OpenMM: added combination rule check, disabled restraint check for now as it's buggy

[gromacs/qmmm-gamess-us.git] / src / kernel / vsite_parm.c

/*
 * 
 *                This source code is part of
 * 
 *                 G   R   O   M   A   C   S
 * 
 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.2.0
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team,
 * check out http://www.gromacs.org for more information.

 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
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 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdio.h>
#include <math.h>
#include <string.h>
#include "vsite_parm.h"
#include "smalloc.h"
#include "resall.h"
#include "add_par.h"
#include "vec.h"
#include "toputil.h"
#include "physics.h"
#include "index.h"
#include "names.h"
#include "gmx_fatal.h"
#include "string2.h"
#include "physics.h"

typedef struct {
  t_iatom a[4];
  real    c;
} t_mybonded;

typedef struct {
  int     ftype;
  t_param *param;
} vsitebondparam_t;

typedef struct {
  int              nr;
  int              ftype;
  vsitebondparam_t *vsbp;
} at2vsitebond_t;

typedef struct {
  int nr;
  int *aj;
} at2vsitecon_t;

static int vsite_bond_nrcheck(int ftype)
{
  int nrcheck;
  
  if ((interaction_function[ftype].flags & (IF_BTYPE | IF_CONSTRAINT | IF_ATYPE)) || (ftype == F_IDIHS))
    nrcheck = NRAL(ftype);
  else
    nrcheck = 0;
  
  return nrcheck;
}

static void enter_bonded(int nratoms, int *nrbonded, t_mybonded **bondeds, 
                         t_param *param)
{
  int j;

  srenew(*bondeds, *nrbonded+1);
  
  /* copy atom numbers */
  for(j=0; j<nratoms; j++)
    (*bondeds)[*nrbonded].a[j] = param->a[j];
  /* copy parameter */
  (*bondeds)[*nrbonded].c = param->C0;
  
  (*nrbonded)++;
}

static void get_bondeds(int nrat, t_iatom atoms[],
                        at2vsitebond_t *at2vb, t_params plist[],
                        int *nrbond, t_mybonded **bonds,
                        int *nrang,  t_mybonded **angles,
                        int *nridih, t_mybonded **idihs )
{
  int     k,i,ftype,nrcheck;
  t_param *param;
  
  for(k=0; k<nrat; k++) {
    for(i=0; i<at2vb[atoms[k]].nr; i++) {
      ftype = at2vb[atoms[k]].vsbp[i].ftype;
      param = at2vb[atoms[k]].vsbp[i].param;
      nrcheck = vsite_bond_nrcheck(ftype);
      /* abuse nrcheck to see if we're adding bond, angle or idih */
      switch (nrcheck) {
      case 2: enter_bonded(nrcheck,nrbond,bonds, param); break;
      case 3: enter_bonded(nrcheck,nrang, angles,param); break;
      case 4: enter_bonded(nrcheck,nridih,idihs, param); break;
      }
    }
  }
}

static at2vsitebond_t *make_at2vsitebond(int natoms,t_params plist[])
{
  bool *bVSI;
  int  ftype,i,j,nrcheck,nr;
  t_iatom *aa;
  at2vsitebond_t *at2vb;

  snew(at2vb,natoms);

  snew(bVSI,natoms);
  for(ftype=0; (ftype<F_NRE); ftype++) {
    if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN) {
      for(i=0; (i<plist[ftype].nr); i++) {
        for(j=0; j<NRAL(ftype); j++)
          bVSI[plist[ftype].param[i].a[j]] = TRUE;
      }
    }
  }
  
  for(ftype=0; (ftype<F_NRE); ftype++) {
    nrcheck = vsite_bond_nrcheck(ftype);
    if (nrcheck > 0) {
      for(i=0; (i<plist[ftype].nr); i++) {
        aa = plist[ftype].param[i].a;
        for(j=0; j<nrcheck; j++) {
          if (bVSI[aa[j]]) {
            nr = at2vb[aa[j]].nr;
            if (nr % 10 == 0)
              srenew(at2vb[aa[j]].vsbp,nr+10);
            at2vb[aa[j]].vsbp[nr].ftype = ftype;
            at2vb[aa[j]].vsbp[nr].param = &plist[ftype].param[i];
            at2vb[aa[j]].nr++;
          }
        }
      }
    }
  }
  sfree(bVSI);

  return at2vb;
}

static void done_at2vsitebond(int natoms,at2vsitebond_t *at2vb)
{
  int i;

  for(i=0; i<natoms; i++)
    if (at2vb[i].nr)
      sfree(at2vb[i].vsbp);
  sfree(at2vb);
}

static at2vsitecon_t *make_at2vsitecon(int natoms,t_params plist[])
{
  bool *bVSI;
  int  ftype,i,j,ai,aj,nr;
  at2vsitecon_t *at2vc;

  snew(at2vc,natoms);

  snew(bVSI,natoms);
  for(ftype=0; (ftype<F_NRE); ftype++) {
    if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN) {
      for(i=0; (i<plist[ftype].nr); i++) {
        for(j=0; j<NRAL(ftype); j++)
          bVSI[plist[ftype].param[i].a[j]] = TRUE;
      }
    }
  }
  
  for(ftype=0; (ftype<F_NRE); ftype++) {
    if (interaction_function[ftype].flags & IF_CONSTRAINT) {
      for(i=0; (i<plist[ftype].nr); i++) {
        ai = plist[ftype].param[i].AI;
        aj = plist[ftype].param[i].AJ;
        if (bVSI[ai] && bVSI[aj]) {
          /* Store forward direction */
          nr = at2vc[ai].nr;
          if (nr % 10 == 0)
            srenew(at2vc[ai].aj,nr+10);
          at2vc[ai].aj[nr] = aj;
          at2vc[ai].nr++;
          /* Store backward direction */
          nr = at2vc[aj].nr;
          if (nr % 10 == 0)
            srenew(at2vc[aj].aj,nr+10);
          at2vc[aj].aj[nr] = ai;
          at2vc[aj].nr++;
        }
      }
    }
  }
  sfree(bVSI);

  return at2vc;
}

static void done_at2vsitecon(int natoms,at2vsitecon_t *at2vc)
{
  int i;

  for(i=0; i<natoms; i++)
    if (at2vc[i].nr)
      sfree(at2vc[i].aj);
  sfree(at2vc);
}

