added Verlet scheme and NxN non-bonded functionality

[gromacs.git] / src / tools / addconf.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
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 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdlib.h>
#include <string.h>
#include "vec.h"
#include "macros.h"
#include "smalloc.h"
#include "addconf.h"
#include "force.h"
#include "gstat.h"
#include "names.h"
#include "nsgrid.h"
#include "mdatoms.h"
#include "nrnb.h"
#include "ns.h"
#include "mtop_util.h"
#include "chargegroup.h"

static real box_margin;

static real max_dist(rvec *x, real *r, int start, int end)
{
  real maxd;
  int i,j;

  maxd=0;
  for(i=start; i<end; i++)
    for(j=i+1; j<end; j++)
      maxd=max(maxd,sqrt(distance2(x[i],x[j]))+0.5*(r[i]+r[j]));

  return 0.5*maxd;
}

static gmx_bool outside_box_minus_margin2(rvec x,matrix box)
{
  return ( (x[XX]<2*box_margin) || (x[XX]>box[XX][XX]-2*box_margin) ||
           (x[YY]<2*box_margin) || (x[YY]>box[YY][YY]-2*box_margin) ||
           (x[ZZ]<2*box_margin) || (x[ZZ]>box[ZZ][ZZ]-2*box_margin) );
}

static gmx_bool outside_box_plus_margin(rvec x,matrix box)
{
  return ( (x[XX]<-box_margin) || (x[XX]>box[XX][XX]+box_margin) ||
           (x[YY]<-box_margin) || (x[YY]>box[YY][YY]+box_margin) ||
           (x[ZZ]<-box_margin) || (x[ZZ]>box[ZZ][ZZ]+box_margin) );
}

static int mark_res(int at, gmx_bool *mark, int natoms, t_atom *atom,int *nmark)
{
  int resind;

  resind = atom[at].resind;
  while( (at > 0) && (resind==atom[at-1].resind) )
    at--;
  while( (at < natoms) && (resind==atom[at].resind) ) {
    if (!mark[at]) {
      mark[at]=TRUE;
      (*nmark)++;
    }
    at++;
  }

  return at;
}

static real find_max_real(int n,real radius[])
{
  int  i;
  real rmax;

  rmax = 0;
  if (n > 0) {
    rmax = radius[0];
    for(i=1; (i<n); i++)
      rmax = max(rmax,radius[i]);
  }
  return rmax;
}

static void combine_atoms(t_atoms *ap,t_atoms *as,
                          rvec xp[],rvec *vp,rvec xs[],rvec *vs,
                          t_atoms **a_comb,rvec **x_comb,rvec **v_comb)
{
  t_atoms *ac;
  rvec    *xc,*vc=NULL;
  int     i,j,natot,res0;

  /* Total number of atoms */
  natot = ap->nr+as->nr;

  snew(ac,1);
  init_t_atoms(ac,natot,FALSE);

  snew(xc,natot);
  if (vp && vs) snew(vc,natot);

  /* Fill the new structures */
  for(i=j=0; (i<ap->nr); i++,j++) {
    copy_rvec(xp[i],xc[j]);
    if (vc) copy_rvec(vp[i],vc[j]);
    memcpy(&(ac->atom[j]),&(ap->atom[i]),sizeof(ap->atom[i]));
    ac->atom[j].type = 0;
  }
  res0 = ap->nres;
  for(i=0; (i<as->nr); i++,j++) {
    copy_rvec(xs[i],xc[j]);
    if (vc) copy_rvec(vs[i],vc[j]);
    memcpy(&(ac->atom[j]),&(as->atom[i]),sizeof(as->atom[i]));
    ac->atom[j].type    = 0;
    ac->atom[j].resind += res0;
  }
  ac->nr   = j;
  ac->nres = ac->atom[j-1].resind+1;
  /* Fill all elements to prevent uninitialized memory */
  for(i=0; i<ac->nr; i++) {
    ac->atom[i].m     = 1;
    ac->atom[i].q     = 0;
    ac->atom[i].mB    = 1;
    ac->atom[i].qB    = 0;
    ac->atom[i].type  = 0;
    ac->atom[i].typeB = 0;
    ac->atom[i].ptype = eptAtom;
  }

