/*
 * 
 *                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:
 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <math.h>
#include "smalloc.h"
#include "sysstuff.h"
#include "macros.h"
#include "string2.h"
#include "topdirs.h"
#include "toputil.h"
#include "topdirs.h"
#include "toputil.h"
#include "symtab.h"
#include "gmx_fatal.h"
#include "gpp_atomtype.h"

/* UTILITIES */

void set_p_string(t_param *p,const char *s)
{
  if (s) {
    if (strlen(s) < sizeof(p->s)-1)
      strncpy(p->s,s,sizeof(p->s));
    else
      gmx_fatal(FARGS,"Increase MAXSLEN in include/grompp.h to at least %d,"
		  " or shorten your definition of bonds like %s to at most %d",
		  strlen(s)+1,s,MAXSLEN-1);
  }
  else
    strcpy(p->s,"");
}

void pr_alloc (int extra, t_params *pr)
{
  int i,j;
  
  /* get new space for arrays */
  if (extra < 0) 
    gmx_fatal(FARGS,"Trying to make array smaller.\n");
  if (extra == 0)
    return;
  if ((pr->nr == 0) && (pr->param != NULL)) {
    fprintf(stderr,"Warning: dangling pointer at %lx\n",
	    (unsigned long)pr->param);
    pr->param = NULL;
  }
  if (pr->nr+extra > pr->maxnr) {
    pr->maxnr = max(1.2*pr->maxnr,pr->maxnr + extra);
    srenew(pr->param,pr->maxnr);
    for(i=pr->nr; (i<pr->maxnr); i++) {
      for(j=0; (j<MAXATOMLIST); j++)
	pr->param[i].a[j]=0;
      for(j=0; (j<MAXFORCEPARAM); j++)
	pr->param[i].c[j]=0;
      set_p_string(&(pr->param[i]),"");
    }
  }
}

void init_plist(t_params plist[])
{
  int i;
  
  for(i=0; (i<F_NRE); i++) {
    plist[i].nr    = 0;
    plist[i].maxnr = 0;
    plist[i].param = NULL;
  
    /* CMAP */
    plist[i].ncmap=0;
    plist[i].cmap=NULL;
    plist[i].grid_spacing = 0;
    plist[i].nc = 0;   
    plist[i].nct        = 0;
    plist[i].cmap_types = NULL;
  }
}

void cp_param(t_param *dest,t_param *src)
{
  int j;
  
  for(j=0; (j<MAXATOMLIST); j++)
    dest->a[j] = src->a[j];
  for(j=0; (j<MAXFORCEPARAM); j++)
    dest->c[j] = src->c[j];
  strncpy(dest->s,src->s,sizeof(dest->s));
}

void add_param_to_list(t_params *list, t_param *b)
{
  int j;
  
  /* allocate one position extra */
  pr_alloc (1,list);

  /* fill the arrays */
  for (j=0; (j < MAXFORCEPARAM); j++) 
    list->param[list->nr].c[j]   = b->c[j];
  for (j=0; (j < MAXATOMLIST); j++) 
    list->param[list->nr].a[j]   = b->a[j];
  memset(list->param[list->nr].s,0,sizeof(list->param[list->nr].s));
  
  list->nr++;
}


void init_molinfo(t_molinfo *mol)
{
  mol->nrexcl = 0;
  mol->excl_set = FALSE;
  mol->bProcessed = FALSE;
  init_plist(mol->plist);
  init_block(&mol->cgs);
  init_block(&mol->mols);
  init_blocka(&mol->excls);
  init_atom(&mol->atoms);
}

/* FREEING MEMORY */

void done_bt (t_params *pl)
{
  sfree(pl->param);
}

void done_mi(t_molinfo *mi)
{
  int i;
  
  done_atom (&(mi->atoms));
  done_block(&(mi->cgs));
  done_block(&(mi->mols));
  for(i=0; (i<F_NRE); i++)
    done_bt(&(mi->plist[i]));
}

/* PRINTING STRUCTURES */

static void print_nbt (FILE *out,char *title,gpp_atomtype_t at,
		       int ftype,t_params *nbt)
{
  int f,i,j,k,l,nrfp,ntype;
  
  if (ftype == F_LJ)
    f=1;
  else
    f=2;
  nrfp=NRFP(ftype);
  
  if (nbt->nr) {
    /* header */
    fprintf (out,"; %s\n",title);
    fprintf (out,"[ %s ]\n",dir2str(d_nonbond_params));
    fprintf (out,"; %6s  %8s","ai","aj");
    fprintf (out,"  %8s","funct");
    for (j=0; (j<nrfp); j++)
      fprintf (out,"  %11c%1d",'c',j);
    fprintf (out,"\n");
    
