4f\n",i,sigma[i],eps[i]);
        for(i=0; (i<atnr); i++) {
            for(j=0; (j<atnr); j++) {
                if (fr->bBHAM)
                    fprintf(debug,"i: %2d  j: %2d  A:  %10.5e  B:  %10.5e  C:  %10.5e\n",i,j,
                            BHAMA(nbfp,atnr,i,j),BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j));
                else
                    fprintf(debug,"i: %2d  j: %2d  c6:  %10.5e  cn:  %10.5e\n",i,j,
                            C6(nbfp,atnr,i,j),C12(nbfp,atnr,i,j));
            }
        }
    }
}
Пример #12
0
static void check_solvent(FILE *fp,t_topology *top,t_forcerec *fr,
			  t_mdatoms *md,t_nsborder *nsb)
{
  /* This routine finds out whether a charge group can be used as
   * solvent in the innerloops. The routine should be called once
   * at the beginning of the MD program.
   */
  t_block *cgs,*excl,*mols;
  atom_id *cgid;
  int     i,j,m,j0,j1,nj,k,aj,ak,tjA,tjB,nl_m,nl_n,nl_o;
  int     warncount;
  bool    bOneCG;
  bool    *bAllExcl,bAE,bOrder;
  bool    *bHaveLJ,*bHaveCoul;
  
  cgs  = &(top->blocks[ebCGS]);
  excl = &(top->atoms.excl);
  mols = &(top->blocks[ebMOLS]);

  if (fp)
    fprintf(fp,"Going to determine what solvent types we have.\n");
  snew(fr->solvent_type,cgs->nr+1);
  snew(fr->mno_index,(cgs->nr+1)*3);
  
  /* Generate charge group number for all atoms */
  cgid = make_invblock(cgs,cgs->nra);
  
  warncount=0;

  /* Loop over molecules */
  if (fp)
    fprintf(fp,"There are %d molecules, %d charge groups and %d atoms\n",
	    mols->nr,cgs->nr,cgs->nra);
  for(i=0; (i<mols->nr); i++) {
    /* Set boolean that determines whether the molecules consists of one CG */
    bOneCG = TRUE;
    /* Set some counters */
    j0     = mols->index[i];
    j1     = mols->index[i+1];
    nj     = j1-j0;
    for(j=j0+1; (j<j1); j++) {
      bOneCG = bOneCG && (cgid[mols->a[j]] == cgid[mols->a[j-1]]);
    }
    if (fr->bSolvOpt && bOneCG && nj>1) {
      /* Check whether everything is excluded */
      snew(bAllExcl,nj);
      bAE = TRUE;
      /* Loop over all atoms in molecule */
      for(j=j0; (j<j1) && bAE; j++) {
	/* Set a flag for each atom in the molecule that determines whether
	 * it is excluded or not 
	 */
	for(k=0; (k<nj); k++)
	  bAllExcl[k] = FALSE;
	/* Now check all the exclusions of this atom */
	for(k=excl->index[j]; (k<excl->index[j+1]); k++) {
	  ak = excl->a[k];
	  /* Consistency and range check */
	  if ((ak < j0) || (ak >= j1)) 
	    fatal_error(0,"Exclusion outside molecule? ak = %d, j0 = %d, j1 = 5d, mol is %d",ak,j0,j1,i);
	  bAllExcl[ak-j0] = TRUE;
	}
	/* Now sum up the booleans */
	for(k=0; (k<nj); k++)
	  bAE = bAE && bAllExcl[k];
      }
      if (bAE) {
	snew(bHaveCoul,nj);
	snew(bHaveLJ,nj);
	for(j=j0; (j<j1); j++) {
	  /* Check for coulomb */
	  aj = mols->a[j];
	  bHaveCoul[j-j0] = ( (fabs(top->atoms.atom[aj].q ) > GMX_REAL_MIN) ||
			      (fabs(top->atoms.atom[aj].qB) > GMX_REAL_MIN));
	  /* Check for LJ. */
	  tjA = top->atoms.atom[aj].type;
	  tjB = top->atoms.atom[aj].typeB;
	  bHaveLJ[j-j0] = FALSE;
	  for(k=0; (k<fr->ntype); k++) {
	    if (fr->bBHAM) 
	      bHaveLJ[j-j0] = (bHaveLJ[j-j0] || 
			       (fabs(BHAMA(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
			       (fabs(BHAMB(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
			       (fabs(BHAMC(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
			       (fabs(BHAMA(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN) ||
			       (fabs(BHAMB(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN) ||
			       (fabs(BHAMC(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN));
	    else
	      bHaveLJ[j-j0] = (bHaveLJ[j-j0] || 
			       (fabs(C6(fr->nbfp,fr->ntype,tjA,k))  > GMX_REAL_MIN) ||
			       (fabs(C12(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
			       (fabs(C6(fr->nbfp,fr->ntype,tjB,k))  > GMX_REAL_MIN) ||
			       (fabs(C12(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN));
	  }
	}
	/* Now we have determined what particles have which interactions 
	 * In the case of water-like molecules we only check for the number
	 * of particles and the LJ, not for the Coulomb. Let's just assume
	 * that the water loops are faster than the MNO loops anyway. DvdS
	 */
	/* No - there's another problem: To optimize the water
	 * innerloop assumes the charge of the first i atom is constant
	 * qO, and charge on atoms 2/3 is constant qH. /EL
	 */
	/* I won't write any altivec versions of the general solvent inner 
         * loops. Thus, when USE_PPC_ALTIVEC is defined it is faster 
	 * to use the normal loops instead of the MNO solvent version. /EL
	 */
	aj=mols->a[j0];
	if((nj==3) && bHaveCoul[0] && bHaveLJ[0] &&
	   !bHaveLJ[1] && !bHaveLJ[2] &&
	   fabs(top->atoms.atom[aj+1].q - top->atoms.atom[aj+2].q) < GMX_REAL_MIN)
	  fr->solvent_type[cgid[aj]] = esolWATER;
	else {
#ifdef USE_PPC_ALTIVEC
          fr->solvent_type[cgid[aj]] = esolNO;
#else
	  /* Time to compute M & N & O */
	  for(k=0; (k<nj) && (bHaveLJ[k] && bHaveCoul[k]); k++)
	    ;
	  nl_n = k;
	  for(; (k<nj) && (!bHaveLJ[k] && bHaveCoul[k]); k++)
	    ;
	  nl_o = k;
	  for(; (k<nj) && (bHaveLJ[k] && !bHaveCoul[k]); k++)
	    ;
	  nl_m = k;
	  /* Now check whether we're at the end of the pack */
	  bOrder = FALSE;
	  for(; (k<nj); k++)
	    bOrder = bOrder || (bHaveLJ[k] || bHaveCoul[k]);
	  if (bOrder) {
	    /* If we have a solvent molecule with LJC everywhere, then
	     * we shouldn't issue a warning. Only if we suspect something
	     * could be better.
	     */
	    if (nl_n != nj) {
	      warncount++;
	      if(warncount<11 && fp) 
 	        fprintf(fp,"The order in molecule %d could be optimized"
		        " for better performance\n",i);
	      if(warncount==10 && fp)
              fprintf(fp,"(More than 10 molecules where the order can be optimized)\n");
	    }
	    nl_m = nl_n = nl_o = nj;
	  }
	  fr->mno_index[cgid[aj]*3]   = nl_m;
	  fr->mno_index[cgid[aj]*3+1] = nl_n;
	  fr->mno_index[cgid[aj]*3+2] = nl_o;
	  fr->solvent_type[cgid[aj]]  = esolMNO;
#endif /* MNO solvent if not using altivec */
	}