/* for debug */
static void print_bad(FILE *fp, 
                      int nrbond, t_mybonded *bonds,
                      int nrang,  t_mybonded *angles,
                      int nridih, t_mybonded *idihs )
{
  int i;
  
  if (nrbond) {
    fprintf(fp,"bonds:");
    for(i=0; i<nrbond; i++)
      fprintf(fp," %u-%u (%g)", 
              bonds[i].AI+1, bonds[i].AJ+1, bonds[i].c);
    fprintf(fp,"\n");
  }
  if (nrang) {
    fprintf(fp,"angles:");
    for(i=0; i<nrang; i++)
      fprintf(fp," %u-%u-%u (%g)", 
              angles[i].AI+1, angles[i].AJ+1, 
              angles[i].AK+1, angles[i].c);
    fprintf(fp,"\n");
  }
  if (nridih) {
    fprintf(fp,"idihs:");
    for(i=0; i<nridih; i++)
      fprintf(fp," %u-%u-%u-%u (%g)", 
              idihs[i].AI+1, idihs[i].AJ+1, 
              idihs[i].AK+1, idihs[i].AL+1, idihs[i].c);
    fprintf(fp,"\n");
  }
}

static void print_param(FILE *fp, int ftype, int i, t_param *param)
{
  static int pass = 0;
  static int prev_ftype= NOTSET;
  static int prev_i    = NOTSET;
  int j;
  
  if ( (ftype!=prev_ftype) || (i!=prev_i) ) {
    pass = 0;
    prev_ftype= ftype;
    prev_i    = i;
  }
  fprintf(fp,"(%d) plist[%s].param[%d]",
          pass,interaction_function[ftype].name,i);
  for(j=0; j<NRFP(ftype); j++)
    fprintf(fp,".c[%d]=%g ",j,param->c[j]);
  fprintf(fp,"\n");
  pass++;
}

static real get_bond_length(int nrbond, t_mybonded bonds[], 
                            t_iatom ai, t_iatom aj)
{
  int  i;
  real bondlen;
  
  bondlen=NOTSET;
  for (i=0; i < nrbond && (bondlen==NOTSET); i++) {
    /* check both ways */
    if ( ( (ai == bonds[i].AI) && (aj == bonds[i].AJ) ) || 
         ( (ai == bonds[i].AJ) && (aj == bonds[i].AI) ) )
      bondlen = bonds[i].c; /* note: bonds[i].c might be NOTSET */
  }
  return bondlen;
}

static real get_angle(int nrang, t_mybonded angles[], 
                      t_iatom ai, t_iatom aj, t_iatom ak)
{
  int  i;
  real angle;
  
  angle=NOTSET;
  for (i=0; i < nrang && (angle==NOTSET); i++) {
    /* check both ways */
    if ( ( (ai==angles[i].AI) && (aj==angles[i].AJ) && (ak==angles[i].AK) ) || 
         ( (ai==angles[i].AK) && (aj==angles[i].AJ) && (ak==angles[i].AI) ) )
      angle = DEG2RAD*angles[i].c;
  }
  return angle;
}

static bool calc_vsite3_param(gpp_atomtype_t atype,
                              t_param *param, t_atoms *at,
                              int nrbond, t_mybonded *bonds,
                              int nrang,  t_mybonded *angles )
{
  /* i = virtual site          |    ,k
   * j = 1st bonded heavy atom | i-j
   * k,l = 2nd bonded atoms    |    `l
   */
  
  bool bXH3,bError;
  real bjk,bjl,a=-1,b=-1;
  /* check if this is part of a NH3 , NH2-umbrella or CH3 group,
   * i.e. if atom k and l are dummy masses (MNH* or MCH3*) */
  if (debug) {
    int i;
    for (i=0; i<4; i++)
      fprintf(debug,"atom %u type %s ",
              param->a[i]+1,
              get_atomtype_name(at->atom[param->a[i]].type,atype));
    fprintf(debug,"\n");
  }
  bXH3 = 
    ( (strncasecmp(get_atomtype_name(at->atom[param->AK].type,atype),"MNH",3)==0) &&
      (strncasecmp(get_atomtype_name(at->atom[param->AL].type,atype),"MNH",3)==0) ) ||
    ( (strncasecmp(get_atomtype_name(at->atom[param->AK].type,atype),"MCH3",4)==0) &&
      (strncasecmp(get_atomtype_name(at->atom[param->AL].type,atype),"MCH3",4)==0) );
  
  bjk = get_bond_length(nrbond, bonds, param->AJ, param->AK);
  bjl = get_bond_length(nrbond, bonds, param->AJ, param->AL);
  bError = (bjk==NOTSET) || (bjl==NOTSET);
  if (bXH3) {
    /* now we get some XH2/XH3 group specific construction */
    /* note: we call the heavy atom 'C' and the X atom 'N' */
    real bMM,bCM,bCN,bNH,aCNH,dH,rH,dM,rM;
    int aN;
    
    /* check if bonds from heavy atom (j) to dummy masses (k,l) are equal: */
    bError = bError || (bjk!=bjl);
    
    /* the X atom (C or N) in the XH2/XH3 group is the first after the masses: */
    aN = max(param->AK,param->AL)+1;
    
    /* get common bonds */
    bMM = get_bond_length(nrbond, bonds, param->AK, param->AL);
    bCM = bjk;
    bCN = get_bond_length(nrbond, bonds, param->AJ, aN);
    bError = bError || (bMM==NOTSET) || (bCN==NOTSET);
    
    /* calculate common things */
    rM  = 0.5*bMM;
    dM  = sqrt( sqr(bCM) - sqr(rM) );
    
    /* are we dealing with the X atom? */
    if ( param->AI == aN ) {
      /* this is trivial */
      a = b = 0.5 * bCN/dM;
      
    } else {
      /* get other bondlengths and angles: */
      bNH = get_bond_length(nrbond, bonds, aN, param->AI);
      aCNH= get_angle      (nrang, angles, param->AJ, aN, param->AI);
      bError = bError || (bNH==NOTSET) || (aCNH==NOTSET);
      