    /* print non-bondtypes */
    ntype = get_atomtype_ntypes(at);
    for (i=k=0; (i<ntype); i++)
      for(j=0; (j<ntype); j++,k++) {
	fprintf (out,"%8s  %8s  %8d",
		 get_atomtype_name(i,at),get_atomtype_name(f,at),f);
	for(l=0; (l<nrfp); l++)
	  fprintf (out,"  %12.5e",nbt->param[k].c[l]);
	fprintf (out,"\n");
      }
  }
  fprintf (out,"\n");
}

void print_bt(FILE *out, directive d, gpp_atomtype_t at,
	      int ftype,int fsubtype,t_params plist[],
	      gmx_bool bFullDih)
{
  /* This dihp is a DIRTY patch because the dih-types do not use
   * all four atoms to determine the type.
   */
  const int dihp[2][2] = { { 1,2 }, { 0,3 } };
  t_params *bt;
  int      i,j,f,nral,nrfp;
  gmx_bool     bDih=FALSE,bSwapParity;
  
  bt=&(plist[ftype]);
  
  if (!bt->nr) 
    return;
  
  f = 0;
  switch(ftype) {
  case F_G96ANGLES:
    f = 1;
    break;
  case F_G96BONDS:
    f = 1;
    break;
  case F_MORSE:
    f = 2;
    break;
  case F_CUBICBONDS:
    f = 3;
    break;
  case F_CONNBONDS:
    f = 4;
    break;
  case F_HARMONIC:
    f = 5;
    break;
  case F_CROSS_BOND_ANGLES:
    f = 2;
    break;
  case F_CROSS_BOND_BONDS:
    f = 3;
    break;
  case F_UREY_BRADLEY:
    f = 4;
    break;
  case F_PDIHS:
  case F_RBDIHS:
  case F_FOURDIHS:
    bDih=TRUE;
    break;
  case F_IDIHS:
    f=1;
    bDih=TRUE;
    break;
  case F_CONSTRNC:
    f=1;
    break;
  case F_VSITE3FD:
    f = 1;
    break;
  case F_VSITE3FAD:
    f = 2;
    break;
  case F_VSITE3OUT:
    f = 3; 
    break;
  case F_VSITE4FDN:
      f = 1;
    break;
  case F_CMAP:
	  f = 1;
	break;
		  		  
  default:
    bDih=FALSE;
  }
  if (bFullDih)
    bDih=FALSE;
  if (fsubtype)
    f = fsubtype-1;
  
  nral = NRAL(ftype);
  nrfp = NRFP(ftype);
  
  /* header */
  fprintf(out,"[ %s ]\n",dir2str(d));
  fprintf(out,"; ");
  if (!bDih) {
    fprintf (out,"%3s  %4s","ai","aj");
    for (j=2; (j<nral); j++)
      fprintf (out,"  %3c%c",'a','i'+j);
  }
  else 
    for (j=0; (j<2); j++)
      fprintf (out,"%3c%c",'a','i'+dihp[f][j]);
  
  fprintf (out," funct");
  for (j=0; (j<nrfp); j++)
    fprintf (out," %12c%1d",'c',j);
  fprintf (out,"\n");
  
  /* print bondtypes */
  for (i=0; (i<bt->nr); i++) {
    bSwapParity = (bt->param[i].C0==NOTSET) && (bt->param[i].C1==-1);
    if (!bDih)
      for (j=0; (j<nral); j++)
	fprintf (out,"%5s ",get_atomtype_name(bt->param[i].a[j],at));
    else 
      for(j=0; (j<2); j++)
	fprintf (out,"%5s ",get_atomtype_name(bt->param[i].a[dihp[f][j]],at));
    fprintf (out,"%5d ", bSwapParity ? -f-1 : f+1);

    if (bt->param[i].s[0])
      fprintf(out,"   %s",bt->param[i].s);
    else
      for (j=0; (j<nrfp && (bt->param[i].c[j] != NOTSET)); j++)
	fprintf (out,"%13.6e ",bt->param[i].c[j]);
    
    fprintf (out,"\n");
  }
  fprintf (out,"\n");
  fflush (out);
}

void print_blocka(FILE *out, const char *szName, 
		  const char *szIndex, const char *szA,
		  t_blocka *block)
{
  int i,j;
  
  fprintf (out,"; %s\n",szName);
  fprintf (out,"; %4s    %s\n",szIndex,szA);
  for (i=0; (i < block->nr); i++) {
    for (i=0; (i < block->nr); i++) {
      fprintf (out,"%6d",i+1);
      for (j=block->index[i]; (j < ((int)block->index[i+1])); j++)
	fprintf (out,"%5d",block->a[j]+1);
      fprintf (out,"\n");
    }
    fprintf (out,"\n");
  }
}