  /* Return values */
  *a_comb = ac;
  *x_comb = xc;
  *v_comb = vc;
}

static t_forcerec *fr=NULL;

void do_nsgrid(FILE *fp,gmx_bool bVerbose,
               matrix box,rvec x[],t_atoms *atoms,real rlong,
               const output_env_t oenv)
{
  gmx_mtop_t *mtop;
  gmx_localtop_t *top;
  t_mdatoms  *md;
  t_block    *cgs;
  t_inputrec *ir;
  t_nrnb     nrnb;
  t_commrec  *cr;
  int        *cg_index;
  gmx_moltype_t *molt;
  gmx_ffparams_t *ffp;
  ivec       *nFreeze;
  int        i,m,natoms;
  rvec       box_size;
  real       *lambda,*dvdl;

  natoms = atoms->nr;

  /* Charge group index */
  snew(cg_index,natoms);
  for(i=0; (i<natoms); i++)
    cg_index[i]=i;

  /* Topology needs charge groups and exclusions */
  snew(mtop,1);
  init_mtop(mtop);
  mtop->natoms = natoms;
  /* Make one moltype that contains the whol system */
  mtop->nmoltype = 1;
  snew(mtop->moltype,mtop->nmoltype);
  molt = &mtop->moltype[0];
  molt->name  = mtop->name;
  molt->atoms = *atoms;
  stupid_fill_block(&molt->cgs,mtop->natoms,FALSE);
  stupid_fill_blocka(&molt->excls,natoms);
  /* Make one molblock for the whole system */
  mtop->nmolblock = 1;
  snew(mtop->molblock,mtop->nmolblock);
  mtop->molblock[0].type = 0;
  mtop->molblock[0].nmol = 1;
  mtop->molblock[0].natoms_mol = natoms;
  /* Initialize a single energy group */
  mtop->groups.grps[egcENER].nr = 1;
  mtop->groups.ngrpnr[egcENER]  = 0;
  mtop->groups.grpnr[egcENER]   = NULL;

  ffp = &mtop->ffparams;

  ffp->ntypes = 1;
  ffp->atnr   = 1;
  ffp->reppow = 12;
  snew(ffp->functype,1);
  snew(ffp->iparams,1);
  ffp->iparams[0].lj.c6  = 1;
  ffp->iparams[0].lj.c12 = 1;

  /* inputrec structure */
  snew(ir,1);
  ir->coulombtype = eelCUT;
  ir->vdwtype     = evdwCUT;
  ir->ndelta      = 2;
  ir->ns_type     = ensGRID;
  snew(ir->opts.egp_flags,1);

  top = gmx_mtop_generate_local_top(mtop,ir);

  /* Some nasty shortcuts */
  cgs  = &(top->cgs);

    /* mdatoms structure */
  snew(nFreeze,2);
  snew(md,1);
  md = init_mdatoms(fp,mtop,FALSE);
  atoms2md(mtop,ir,0,NULL,0,mtop->natoms,md);
  sfree(nFreeze);

  /* forcerec structure */
  if (fr == NULL)
    fr = mk_forcerec();
  snew(cr,1);
  cr->nnodes   = 1;
  /* cr->nthreads = 1; */

  /*    ir->rlist       = ir->rcoulomb = ir->rvdw = rlong;
        printf("Neighborsearching with a cut-off of %g\n",rlong);
        init_forcerec(stdout,fr,ir,top,cr,md,box,FALSE,NULL,NULL,NULL,TRUE);*/
  fr->cg0 = 0;
  fr->hcg = top->cgs.nr;
  fr->nWatMol = 0;

  /* Prepare for neighboursearching */
  init_nrnb(&nrnb);