      /* calculate */
      dH  = bCN - bNH * cos(aCNH);
      rH  = bNH * sin(aCNH);
      
      a = 0.5 * ( dH/dM + rH/rM );
      b = 0.5 * ( dH/dM - rH/rM );
    }
  } else
    gmx_fatal(FARGS,"calc_vsite3_param not implemented for the general case "
                "(atom %d)",param->AI+1);
  
  param->C0 = a;
  param->C1 = b;
  
  if (debug)
    fprintf(debug,"params for vsite3 %u: %g %g\n",
            param->AI+1,param->C0,param->C1);
  
  return bError;
}

static bool calc_vsite3fd_param(t_param *param,
                                int nrbond, t_mybonded *bonds,
                                int nrang,  t_mybonded *angles)
{
  /* i = virtual site          |    ,k
   * j = 1st bonded heavy atom | i-j
   * k,l = 2nd bonded atoms    |    `l
   */

  bool bError;
  real bij,bjk,bjl,aijk,aijl,rk,rl;
  
  bij = get_bond_length(nrbond, bonds, param->AI, param->AJ);
  bjk = get_bond_length(nrbond, bonds, param->AJ, param->AK);
  bjl = get_bond_length(nrbond, bonds, param->AJ, param->AL);
  aijk= get_angle      (nrang, angles, param->AI, param->AJ, param->AK);
  aijl= get_angle      (nrang, angles, param->AI, param->AJ, param->AL);
  bError = (bij==NOTSET) || (bjk==NOTSET) || (bjl==NOTSET) || 
    (aijk==NOTSET) || (aijl==NOTSET);
  
  rk = bjk * sin(aijk);
  rl = bjl * sin(aijl);
  param->C0 = rk / (rk + rl);
  param->C1 = -bij; /* 'bond'-length for fixed distance vsite */
  
  if (debug)
    fprintf(debug,"params for vsite3fd %u: %g %g\n",
            param->AI+1,param->C0,param->C1);
  return bError;
}

static bool calc_vsite3fad_param(t_param *param,
                                 int nrbond, t_mybonded *bonds,
                                 int nrang,  t_mybonded *angles)
{
  /* i = virtual site          |
   * j = 1st bonded heavy atom | i-j
   * k = 2nd bonded heavy atom |    `k-l
   * l = 3d bonded heavy atom  |
   */

  bool bSwapParity,bError;
  real bij,aijk;
  
  bSwapParity = ( param->C1 == -1 );
  
  bij  = get_bond_length(nrbond, bonds, param->AI, param->AJ);
  aijk = get_angle      (nrang, angles, param->AI, param->AJ, param->AK);
  bError = (bij==NOTSET) || (aijk==NOTSET);
  
  param->C1 = bij;          /* 'bond'-length for fixed distance vsite */
  param->C0 = RAD2DEG*aijk; /* 'bond'-angle for fixed angle vsite */
  
  if (bSwapParity)
    param->C0 = 360 - param->C0;
  
  if (debug)
    fprintf(debug,"params for vsite3fad %u: %g %g\n",
            param->AI+1,param->C0,param->C1);
  return bError;
}

static bool calc_vsite3out_param(gpp_atomtype_t atype,
                                 t_param *param, t_atoms *at,
                                 int nrbond, t_mybonded *bonds,
                                 int nrang,  t_mybonded *angles)
{
  /* i = virtual site          |    ,k
   * j = 1st bonded heavy atom | i-j
   * k,l = 2nd bonded atoms    |    `l
   * NOTE: i is out of the j-k-l plane!
   */
  
  bool bXH3,bError,bSwapParity;
  real bij,bjk,bjl,aijk,aijl,akjl,pijk,pijl,a,b,c;
  
  /* check if this is part of a NH2-umbrella, NH3 or CH3 group,
   * i.e. if atom k and l are dummy masses (MNH* or MCH3*) */
  if (debug) {
    int i;
    for (i=0; i<4; i++)
      fprintf(debug,"atom %u type %s ",
              param->a[i]+1,get_atomtype_name(at->atom[param->a[i]].type,atype));
    fprintf(debug,"\n");
  }
  bXH3 = 
    ( (strncasecmp(get_atomtype_name(at->atom[param->AK].type,atype),"MNH",3)==0) &&
      (strncasecmp(get_atomtype_name(at->atom[param->AL].type,atype),"MNH",3)==0) ) ||
    ( (strncasecmp(get_atomtype_name(at->atom[param->AK].type,atype),"MCH3",4)==0) &&
      (strncasecmp(get_atomtype_name(at->atom[param->AL].type,atype),"MCH3",4)==0) );
  
  /* check if construction parity must be swapped */  
  bSwapParity = ( param->C1 == -1 );
  
  bjk = get_bond_length(nrbond, bonds, param->AJ, param->AK);
  bjl = get_bond_length(nrbond, bonds, param->AJ, param->AL);
  bError = (bjk==NOTSET) || (bjl==NOTSET);
  if (bXH3) {
    /* now we get some XH3 group specific construction */
    /* note: we call the heavy atom 'C' and the X atom 'N' */
    real bMM,bCM,bCN,bNH,aCNH,dH,rH,rHx,rHy,dM,rM;
    int aN;
    
    /* check if bonds from heavy atom (j) to dummy masses (k,l) are equal: */
    bError = bError || (bjk!=bjl);
    
    /* the X atom (C or N) in the XH3 group is the first after the masses: */
    aN = max(param->AK,param->AL)+1;
    
    /* get all bondlengths and angles: */
    bMM = get_bond_length(nrbond, bonds, param->AK, param->AL);
    bCM = bjk;
    bCN = get_bond_length(nrbond, bonds, param->AJ, aN);
    bNH = get_bond_length(nrbond, bonds, aN, param->AI);
    aCNH= get_angle      (nrang, angles, param->AJ, aN, param->AI);
    bError = bError || 
      (bMM==NOTSET) || (bCN==NOTSET) || (bNH==NOTSET) || (aCNH==NOTSET);
    