void print_excl(FILE *out, int natoms, t_excls excls[])
{
  atom_id i;
  gmx_bool    have_excl;
  int     j;
  
  have_excl=FALSE;
  for(i=0; i<natoms && !have_excl; i++)
    have_excl = (excls[i].nr > 0);
  
  if (have_excl) {
    fprintf (out,"[ %s ]\n",dir2str(d_exclusions));
    fprintf (out,"; %4s    %s\n","i","excluded from i");
    for(i=0; i<natoms; i++)
      if (excls[i].nr > 0) {
	fprintf (out,"%6d ",i+1);
	for(j=0; j<excls[i].nr; j++)
	  fprintf (out," %5d",excls[i].e[j]+1);
	fprintf (out,"\n");
      }
    fprintf (out,"\n");
    fflush(out);
  }
}

static double get_residue_charge(const t_atoms *atoms,int at)
{
  int ri;
  double q;
  
  ri = atoms->atom[at].resind;
  q = 0;
  while (at < atoms->nr && atoms->atom[at].resind == ri) {
    q += atoms->atom[at].q;
    at++;
  }

  return q;
}

void print_atoms(FILE *out,gpp_atomtype_t atype,t_atoms *at,int *cgnr,
		 gmx_bool bRTPresname)
{
  int  i,ri;
  int  tpA,tpB;
  const char *as;
  char *tpnmA,*tpnmB;
  double qres,qtot;
  
  as=dir2str(d_atoms);
  fprintf(out,"[ %s ]\n",as);
  fprintf(out,"; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
	  "nr","type","resnr","residue","atom","cgnr","charge","mass","typeB","chargeB","massB");
    
  qtot  = 0;
  
  if (debug)
    fprintf(debug,"This molecule has %d atoms and %d residues\n",
	    at->nr,at->nres);
  
  if (at->nres) {
    /* if the information is present... */
    for (i=0; (i < at->nr); i++) {
      ri = at->atom[i].resind;
      if ((i == 0 || ri != at->atom[i-1].resind) &&
	  at->resinfo[ri].rtp != NULL) {
	qres = get_residue_charge(at,i);
	fprintf(out,"; residue %3d %-3s rtp %-4s q ",
		at->resinfo[ri].nr,
		*at->resinfo[ri].name,
		*at->resinfo[ri].rtp);
	if (fabs(qres) < 0.001) {
	  fprintf(out," %s","0.0");
	} else {
	  fprintf(out,"%+3.1f",qres);
	}
	fprintf(out,"\n");
      }
      tpA = at->atom[i].type;
      if ((tpnmA = get_atomtype_name(tpA,atype)) == NULL)
	gmx_fatal(FARGS,"tpA = %d, i= %d in print_atoms",tpA,i);
      
      fprintf(out,"%6d %10s %6d%c %5s %6s %6d %10g %10g",
	      i+1,tpnmA,
	      at->resinfo[ri].nr,
	      at->resinfo[ri].ic,
	      bRTPresname ?
	      *(at->resinfo[at->atom[i].resind].rtp) :
	      *(at->resinfo[at->atom[i].resind].name),
	      *(at->atomname[i]),cgnr[i],
	      at->atom[i].q,at->atom[i].m);
      if (PERTURBED(at->atom[i])) {
	tpB = at->atom[i].typeB;
	if ((tpnmB = get_atomtype_name(tpB,atype)) == NULL)
	  gmx_fatal(FARGS,"tpB = %d, i= %d in print_atoms",tpB,i);
	fprintf(out," %6s %10g %10g",
		tpnmB,at->atom[i].qB,at->atom[i].mB);
      }
      qtot += (double)at->atom[i].q;
      if ( fabs(qtot) < 4*GMX_REAL_EPS ) 
	qtot=0;
      fprintf(out,"   ; qtot %.4g\n",qtot);
    }
  }
  fprintf(out,"\n");
  fflush(out);
}

void print_bondeds(FILE *out,int natoms,directive d,
		   int ftype,int fsubtype,t_params plist[])
{
  t_symtab   stab;
  gpp_atomtype_t atype;
  t_param    *param;
  t_atom     *a;
  int i;
    
  atype = init_atomtype();
  snew(a,1);
  snew(param,1);
  open_symtab(&stab);
  for (i=0; (i < natoms); i++) {
    char buf[12];
    sprintf(buf,"%4d",(i+1));
    add_atomtype(atype,&stab,a,buf,param,0,0,0,0,0,0,0);
  }
  print_bt(out,d,atype,ftype,fsubtype,plist,TRUE);
    
  done_symtab(&stab);
  sfree(a);
  sfree(param);
  done_atomtype(atype);
}