  /* Init things dependent on parameters */
  ir->rlistlong = ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
  /* create free energy data to avoid NULLs */
  snew(ir->fepvals,1);
  printf("Neighborsearching with a cut-off of %g\n",rlong);
  init_forcerec(stdout,oenv,fr,NULL,ir,mtop,cr,box,FALSE,
                NULL,NULL,NULL,NULL,NULL,TRUE,-1);
  if (debug)
    pr_forcerec(debug,fr,cr);

  /* Calculate new stuff dependent on coords and box */
  for(m=0; (m<DIM); m++)
    box_size[m] = box[m][m];
  calc_shifts(box,fr->shift_vec);
  put_charge_groups_in_box(fp,0,cgs->nr,fr->ePBC,box,cgs,x,fr->cg_cm);

  /* Do the actual neighboursearching */
  snew(lambda,efptNR);
  snew(dvdl,efptNR);
  init_neighbor_list(fp,fr,md->homenr);
  search_neighbours(fp,fr,x,box,top,
                    &mtop->groups,cr,&nrnb,md,lambda,dvdl,NULL,
                    TRUE,FALSE,FALSE,NULL);

  if (debug)
    dump_nblist(debug,cr,fr,0);

  if (bVerbose)
    fprintf(stderr,"Successfully made neighbourlist\n");
}

gmx_bool bXor(gmx_bool b1,gmx_bool b2)
{
  return (b1 && !b2) || (b2 && !b1);
}

void add_conf(t_atoms *atoms, rvec **x, rvec **v, real **r, gmx_bool bSrenew,
              int ePBC, matrix box, gmx_bool bInsert,
              t_atoms *atoms_solvt,rvec *x_solvt,rvec *v_solvt,real *r_solvt,
              gmx_bool bVerbose,real rshell,int max_sol, const output_env_t oenv)
{
  t_nblist   *nlist;
  t_atoms    *atoms_all;
  real       max_vdw,*r_prot,*r_all,n2,r2,ib1,ib2;
  int        natoms_prot,natoms_solvt;
  int        i,j,jj,m,j0,j1,jjj,jnres,jnr,inr,iprot,is1,is2;
  int        prev,resnr,nresadd,d,k,ncells,maxincell;
  int        dx0,dx1,dy0,dy1,dz0,dz1;
  int        ntest,nremove,nkeep;
  rvec       dx,xi,xj,xpp,*x_all,*v_all;
  gmx_bool       *remove,*keep;
  int        bSolSol;

  natoms_prot  = atoms->nr;
  natoms_solvt = atoms_solvt->nr;
  if (natoms_solvt <= 0) {
    fprintf(stderr,"WARNING: Nothing to add\n");
    return;
  }

  if (ePBC == epbcSCREW)
    gmx_fatal(FARGS,"Sorry, %s pbc is not yet supported",epbc_names[ePBC]);

  if (bVerbose)
    fprintf(stderr,"Calculating Overlap...\n");

  /* Set margin around box edges to largest solvent dimension.
   * The maximum distance between atoms in a solvent molecule should
   * be calculated. At the moment a fudge factor of 3 is used.
   */
  r_prot     = *r;
  box_margin = 3*find_max_real(natoms_solvt,r_solvt);
  max_vdw    = max(3*find_max_real(natoms_prot,r_prot),box_margin);
  fprintf(stderr,"box_margin = %g\n",box_margin);

  snew(remove,natoms_solvt);

  nremove = 0;
  if (!bInsert) {
    for(i=0; i<atoms_solvt->nr; i++)
      if ( outside_box_plus_margin(x_solvt[i],box) )
        i=mark_res(i,remove,atoms_solvt->nr,atoms_solvt->atom,&nremove);
    fprintf(stderr,"Removed %d atoms that were outside the box\n",nremove);
  }

  /* Define grid stuff for genbox */
  /* Largest VDW radius */
  snew(r_all,natoms_prot+natoms_solvt);
  for(i=j=0; i<natoms_prot; i++,j++)
    r_all[j]=r_prot[i];
  for(i=0; i<natoms_solvt; i++,j++)
    r_all[j]=r_solvt[i];

