/*
 * 
 *                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.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
 * bugs must be traceable. We will be happy to consider code for
 * inclusion in the official distribution, but derived work must not
 * be called official GROMACS. Details are found in the README & COPYING
 * files - if they are missing, get the official version at www.gromacs.org.
 * 
 * To help us fund GROMACS development, we humbly ask that you cite
 * the papers on the package - you can find them in the top README file.
 * 
 * For more info, check our website at http://www.gromacs.org
 * 
 * And Hey:
 * Green Red Orange Magenta Azure Cyan Skyblue
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <math.h>
#include <string.h>
#include "statutil.h"
#include "sysstuff.h"
#include "typedefs.h"
#include "smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
#include "copyrite.h"
#include "futil.h"
#include "statutil.h"
#include "index.h"
#include "mshift.h"
#include "xvgr.h"
#include "princ.h"
#include "rmpbc.h"
#include "txtdump.h"
#include "tpxio.h"
#include "gmx_ana.h"

typedef struct {
  atom_id i;
  real    d2;
} t_order;

t_order *order;

static int ocomp(const void *a,const void *b)
{
  t_order *oa,*ob;
  
  oa = (t_order *)a;
  ob = (t_order *)b;
  
  if (oa->d2 < ob->d2)
    return -1;
  else
    return 1;  
}

int gmx_trjorder(int argc,char *argv[])
{
  const char *desc[] = {
    "[TT]trjorder[tt] orders molecules according to the smallest distance",
    "to atoms in a reference group",
    "or on z-coordinate (with option [TT]-z[tt]).",
    "With distance ordering, it will ask for a group of reference",
    "atoms and a group of molecules. For each frame of the trajectory",
    "the selected molecules will be reordered according to the shortest",
    "distance between atom number [TT]-da[tt] in the molecule and all the",
    "atoms in the reference group. The center of mass of the molecules can",
    "be used instead of a reference atom by setting [TT]-da[tt] to 0.",
    "All atoms in the trajectory are written",
    "to the output trajectory.[PAR]",
    "[TT]trjorder[tt] can be useful for e.g. analyzing the n waters closest to a",
    "protein.",
    "In that case the reference group would be the protein and the group",
    "of molecules would consist of all the water atoms. When an index group",
    "of the first n waters is made, the ordered trajectory can be used",
    "with any Gromacs program to analyze the n closest waters.",
    "[PAR]",
    "If the output file is a [TT].pdb[tt] file, the distance to the reference target",
    "will be stored in the B-factor field in order to color with e.g. Rasmol.",
    "[PAR]",
    "With option [TT]-nshell[tt] the number of molecules within a shell",
    "of radius [TT]-r[tt] around the reference group are printed."
  };
  static int na=3,ref_a=1;
  static real rcut=0;
  static gmx_bool bCOM=FALSE,bZ=FALSE;
  t_pargs pa[] = {
    { "-na", FALSE, etINT,  {&na},
      "Number of atoms in a molecule" },
    { "-da", FALSE, etINT,  {&ref_a},
      "Atom used for the distance calculation, 0 is COM" },
    { "-com", FALSE, etBOOL, {&bCOM},
      "Use the distance to the center of mass of the reference group" },
    { "-r",  FALSE, etREAL, {&rcut},
      "Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein" },
    { "-z", FALSE, etBOOL, {&bZ},
      "Order molecules on z-coordinate" }
  };
  FILE       *fp;
  t_trxstatus *out;
  t_trxstatus *status;
  gmx_bool       bNShell,bPDBout;
  t_topology top;
  int        ePBC;
  rvec       *x,*xsol,xcom,dx;
  matrix     box;
  t_pbc      pbc;
  gmx_rmpbc_t gpbc;
  real       t,totmass,mass,rcut2=0,n2;
  int        natoms,nwat,ncut;
  char       **grpname,title[256];
  int        i,j,d,*isize,isize_ref=0,isize_sol;
  atom_id    sa,sr,*swi,**index,*ind_ref=NULL,*ind_sol;
  output_env_t oenv;
  t_filenm fnm[] = { 
    { efTRX, "-f", NULL, ffREAD  }, 
    { efTPS, NULL, NULL, ffREAD  }, 
    { efNDX, NULL, NULL, ffOPTRD },
    { efTRO, "-o", "ordered", ffOPTWR },
    { efXVG, "-nshell", "nshell", ffOPTWR } 
  }; 
#define NFILE asize(fnm) 

  CopyRight(stderr,argv[0]); 
  parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
		    NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv); 

  read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&x,NULL,box,TRUE);
  sfree(x);

