gmx_rmpbc gets natoms passed again, without natoms many tool could not parse trajecto...

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

#include <string.h>
#include <ctype.h>
#include <math.h>

#include "sysstuff.h"
#include "smalloc.h"
#include "macros.h"
#include "statutil.h"
#include "maths.h"
#include "futil.h"
#include "index.h"
#include "copyrite.h"
#include "typedefs.h"
#include "xvgr.h"
#include "gstat.h"
#include "gmx_statistics.h"
#include "tpxio.h"
#include "pbc.h"
#include "vec.h"
#include "confio.h"
#include "gmx_ana.h"


#define FACTOR  1000.0  /* Convert nm^2/ps to 10e-5 cm^2/s */
/* NORMAL = total diffusion coefficient (default). X,Y,Z is diffusion 
   coefficient in X,Y,Z direction. LATERAL is diffusion coefficient in
   plane perpendicular to axis
*/
typedef enum { NOT_USED, NORMAL, X, Y, Z, LATERAL } msd_type;

typedef struct {
  real    t0;           /* start time and time increment between  */
  real    delta_t;      /* time between restart points */
  real    beginfit,     /* the begin/end time for fits as reals between */
          endfit;       /* 0 and 1 */
  real    dim_factor;   /* the dimensionality factor for the diffusion 
                           constant */
  real    **data;       /* the displacement data. First index is the group 
                           number, second is frame number */
  real    *time;        /* frame time */
  real    *mass;        /* masses for mass-weighted msd */
  matrix  **datam;
  rvec    **x0;         /* original positions */
  rvec    *com;         /* center of mass correction for each frame */
  gmx_stats_t **lsq;    /* fitting stats for individual molecule msds */
  msd_type type;        /* the type of msd to calculate (lateral, etc.)*/
  int       axis;       /* the axis along which to calculate */
  int       ncoords;
  int       nrestart;   /* number of restart points */
  int       nmol;       /* number of molecules (for bMol) */
  int       nframes;    /* number of frames */ 
  int       nlast;
  int       ngrp;       /* number of groups to use for msd calculation */
  int       *n_offs;
  int       **ndata;    /* the number of msds (particles/mols) per data 
                           point. */
} t_corr;

typedef real t_calc_func(t_corr *,int,atom_id[],int,rvec[],rvec,bool,matrix,
                         const output_env_t oenv);
                              
static real thistime(t_corr *curr) 
{
  return curr->time[curr->nframes]; 
}

static bool in_data(t_corr *curr,int nx00) 
{ 
  return curr->nframes-curr->n_offs[nx00]; 
}

t_corr *init_corr(int nrgrp,int type,int axis,real dim_factor,
                  int nmol,bool bTen,bool bMass,real dt,t_topology *top,
                  real beginfit,real endfit)
{
  t_corr  *curr;
  t_atoms *atoms;
  int     i;

  snew(curr,1);
  curr->type      = (msd_type)type;
  curr->axis      = axis;
  curr->ngrp      = nrgrp;
  curr->nrestart  = 0;
  curr->delta_t   = dt;
  curr->beginfit  = (1 - 2*GMX_REAL_EPS)*beginfit;
  curr->endfit    = (1 + 2*GMX_REAL_EPS)*endfit;
  curr->x0        = NULL;
  curr->n_offs    = NULL;
  curr->nframes   = 0;
  curr->nlast     = 0;
  curr->dim_factor = dim_factor;
  
  snew(curr->ndata,nrgrp);
  snew(curr->data,nrgrp);
  if (bTen)
    snew(curr->datam,nrgrp);
  for(i=0; (i<nrgrp); i++) {
    curr->ndata[i] = NULL;
    curr->data[i]  = NULL;
    if (bTen)
      curr->datam[i] = NULL;
  }
  curr->time = NULL;
  curr->lsq  = NULL;
  curr->nmol = nmol;
  if (curr->nmol > 0) {
    snew(curr->mass,curr->nmol);
    for(i=0; i<curr->nmol; i++)
      curr->mass[i] = 1;
  }
  else {
    if (bMass) {
      atoms = &top->atoms;
      snew(curr->mass,atoms->nr);
      for(i=0; (i<atoms->nr); i++) {
        curr->mass[i] = atoms->atom[i].m;
      }
    }
  }