	/* Last check for perturbed atoms */
	for(j=j0; (j<j1); j++)
	  if (md->bPerturbed[mols->a[j]])
	    fr->solvent_type[cgid[mols->a[j0]]] = esolNO;
	
	sfree(bHaveLJ);
	sfree(bHaveCoul);
      }
      else {
	/* Turn off solvent optimization for all cg's in the molecule,
	 * here there is only one.
	 */
	fr->solvent_type[cgid[mols->a[j0]]] = esolNO;
      }
      sfree(bAllExcl);
    }
    else {
      /* Turn off solvent optimization for all cg's in the molecule */
      for(j=mols->index[i]; (j<mols->index[i+1]); j++) {
	fr->solvent_type[cgid[mols->a[j]]] = esolNO;
      }
    }
  }
  if (debug) {
    for(i=0; (i<cgs->nr); i++) 
      fprintf(debug,"MNO: cg = %5d, m = %2d, n = %2d, o = %2d\n",
	      i,fr->mno_index[3*i],fr->mno_index[3*i+1],fr->mno_index[3*i+2]);
  }

  /* Now compute the number of solvent molecules, could be merged with code above */
  fr->nMNOMol = 0;
  fr->nWatMol = 0;
  for(m=0; m<3; m++)
    fr->nMNOav[m] = 0;
  for(i=0; i<mols->nr; i++) {
    j = mols->a[mols->index[i]];
    if (j>=START(nsb) && j<START(nsb)+HOMENR(nsb)) {
	if (fr->solvent_type[cgid[j]] == esolMNO) {
	  fr->nMNOMol++;
	  for(m=0; m<3; m++)
	    fr->nMNOav[m] += fr->mno_index[3*cgid[j]+m];
	}
	else if (fr->solvent_type[cgid[j]] == esolWATER)
	  fr->nWatMol++;
    }
  }
  if (fr->nMNOMol > 0)
    for(m=0; (m<3); m++)
      fr->nMNOav[m] /= fr->nMNOMol;
  
  sfree(cgid);

  if (fp) {
    fprintf(fp,"There are %d optimized solvent molecules on node %d\n",
	    fr->nMNOMol,nsb->nodeid);
    if (fr->nMNOMol > 0)
      fprintf(fp,"  aver. nr. of atoms per molecule: vdwc %.1f coul %.1f vdw %.1f\n",
	      fr->nMNOav[1],fr->nMNOav[2]-fr->nMNOav[1],fr->nMNOav[0]-fr->nMNOav[2]);
    fprintf(fp,"There are %d optimized water molecules on node %d\n",
	    fr->nWatMol,nsb->nodeid);
  }
}