    /* calculate */
    dH  = bCN - bNH * cos(aCNH);
    rH  = bNH * sin(aCNH);
    /* we assume the H's are symmetrically distributed */
    rHx = rH*cos(DEG2RAD*30);
    rHy = rH*sin(DEG2RAD*30);
    rM  = 0.5*bMM;
    dM  = sqrt( sqr(bCM) - sqr(rM) );
    a   = 0.5*( (dH/dM) - (rHy/rM) );
    b   = 0.5*( (dH/dM) + (rHy/rM) );
    c   = rHx / (2*dM*rM);
    
  } else {
    /* this is the general construction */
    
    bij = get_bond_length(nrbond, bonds, param->AI, param->AJ);
    aijk= get_angle      (nrang, angles, param->AI, param->AJ, param->AK);
    aijl= get_angle      (nrang, angles, param->AI, param->AJ, param->AL);
    akjl= get_angle      (nrang, angles, param->AK, param->AJ, param->AL);
    bError = bError || 
      (bij==NOTSET) || (aijk==NOTSET) || (aijl==NOTSET) || (akjl==NOTSET);
  
    pijk = cos(aijk)*bij;
    pijl = cos(aijl)*bij;
    a = ( pijk + (pijk*cos(akjl)-pijl) * cos(akjl) / sqr(sin(akjl)) ) / bjk;
    b = ( pijl + (pijl*cos(akjl)-pijk) * cos(akjl) / sqr(sin(akjl)) ) / bjl;
    c = - sqrt( sqr(bij) - 
                ( sqr(pijk) - 2*pijk*pijl*cos(akjl) + sqr(pijl) ) 
                / sqr(sin(akjl)) )
      / ( bjk*bjl*sin(akjl) );
  }
  
  param->C0 = a;
  param->C1 = b;
  if (bSwapParity)
    param->C2 = -c;
  else
    param->C2 =  c;
  if (debug)
    fprintf(debug,"params for vsite3out %u: %g %g %g\n",
            param->AI+1,param->C0,param->C1,param->C2);
  return bError;
}

static bool calc_vsite4fd_param(t_param *param,
                                int nrbond, t_mybonded *bonds,
                                int nrang,  t_mybonded *angles)
{
  /* i = virtual site          |    ,k
   * j = 1st bonded heavy atom | i-j-m
   * k,l,m = 2nd bonded atoms  |    `l
   */
  
  bool bError;
  real bij,bjk,bjl,bjm,aijk,aijl,aijm,akjm,akjl;
  real pk,pl,pm,cosakl,cosakm,sinakl,sinakm,cl,cm;
  
  bij = get_bond_length(nrbond, bonds, param->AI, param->AJ);
  bjk = get_bond_length(nrbond, bonds, param->AJ, param->AK);
  bjl = get_bond_length(nrbond, bonds, param->AJ, param->AL);
  bjm = get_bond_length(nrbond, bonds, param->AJ, param->AM);
  aijk= get_angle      (nrang, angles, param->AI, param->AJ, param->AK);
  aijl= get_angle      (nrang, angles, param->AI, param->AJ, param->AL);
  aijm= get_angle      (nrang, angles, param->AI, param->AJ, param->AM);
  akjm= get_angle      (nrang, angles, param->AK, param->AJ, param->AM);
  akjl= get_angle      (nrang, angles, param->AK, param->AJ, param->AL);
  bError = (bij==NOTSET) || (bjk==NOTSET) || (bjl==NOTSET) || (bjm==NOTSET) ||
    (aijk==NOTSET) || (aijl==NOTSET) || (aijm==NOTSET) || (akjm==NOTSET) || 
    (akjl==NOTSET);
  
  if (!bError) {
    pk = bjk*sin(aijk);
    pl = bjl*sin(aijl);
    pm = bjm*sin(aijm);
    cosakl = (cos(akjl) - cos(aijk)*cos(aijl)) / (sin(aijk)*sin(aijl));
    cosakm = (cos(akjm) - cos(aijk)*cos(aijm)) / (sin(aijk)*sin(aijm));
    if ( cosakl < -1 || cosakl > 1 || cosakm < -1 || cosakm > 1 ) {
      fprintf(stderr,"virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f\n",
              param->AI+1,RAD2DEG*aijk,RAD2DEG*aijl,RAD2DEG*aijm);
      gmx_fatal(FARGS,"invalid construction in calc_vsite4fd for atom %d: "
                  "cosakl=%f, cosakm=%f\n",param->AI+1,cosakl,cosakm);
    }
    sinakl = sqrt(1-sqr(cosakl));
    sinakm = sqrt(1-sqr(cosakm));
    
    /* note: there is a '+' because of the way the sines are calculated */
    cl = -pk / ( pl*cosakl - pk + pl*sinakl*(pm*cosakm-pk)/(pm*sinakm) );
    cm = -pk / ( pm*cosakm - pk + pm*sinakm*(pl*cosakl-pk)/(pl*sinakl) );
    
    param->C0 = cl;
    param->C1 = cm;
    param->C2 = -bij;
    if (debug)
      fprintf(debug,"params for vsite4fd %u: %g %g %g\n",
              param->AI+1,param->C0,param->C1,param->C2);
  }
  
  return bError;
}


static bool 
calc_vsite4fdn_param(t_param *param,
                     int nrbond, t_mybonded *bonds,
                     int nrang,  t_mybonded *angles)
{
    /* i = virtual site          |    ,k
    * j = 1st bonded heavy atom | i-j-m
    * k,l,m = 2nd bonded atoms  |    `l
    */
    
    bool bError;
    real bij,bjk,bjl,bjm,aijk,aijl,aijm;
    real pk,pl,pm,a,b;
    
    bij = get_bond_length(nrbond, bonds, param->AI, param->AJ);
    bjk = get_bond_length(nrbond, bonds, param->AJ, param->AK);
    bjl = get_bond_length(nrbond, bonds, param->AJ, param->AL);
    bjm = get_bond_length(nrbond, bonds, param->AJ, param->AM);
    aijk= get_angle      (nrang, angles, param->AI, param->AJ, param->AK);
    aijl= get_angle      (nrang, angles, param->AI, param->AJ, param->AL);
    aijm= get_angle      (nrang, angles, param->AI, param->AJ, param->AM);

    bError = (bij==NOTSET) || (bjk==NOTSET) || (bjl==NOTSET) || (bjm==NOTSET) ||
        (aijk==NOTSET) || (aijl==NOTSET) || (aijm==NOTSET);
    
    if (!bError) {
        
        /* Calculate component of bond j-k along the direction i-j */
        pk = -bjk*cos(aijk);