  /* Combine arrays */
  combine_atoms(atoms,atoms_solvt,*x,v?*v:NULL,x_solvt,v_solvt,
                &atoms_all,&x_all,&v_all);

  /* Do neighboursearching step */
  do_nsgrid(stdout,bVerbose,box,x_all,atoms_all,max_vdw,oenv);

  /* check solvent with solute */
  nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
  fprintf(stderr,"nri = %d, nrj = %d\n",nlist->nri,nlist->nrj);
  for(bSolSol=0; (bSolSol<=(bInsert ? 0 : 1)); bSolSol++) {
    ntest = nremove = 0;
    fprintf(stderr,"Checking %s-Solvent overlap:",
            bSolSol ? "Solvent" : "Protein");
    for(i=0; (i<nlist->nri && nremove<natoms_solvt); i++) {
      inr = nlist->iinr[i];
      j0  = nlist->jindex[i];
      j1  = nlist->jindex[i+1];
      rvec_add(x_all[inr],fr->shift_vec[nlist->shift[i]],xi);

      for(j=j0; (j<j1 && nremove<natoms_solvt); j++) {
        jnr = nlist->jjnr[j];
        copy_rvec(x_all[jnr],xj);

        /* Check solvent-protein and solvent-solvent */
        is1 = inr-natoms_prot;
        is2 = jnr-natoms_prot;

        /* Check if at least one of the atoms is a solvent that is not yet
         * listed for removal, and if both are solvent, that they are not in the
         * same residue.
         */
        if ((!bSolSol &&
             bXor((is1 >= 0),(is2 >= 0)) &&  /* One atom is protein */
             ((is1 < 0) || ((is1 >= 0) && !remove[is1])) &&
             ((is2 < 0) || ((is2 >= 0) && !remove[is2]))) ||

            (bSolSol  &&
             (is1 >= 0) && (!remove[is1]) &&   /* is1 is solvent */
             (is2 >= 0) && (!remove[is2]) &&   /* is2 is solvent */
             (bInsert || /* when inserting also check inside the box */
              (outside_box_minus_margin2(x_solvt[is1],box) && /* is1 on edge */
               outside_box_minus_margin2(x_solvt[is2],box))   /* is2 on edge */
              ) &&
             (atoms_solvt->atom[is1].resind !=  /* Not the same residue */
              atoms_solvt->atom[is2].resind))) {

          ntest++;
          rvec_sub(xi,xj,dx);
          n2 = norm2(dx);
          r2 = sqr(r_all[inr]+r_all[jnr]);
          if (n2 < r2) {
            if (bInsert) {
              nremove = natoms_solvt;
              for(k=0; k<nremove; k++) {
                remove[k] = TRUE;
              }
            }
            /* Need only remove one of the solvents... */
            if (is2 >= 0)
              (void) mark_res(is2,remove,natoms_solvt,atoms_solvt->atom,
                              &nremove);
            else if (is1 >= 0)
              (void) mark_res(is1,remove,natoms_solvt,atoms_solvt->atom,
                              &nremove);
            else
              fprintf(stderr,"Neither atom is solvent%d %d\n",is1,is2);
          }
        }
      }
    }
    if (!bInsert) {
      fprintf(stderr," tested %d pairs, removed %d atoms.\n",ntest,nremove);
    }
  }
  if (debug)
    for(i=0; i<natoms_solvt; i++)
      fprintf(debug,"remove[%5d] = %s\n",i,bool_names[remove[i]]);

  /* Search again, now with another cut-off */
  if (rshell > 0) {
    do_nsgrid(stdout,bVerbose,box,x_all,atoms_all,rshell,oenv);
    nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
    fprintf(stderr,"nri = %d, nrj = %d\n",nlist->nri,nlist->nrj);
    nkeep = 0;
    snew(keep,natoms_solvt);
    for(i=0; i<nlist->nri; i++) {
      inr = nlist->iinr[i];
      j0  = nlist->jindex[i];
      j1  = nlist->jindex[i+1];

      for(j=j0; j<j1; j++) {
        jnr = nlist->jjnr[j];