  /* get index groups */
  printf("Select %sa group of molecules to be ordered:\n",
	 bZ ? "" : "a group of reference atoms and "); 
  snew(grpname,2);
  snew(index,2);
  snew(isize,2);
  get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),bZ ? 1 : 2,
	    isize,index,grpname);

  if (!bZ) {
    isize_ref = isize[0];
    isize_sol = isize[1];
    ind_ref   = index[0];
    ind_sol   = index[1];
  } else {
    isize_sol = isize[0];
    ind_sol   = index[0];
  }

  natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box); 
  if (natoms > top.atoms.nr)
    gmx_fatal(FARGS,"Number of atoms in the run input file is larger than in the trjactory");
  for(i=0; (i<2); i++)
    for(j=0; (j<isize[i]); j++)
      if (index[i][j] > natoms)
	gmx_fatal(FARGS,"An atom number in group %s is larger than the number of atoms in the trajectory");
  
  if ((isize_sol % na) != 0)
    gmx_fatal(FARGS,"Number of atoms in the molecule group (%d) is not a multiple of na (%d)",
		isize[1],na);
		
  nwat = isize_sol/na;
  if (ref_a > na)
    gmx_fatal(FARGS,"The reference atom can not be larger than the number of atoms in a molecule");
  ref_a--;
  snew(xsol,nwat);
  snew(order,nwat);
  snew(swi,natoms);
  for(i=0; (i<natoms); i++)
    swi[i] = i;

  out     = NULL;
  fp      = NULL;
  bNShell = ((opt2bSet("-nshell",NFILE,fnm)) ||
	     (opt2parg_bSet("-r",asize(pa),pa)));
  bPDBout = FALSE;
  if (bNShell) {
    rcut2   = rcut*rcut;
    fp = xvgropen(opt2fn("-nshell",NFILE,fnm),"Number of molecules",
		  "Time (ps)","N",oenv);
    printf("Will compute the number of molecules within a radius of %g\n",
	   rcut);
  }
  if (!bNShell || opt2bSet("-o",NFILE,fnm)) {
    bPDBout = (fn2ftp(opt2fn("-o",NFILE,fnm)) == efPDB);
    if (bPDBout && !top.atoms.pdbinfo) {
      fprintf(stderr,"Creating pdbfino records\n");
      snew(top.atoms.pdbinfo,top.atoms.nr);
    }
    out = open_trx(opt2fn("-o",NFILE,fnm),"w");
  }
  gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
  do {
    gmx_rmpbc(gpbc,natoms,box,x);
    set_pbc(&pbc,ePBC,box);

    if (ref_a == -1) {
      /* Calculate the COM of all solvent molecules */
      for(i=0; i<nwat; i++) {
	totmass = 0;
	clear_rvec(xsol[i]);
	for(j=0; j<na; j++) {
	  sa = ind_sol[i*na+j];
	  mass = top.atoms.atom[sa].m;
	  totmass += mass;
	  for(d=0; d<DIM; d++) {
	    xsol[i][d] += mass*x[sa][d];
	  }
	}
	svmul(1/totmass,xsol[i],xsol[i]);
      }
    } else {
      /* Copy the reference atom of all solvent molecules */
      for(i=0; i<nwat; i++) {
	copy_rvec(x[ind_sol[i*na+ref_a]],xsol[i]);
      }
    }

    if (bZ) {
      for(i=0; (i<nwat); i++) {
	sa = ind_sol[na*i];
	order[i].i   = sa;
	order[i].d2  = xsol[i][ZZ]; 
      }
    } else if (bCOM) {
      totmass = 0;
      clear_rvec(xcom);
      for(i=0; i<isize_ref; i++) {
	mass = top.atoms.atom[ind_ref[i]].m;
	totmass += mass;
	for(j=0; j<DIM; j++)
	  xcom[j] += mass*x[ind_ref[i]][j];
      }
      svmul(1/totmass,xcom,xcom);
      for(i=0; (i<nwat); i++) {
	sa = ind_sol[na*i];
	pbc_dx(&pbc,xcom,xsol[i],dx);
	order[i].i   = sa;
	order[i].d2  = norm2(dx); 
      }
    } else {
      /* Set distance to first atom */
      for(i=0; (i<nwat); i++) {
	sa = ind_sol[na*i];
	pbc_dx(&pbc,x[ind_ref[0]],xsol[i],dx);
	order[i].i   = sa;
	order[i].d2  = norm2(dx); 
      }
      for(j=1; (j<isize_ref); j++) {
	sr = ind_ref[j];
	for(i=0; (i<nwat); i++) {
	  sa = ind_sol[na*i];
	  pbc_dx(&pbc,x[sr],xsol[i],dx);
	  n2 = norm2(dx);
	  if (n2 < order[i].d2)
	    order[i].d2  = n2;
	}
      }
    }

    if (bNShell) {
      ncut = 0;
      for(i=0; (i<nwat); i++)
	if (order[i].d2 <= rcut2)
	  ncut++;
      fprintf(fp,"%10.3f  %8d\n",t,ncut);
    }
    if (out) {
      qsort(order,nwat,sizeof(*order),ocomp);
      for(i=0; (i<nwat); i++)
	for(j=0; (j<na); j++) 
	  swi[ind_sol[na*i]+j] = order[i].i+j;
      
      /* Store the distance as the B-factor */
      if (bPDBout) {
	for(i=0; (i<nwat); i++) {
	  for(j=0; (j<na); j++) {
	    top.atoms.pdbinfo[order[i].i+j].bfac = sqrt(order[i].d2);
	  }
	}
      }
      write_trx(out,natoms,swi,&top.atoms,0,t,box,x,NULL,NULL);
    }
  } while(read_next_x(oenv,status,&t,natoms,x,box));
  close_trj(status);
  if (out)
    close_trx(out);
  if (fp)
    ffclose(fp);
  gmx_rmpbc_done(gpbc);
  
  thanx(stderr);
  
  return 0;
}