        /* Calculate component of bond j-l along the direction i-j */
        pl = -bjl*cos(aijl);

        /* Calculate component of bond j-m along the direction i-j */
        pm = -bjm*cos(aijm);
        
        if(fabs(pl)<1000*GMX_REAL_MIN || fabs(pm)<1000*GMX_REAL_MIN)
        {
            fprintf(stderr,"virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f\n",
                    param->AI+1,RAD2DEG*aijk,RAD2DEG*aijl,RAD2DEG*aijm);
            gmx_fatal(FARGS,"invalid construction in calc_vsite4fdn for atom %d: "
                      "pl=%f, pm=%f\n",param->AI+1,pl,pm);
        }
        
        a = pk/pl;
        b = pk/pm;
          
        param->C0 = a;
        param->C1 = b;
        param->C2 = bij;
        
        if (debug)
            fprintf(debug,"params for vsite4fdn %u: %g %g %g\n",
                    param->AI+1,param->C0,param->C1,param->C2);
    }
    
    return bError;
}



int set_vsites(bool bVerbose, t_atoms *atoms, gpp_atomtype_t atype,
                t_params plist[])
{
  int i,j,ftype;
  int nvsite,nrbond,nrang,nridih,nrset;
  bool bFirst,bSet,bERROR;
  at2vsitebond_t *at2vb;
  t_mybonded *bonds;
  t_mybonded *angles;
  t_mybonded *idihs;
  
  bFirst = TRUE;
  bERROR = TRUE;
  nvsite=0;
  if (debug)
    fprintf(debug, "\nCalculating parameters for virtual sites\n");

  /* Make a reverse list to avoid ninteractions^2 operations */
  at2vb = make_at2vsitebond(atoms->nr,plist);

  for(ftype=0; (ftype<F_NRE); ftype++)
    if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN) {
      nrset=0;
      nvsite+=plist[ftype].nr;
      for(i=0; (i<plist[ftype].nr); i++) {
        /* check if all parameters are set */
        bSet=TRUE;
        for(j=0; j<NRFP(ftype) && bSet; j++)
          bSet = plist[ftype].param[i].c[j]!=NOTSET;

        if (debug) {
          fprintf(debug,"bSet=%s ",bool_names[bSet]);
          print_param(debug,ftype,i,&plist[ftype].param[i]);
        }
        if (!bSet) {
          if (bVerbose && bFirst) {
            fprintf(stderr,"Calculating parameters for virtual sites\n");
            bFirst=FALSE;
          }
          
          nrbond=nrang=nridih=0;
          bonds = NULL;
          angles= NULL;
          idihs = NULL;
          nrset++;
          /* now set the vsite parameters: */
          get_bondeds(NRAL(ftype), plist[ftype].param[i].a, at2vb, plist, 
                      &nrbond, &bonds, &nrang,  &angles, &nridih, &idihs);
          if (debug) {
            fprintf(debug, "Found %d bonds, %d angles and %d idihs "
                    "for virtual site %u (%s)\n",nrbond,nrang,nridih,
                    plist[ftype].param[i].AI+1,
                    interaction_function[ftype].longname);
            print_bad(debug, nrbond, bonds, nrang, angles, nridih, idihs);
          } /* debug */
          switch(ftype) {
          case F_VSITE3: 
            bERROR = 
              calc_vsite3_param(atype, &(plist[ftype].param[i]), atoms,
                                nrbond, bonds, nrang, angles);
            break;
          case F_VSITE3FD:
            bERROR = 
              calc_vsite3fd_param(&(plist[ftype].param[i]),
                                  nrbond, bonds, nrang, angles);
            break;
          case F_VSITE3FAD:
            bERROR = 
              calc_vsite3fad_param(&(plist[ftype].param[i]),
                                   nrbond, bonds, nrang, angles);
            break;
          case F_VSITE3OUT:
            bERROR = 
              calc_vsite3out_param(atype, &(plist[ftype].param[i]), atoms,
                                   nrbond, bonds, nrang, angles);
            break;
          case F_VSITE4FD:
            bERROR = 
              calc_vsite4fd_param(&(plist[ftype].param[i]), 
                                  nrbond, bonds, nrang, angles);
            break;
          case F_VSITE4FDN:
          bERROR = 
              calc_vsite4fdn_param(&(plist[ftype].param[i]), 
                               nrbond, bonds, nrang, angles);
          break;
          default:
            gmx_fatal(FARGS,"Automatic parameter generation not supported "
                        "for %s atom %d",
                        interaction_function[ftype].longname,
                        plist[ftype].param[i].AI+1);
          } /* switch */
          if (bERROR)
            gmx_fatal(FARGS,"Automatic parameter generation not supported "
                        "for %s atom %d for this bonding configuration",
                        interaction_function[ftype].longname,
                        plist[ftype].param[i].AI+1);
          sfree(bonds);
          sfree(angles);
          sfree(idihs);
        } /* if bSet */
      } /* for i */
      if (debug && plist[ftype].nr)
        fprintf(stderr,"Calculated parameters for %d out of %d %s atoms\n",
                nrset,plist[ftype].nr,interaction_function[ftype].longname);
    } /* if IF_VSITE */

  done_at2vsitebond(atoms->nr,at2vb);
  
  return nvsite;
}

void set_vsites_ptype(bool bVerbose, gmx_moltype_t *molt)
{
  int ftype,i;
  int nra,nrd;
  t_ilist *il;
  t_iatom *ia,avsite;
  
  if (bVerbose)
    fprintf(stderr,"Setting particle type to V for virtual sites\n");
  if (debug)
    fprintf(stderr,"checking %d functypes\n",F_NRE);
  for(ftype=0; ftype<F_NRE; ftype++) {
    il = &molt->ilist[ftype];
    if (interaction_function[ftype].flags & IF_VSITE) {
      nra    = interaction_function[ftype].nratoms;
      nrd    = il->nr;
      ia     = il->iatoms;
      