        /* Check solvent-protein and solvent-solvent */
        is1 = inr-natoms_prot;
        is2 = jnr-natoms_prot;

        /* Check if at least one of the atoms is a solvent that is not yet
         * listed for removal, and if both are solvent, that they are not in the
         * same residue.
         */
        if (is1>=0 && is2<0)
          mark_res(is1,keep,natoms_solvt,atoms_solvt->atom,&nkeep);
        else if (is1<0 && is2>=0)
          mark_res(is2,keep,natoms_solvt,atoms_solvt->atom,&nkeep);
      }
    }
    fprintf(stderr,"Keeping %d solvent atoms after proximity check\n",
            nkeep);
    for (i=0; i<natoms_solvt; i++)
      remove[i] = remove[i] || !keep[i];
    sfree(keep);
  }
  /* count how many atoms and residues will be added and make space */
  if (bInsert) {
    j     = atoms_solvt->nr;
    jnres = atoms_solvt->nres;
  } else {
    j     = 0;
    jnres = 0;
    for (i=0; ((i<atoms_solvt->nr) &&
               ((max_sol == 0) || (jnres < max_sol))); i++) {
      if (!remove[i]) {
        j++;
        if ((i == 0) ||
            (atoms_solvt->atom[i].resind != atoms_solvt->atom[i-1].resind))
          jnres++;
      }
    }
  }
  if (debug)
    fprintf(debug,"Will add %d atoms in %d residues\n",j,jnres);
  if (!bInsert) {
    /* Flag the remaing solvent atoms to be removed */
    jjj = atoms_solvt->atom[i-1].resind;
    for ( ; (i<atoms_solvt->nr); i++) {
      if (atoms_solvt->atom[i].resind > jjj)
        remove[i] = TRUE;
      else
        j++;
    }
  }

  if (bSrenew) {
    srenew(atoms->resinfo,  atoms->nres+jnres);
    srenew(atoms->atomname, atoms->nr+j);
    srenew(atoms->atom,     atoms->nr+j);
    srenew(*x,              atoms->nr+j);
    if (v) srenew(*v,       atoms->nr+j);
    srenew(*r,              atoms->nr+j);
  }

  /* add the selected atoms_solvt to atoms */
  if (atoms->nr > 0) {
    resnr = atoms->resinfo[atoms->atom[atoms->nr-1].resind].nr;
  } else {
    resnr = 0;
  }
  prev = -1;
  nresadd = 0;
  for (i=0; i<atoms_solvt->nr; i++) {
    if (!remove[i]) {
      if (prev == -1 ||
          atoms_solvt->atom[i].resind != atoms_solvt->atom[prev].resind) {
        nresadd ++;
        atoms->nres++;
        resnr++;
        atoms->resinfo[atoms->nres-1] =
          atoms_solvt->resinfo[atoms_solvt->atom[i].resind];
        atoms->resinfo[atoms->nres-1].nr = resnr;
        /* calculate shift of the solvent molecule using the first atom */
        copy_rvec(x_solvt[i],dx);
        put_atoms_in_box(ePBC,box,1,&dx);
        rvec_dec(dx,x_solvt[i]);
      }
      atoms->atom[atoms->nr] = atoms_solvt->atom[i];
      atoms->atomname[atoms->nr] = atoms_solvt->atomname[i];
      rvec_add(x_solvt[i],dx,(*x)[atoms->nr]);
      if (v) copy_rvec(v_solvt[i],(*v)[atoms->nr]);
      (*r)[atoms->nr]   = r_solvt[i];
      atoms->atom[atoms->nr].resind = atoms->nres-1;
      atoms->nr++;
      prev=i;
    }
  }
  if (bSrenew)
    srenew(atoms->resinfo,  atoms->nres+nresadd);

  if (bVerbose)
    fprintf(stderr,"Added %d molecules\n",nresadd);

  sfree(remove);
  done_atom(atoms_all);
  sfree(x_all);
  sfree(v_all);
}