      if (debug && nrd)
        fprintf(stderr,"doing %d %s virtual sites\n",
                (nrd / (nra+1)),interaction_function[ftype].longname);
      
      for(i=0; (i<nrd); ) {
        /* The virtual site */
        avsite = ia[1];
        molt->atoms.atom[avsite].ptype = eptVSite;
        
        i  += nra+1;
        ia += nra+1;
      }
    }
  }
  
}

typedef struct { 
  int ftype,parnr;
} t_pindex;

static void check_vsite_constraints(t_params *plist, 
                                    int cftype, int vsite_type[])
{
  int      i,k,n;
  atom_id  atom;
  t_params *ps;
  
  n=0;
  ps = &(plist[cftype]);
  for(i=0; (i<ps->nr); i++)
    for(k=0; k<2; k++) {
      atom = ps->param[i].a[k];
      if (vsite_type[atom]!=NOTSET) {
        fprintf(stderr,"ERROR: Cannot have constraint (%u-%u) with virtual site (%u)\n",
                ps->param[i].AI+1, ps->param[i].AJ+1, atom+1);
        n++;
      }
    }
  if (n)
    gmx_fatal(FARGS,"There were %d virtual sites involved in constraints",n);
}

static void clean_vsite_bonds(t_params *plist, t_pindex pindex[], 
                            int cftype, int vsite_type[])
{
  int      ftype,i,j,parnr,k,l,m,n,nvsite,nOut,kept_i,vsnral,vsitetype;
  int      nconverted,nremoved;
  atom_id  atom,oatom,constr,at1,at2;
  atom_id  vsiteatoms[MAXATOMLIST];
  bool     bKeep,bRemove,bUsed,bPresent,bThisFD,bThisOUT,bAllFD,bFirstTwo;
  t_params *ps;

  if (cftype == F_CONNBONDS)
    return;
  
  ps = &(plist[cftype]);
  vsnral=0;
  kept_i=0;
  nconverted=0;
  nremoved=0;
  nOut=0;
  for(i=0; (i<ps->nr); i++) { /* for all bonds in the plist */
    bKeep=FALSE;
    bRemove=FALSE;
    bAllFD=TRUE;
    /* check if all virtual sites are constructed from the same atoms */
    nvsite=0;
    if(debug) 
      fprintf(debug,"constr %u %u:",ps->param[i].AI+1,ps->param[i].AJ+1);
    for(k=0; (k<2) && !bKeep && !bRemove; k++) { 
      /* for all atoms in the bond */
      atom = ps->param[i].a[k];
      if (vsite_type[atom]!=NOTSET) {
        if(debug) {
          fprintf(debug," d%d[%d: %d %d %d]",k,atom+1,
                  plist[pindex[atom].ftype].param[pindex[atom].parnr].AJ+1,
                  plist[pindex[atom].ftype].param[pindex[atom].parnr].AK+1,
                  plist[pindex[atom].ftype].param[pindex[atom].parnr].AL+1);
        }
        nvsite++;
        bThisFD = ( (pindex[atom].ftype == F_VSITE3FD ) ||
                (pindex[atom].ftype == F_VSITE3FAD) ||
                (pindex[atom].ftype == F_VSITE4FD ) ||
                (pindex[atom].ftype == F_VSITE4FDN ) );
        bThisOUT= ( (pindex[atom].ftype == F_VSITE3OUT) &&
                    (interaction_function[cftype].flags & IF_CONSTRAINT) );
        bAllFD = bAllFD && bThisFD;
        if (bThisFD || bThisOUT) {
          if(debug)fprintf(debug," %s",bThisOUT?"out":"fd");
          oatom = ps->param[i].a[1-k]; /* the other atom */
          if ( vsite_type[oatom]==NOTSET &&
               oatom==plist[pindex[atom].ftype].param[pindex[atom].parnr].AJ ){
            /* if the other atom isn't a vsite, and it is AI */
            bRemove=TRUE;
            if (bThisOUT)
              nOut++;
            if(debug)fprintf(debug," D-AI");
          }
        }
        if (!bRemove) {
          if (nvsite==1) {
            /* if this is the first vsite we encounter then
               store construction atoms */
            vsnral=NRAL(pindex[atom].ftype)-1;
            for(m=0; (m<vsnral); m++)
              vsiteatoms[m]=
                plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
          } else {
            /* if it is not the first then
               check if this vsite is constructed from the same atoms */
            if (vsnral == NRAL(pindex[atom].ftype)-1 )
              for(m=0; (m<vsnral) && !bKeep; m++) {
                bPresent=FALSE;
                constr=
                  plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
                for(n=0; (n<vsnral) && !bPresent; n++)
                  if (constr == vsiteatoms[n])
                    bPresent=TRUE;
                if (!bPresent) {
                  bKeep=TRUE;
                  if(debug)fprintf(debug," !present");
                }
              }
            else {
              bKeep=TRUE;
              if(debug)fprintf(debug," !same#at");
            }
          }
        }
      }
    }
    
    if (bRemove) 
      bKeep=FALSE;
    else {
      /* if we have no virtual sites in this bond, keep it */
      if (nvsite==0) {
        if (debug)fprintf(debug," no vsite");
        bKeep=TRUE;
      }
    
      /* check if all non-vsite atoms are used in construction: */
      bFirstTwo=TRUE;
      for(k=0; (k<2) && !bKeep; k++) { /* for all atoms in the bond */
        atom = ps->param[i].a[k];
        if (vsite_type[atom]==NOTSET) {
          bUsed=FALSE;
          for(m=0; (m<vsnral) && !bUsed; m++)
            if (atom == vsiteatoms[m]) {
              bUsed=TRUE;
              bFirstTwo = bFirstTwo && m<2;
            }
          if (!bUsed) {
            bKeep=TRUE;
            if(debug)fprintf(debug," !used");
          }
        }
      }
      
      if ( ! ( bAllFD && bFirstTwo ) )
        /* check if all constructing atoms are constrained together */
        for (m=0; m<vsnral && !bKeep; m++) { /* all constr. atoms */
          at1 = vsiteatoms[m];
          at2 = vsiteatoms[(m+1) % vsnral];
          bPresent=FALSE;
          for (ftype=0; ftype<F_NRE; ftype++)
            if ( interaction_function[ftype].flags & IF_CONSTRAINT )
              for (j=0; (j<plist[ftype].nr) && !bPresent; j++)
                /* all constraints until one matches */
                bPresent = ( ( (plist[ftype].param[j].AI == at1) &&
                               (plist[ftype].param[j].AJ == at2) ) || 
                             ( (plist[ftype].param[j].AI == at2) &&
                               (plist[ftype].param[j].AJ == at1) ) );
          if (!bPresent) {
            bKeep=TRUE;
            if(debug)fprintf(debug," !bonded");
          }
        }
    }
    
    if ( bKeep ) {
      if(debug)fprintf(debug," keeping");
      /* now copy the bond to the new array */
      memcpy(&(ps->param[kept_i]),
             &(ps->param[i]),(size_t)sizeof(ps->param[0]));
      kept_i++;
    } else if (IS_CHEMBOND(cftype)) {
      srenew(plist[F_CONNBONDS].param,plist[F_CONNBONDS].nr+1);
      memcpy(&(plist[F_CONNBONDS].param[plist[F_CONNBONDS].nr]),
             &(ps->param[i]),(size_t)sizeof(plist[F_CONNBONDS].param[0]));
      plist[F_CONNBONDS].nr++;
      nconverted++;
    } else
      nremoved++;
    if(debug)fprintf(debug,"\n");
  }
  
  if (nremoved)
    fprintf(stderr,"Removed   %4d %15ss with virtual sites, %5d left\n",
            nremoved, interaction_function[cftype].longname, kept_i);
  if (nconverted)
    fprintf(stderr,"Converted %4d %15ss with virtual sites to connections, %5d left\n",
            nconverted, interaction_function[cftype].longname, kept_i);
  if (nOut)
    fprintf(stderr,"Warning: removed %d %ss with vsite with %s construction\n"
            "         This vsite construction does not guarantee constant "
            "bond-length\n"
            "         If the constructions were generated by pdb2gmx ignore "
            "this warning\n",
            nOut, interaction_function[cftype].longname, 
            interaction_function[F_VSITE3OUT].longname );
  ps->nr=kept_i;
}

static void clean_vsite_angles(t_params *plist, t_pindex pindex[], 
                               int cftype, int vsite_type[],
                               at2vsitecon_t *at2vc)
{
  int      i,j,parnr,k,l,m,n,nvsite,kept_i,vsnral,vsitetype;
  atom_id  atom,constr,at1,at2;
  atom_id  vsiteatoms[MAXATOMLIST];
  bool     bKeep,bUsed,bPresent,bAll3FAD,bFirstTwo;
  t_params *ps;
  
  ps = &(plist[cftype]);
  vsnral=0;
  kept_i=0;
  for(i=0; (i<ps->nr); i++) { /* for all angles in the plist */
    bKeep=FALSE;
    bAll3FAD=TRUE;
    /* check if all virtual sites are constructed from the same atoms */
    nvsite=0;
    for(k=0; (k<3) && !bKeep; k++) { /* for all atoms in the angle */
      atom = ps->param[i].a[k];
      if (vsite_type[atom]!=NOTSET) {
        nvsite++;
        bAll3FAD = bAll3FAD && (pindex[atom].ftype == F_VSITE3FAD);
        if (nvsite==1) {
          /* store construction atoms of first vsite */
          vsnral=NRAL(pindex[atom].ftype)-1;
          for(m=0; (m<vsnral); m++)
            vsiteatoms[m]=
              plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
        } else 
          /* check if this vsite is constructed from the same atoms */
          if (vsnral == NRAL(pindex[atom].ftype)-1 )
            for(m=0; (m<vsnral) && !bKeep; m++) {
              bPresent=FALSE;
              constr=
                plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
              for(n=0; (n<vsnral) && !bPresent; n++)
                if (constr == vsiteatoms[n])
                  bPresent=TRUE;
              if (!bPresent)
                bKeep=TRUE;
            }
          else
            bKeep=TRUE;
      }
    }
    
    /* keep all angles with no virtual sites in them or 
       with virtual sites with more than 3 constr. atoms */
    if ( nvsite == 0 && vsnral > 3 )
      bKeep=TRUE;
    
    /* check if all non-vsite atoms are used in construction: */
    bFirstTwo=TRUE;
    for(k=0; (k<3) && !bKeep; k++) { /* for all atoms in the angle */
      atom = ps->param[i].a[k];
      if (vsite_type[atom]==NOTSET) {
        bUsed=FALSE;
        for(m=0; (m<vsnral) && !bUsed; m++)
          if (atom == vsiteatoms[m]) {
            bUsed=TRUE;
            bFirstTwo = bFirstTwo && m<2;
          }
        if (!bUsed)
          bKeep=TRUE;
      }
    }
    
    if ( ! ( bAll3FAD && bFirstTwo ) )
      /* check if all constructing atoms are constrained together */
      for (m=0; m<vsnral && !bKeep; m++) { /* all constr. atoms */
        at1 = vsiteatoms[m];
        at2 = vsiteatoms[(m+1) % vsnral];
        bPresent=FALSE;
        for(j=0; j<at2vc[at1].nr; j++) {
          if (at2vc[at1].aj[j] == at2)
            bPresent = TRUE;
        }
        if (!bPresent)
          bKeep=TRUE;
      }
    
    if ( bKeep ) {
      /* now copy the angle to the new array */
      memcpy(&(ps->param[kept_i]),
             &(ps->param[i]),(size_t)sizeof(ps->param[0]));
      kept_i++;
    }
  }
  
  if (ps->nr != kept_i)
    fprintf(stderr,"Removed   %4d %15ss with virtual sites, %5d left\n",
            ps->nr-kept_i, interaction_function[cftype].longname, kept_i);
  ps->nr=kept_i;
}

static void clean_vsite_dihs(t_params *plist, t_pindex pindex[], 
                           int cftype, int vsite_type[])
{
  int      ftype,i,parnr,k,l,m,n,nvsite,kept_i,vsnral;
  atom_id  atom,constr;
  atom_id  vsiteatoms[3];
  bool     bKeep,bUsed,bPresent;
  t_params *ps;
  
  ps = &(plist[cftype]);
  
  vsnral=0;
  kept_i=0;
  for(i=0; (i<ps->nr); i++) { /* for all dihedrals in the plist */
    bKeep=FALSE;
    /* check if all virtual sites are constructed from the same atoms */
    nvsite=0;
    for(k=0; (k<4) && !bKeep; k++) { /* for all atoms in the dihedral */
      atom = ps->param[i].a[k];
      if (vsite_type[atom]!=NOTSET) {
        nvsite++;
        if (nvsite==1) {
          /* store construction atoms of first vsite */
          vsnral=NRAL(pindex[atom].ftype)-1;
          for(m=0; (m<vsnral); m++)
            vsiteatoms[m]=
              plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
          if (debug) {
            fprintf(debug,"dih w. vsite: %u %u %u %u\n",
                    ps->param[i].AI+1,ps->param[i].AJ+1,
                    ps->param[i].AK+1,ps->param[i].AL+1);
            fprintf(debug,"vsite %u from: %u %u %u\n",
                    atom+1,vsiteatoms[0]+1,vsiteatoms[1]+1,vsiteatoms[2]+1);
          }
        } else 
          /* check if this vsite is constructed from the same atoms */
          if (vsnral == NRAL(pindex[atom].ftype)-1 )
            for(m=0; (m<vsnral) && !bKeep; m++) {
              bPresent=FALSE;
              constr=
                plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
              for(n=0; (n<vsnral) && !bPresent; n++)
                if (constr == vsiteatoms[n])
                  bPresent=TRUE;
              if (!bPresent)
                bKeep=TRUE;
            }
      }
    }
    
    /* keep all dihedrals with no virtual sites in them */
    if (nvsite==0)
      bKeep=TRUE;
    
    /* check if all atoms in dihedral are either virtual sites, or used in 
       construction of virtual sites. If so, keep it, if not throw away: */
    for(k=0; (k<4) && !bKeep; k++) { /* for all atoms in the dihedral */
      atom = ps->param[i].a[k];
      if (vsite_type[atom]==NOTSET) {
        bUsed=FALSE;
        for(m=0; (m<vsnral) && !bUsed; m++)
          if (atom == vsiteatoms[m])
            bUsed=TRUE;
        if (!bUsed) {
          bKeep=TRUE;
          if (debug) fprintf(debug,"unused atom in dih: %u\n",atom+1);
        }
      }
    }
      
    if ( bKeep ) {
      memcpy(&(ps->param[kept_i]),
             &(ps->param[i]),(size_t)sizeof(ps->param[0]));
      kept_i++;
    }
  }

  if (ps->nr != kept_i)
    fprintf(stderr,"Removed   %4d %15ss with virtual sites, %5d left\n", 
            ps->nr-kept_i, interaction_function[cftype].longname, kept_i);
  ps->nr=kept_i;
}

void clean_vsite_bondeds(t_params *plist, int natoms, bool bRmVSiteBds)
{
  int i,k,nvsite,ftype,vsite,parnr;
  int *vsite_type;
  t_pindex *pindex;
  at2vsitecon_t *at2vc;

  pindex=0; /* avoid warnings */
  /* make vsite_type array */
  snew(vsite_type,natoms);
  for(i=0; i<natoms; i++)
    vsite_type[i]=NOTSET;
  nvsite=0;
  for(ftype=0; ftype<F_NRE; ftype++)
    if (interaction_function[ftype].flags & IF_VSITE) {
      nvsite+=plist[ftype].nr;
      i = 0;
      while (i < plist[ftype].nr) {
        vsite = plist[ftype].param[i].AI;
        if ( vsite_type[vsite] == NOTSET)
          vsite_type[vsite] = ftype;
        else
          gmx_fatal(FARGS,"multiple vsite constructions for atom %d",vsite+1);
        if (ftype == F_VSITEN) {
          while (i < plist[ftype].nr && plist[ftype].param[i].AI == vsite)
            i++;
        } else {
          i++;
        }
      }
    }
  
  /* the rest only if we have virtual sites: */
  if (nvsite) {
    fprintf(stderr,"Cleaning up constraints %swith virtual sites\n",
            bRmVSiteBds?"and constant bonded interactions ":"");

    /* Make a reverse list to avoid ninteractions^2 operations */
    at2vc = make_at2vsitecon(natoms,plist);

    snew(pindex,natoms);
    for(ftype=0; ftype<F_NRE; ftype++) {
      if ((interaction_function[ftype].flags & IF_VSITE) &&
          ftype != F_VSITEN) {
        for (parnr=0; (parnr<plist[ftype].nr); parnr++) {
          k=plist[ftype].param[parnr].AI;
          pindex[k].ftype=ftype;
          pindex[k].parnr=parnr;
        }
      }
    }

    if (debug)
      for(i=0; i<natoms; i++)
        fprintf(debug,"atom %d vsite_type %s\n",i, 
                vsite_type[i]==NOTSET ? "NOTSET" : 
                interaction_function[vsite_type[i]].name);
    
    /* remove things with vsite atoms */
    for(ftype=0; ftype<F_NRE; ftype++)
      if ( ( ( interaction_function[ftype].flags & IF_BOND ) && bRmVSiteBds ) ||
           ( interaction_function[ftype].flags & IF_CONSTRAINT ) ) {
        if (interaction_function[ftype].flags & (IF_BTYPE | IF_CONSTRAINT) )
          clean_vsite_bonds (plist, pindex, ftype, vsite_type);
        else if (interaction_function[ftype].flags & IF_ATYPE)
          clean_vsite_angles(plist, pindex, ftype, vsite_type, at2vc);
        else if ( (ftype==F_PDIHS) || (ftype==F_IDIHS) )
          clean_vsite_dihs  (plist, pindex, ftype, vsite_type);
      }
    /* check if we have constraints left with virtual sites in them */
    for(ftype=0; ftype<F_NRE; ftype++)
      if (interaction_function[ftype].flags & IF_CONSTRAINT)
        check_vsite_constraints(plist, ftype, vsite_type);

    done_at2vsitecon(natoms,at2vc);
  }
  sfree(pindex);
  sfree(vsite_type);
}