  return curr;
}

static void done_corr(t_corr *curr)
{
  int i;
  
  sfree(curr->n_offs);
  for(i=0; (i<curr->nrestart); i++)
    sfree(curr->x0[i]);
  sfree(curr->x0);
}

static void corr_print(t_corr *curr,bool bTen,const char *fn,const char *title,
                       const char *yaxis,
                       real msdtime,real beginfit,real endfit,
                       real *DD,real *SigmaD,char *grpname[],
                       const output_env_t oenv)
{
  FILE *out;
  int  i,j;
  
  out=xvgropen(fn,title,output_env_get_xvgr_tlabel(oenv),yaxis,oenv);
  if (DD) {
    fprintf(out,"# MSD gathered over %g %s with %d restarts\n",
            msdtime,output_env_get_time_unit(oenv),curr->nrestart);
    fprintf(out,"# Diffusion constants fitted from time %g to %g %s\n",
            beginfit,endfit,output_env_get_time_unit(oenv));
    for(i=0; i<curr->ngrp; i++) 
      fprintf(out,"# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n",
              grpname[i],DD[i],SigmaD[i]);
  }
  for(i=0; i<curr->nframes; i++) {
    fprintf(out,"%10g",output_env_conv_time(oenv,curr->time[i]));
    for(j=0; j<curr->ngrp; j++) {
      fprintf(out,"  %10g",curr->data[j][i]);
      if (bTen) {
        fprintf(out," %10g %10g %10g %10g %10g %10g",
                curr->datam[j][i][XX][XX],
                curr->datam[j][i][YY][YY],
                curr->datam[j][i][ZZ][ZZ],
                curr->datam[j][i][YY][XX],
                curr->datam[j][i][ZZ][XX],
                curr->datam[j][i][ZZ][YY]);
      }
    }
    fprintf(out,"\n");
  }
  ffclose(out);
}

/* called from corr_loop, to do the main calculations */
static void calc_corr(t_corr *curr,int nr,int nx,atom_id index[],rvec xc[],
                      bool bRmCOMM,rvec com,t_calc_func *calc1,bool bTen,
                      const output_env_t oenv)
{
  int  nx0;
  real g;
  matrix mat;
  rvec dcom;
  
  /* Check for new starting point */
  if (curr->nlast < curr->nrestart) {
    if ((thistime(curr) >= (curr->nlast*curr->delta_t)) && (nr==0)) {
      memcpy(curr->x0[curr->nlast],xc,curr->ncoords*sizeof(xc[0]));
      curr->n_offs[curr->nlast]=curr->nframes;
      copy_rvec(com,curr->com[curr->nlast]);
      curr->nlast++;
    }
  }

  /* nx0 appears to be the number of new starting points,
   * so for all starting points, call calc1. 
   */
  for(nx0=0; (nx0<curr->nlast); nx0++) {
    if (bRmCOMM) {
      rvec_sub(com,curr->com[nx0],dcom);
    } else {
      clear_rvec(dcom);
    }
    g = calc1(curr,nx,index,nx0,xc,dcom,bTen,mat,oenv);
#ifdef DEBUG2
    printf("g[%d]=%g\n",nx0,g);
#endif
    curr->data[nr][in_data(curr,nx0)] += g;
    if (bTen) {
      m_add(curr->datam[nr][in_data(curr,nx0)],mat,
            curr->datam[nr][in_data(curr,nx0)]);
    }
    curr->ndata[nr][in_data(curr,nx0)]++;
  }
}

/* the non-mass-weighted mean-squared displacement calcuation */
static real calc1_norm(t_corr *curr,int nx,atom_id index[],int nx0,rvec xc[],
                      rvec dcom,bool bTen,matrix mat, const output_env_t oenv)
{
  int  i,ix,m,m2;
  real g,r,r2;
  rvec rv;
  
  g=0.0;
  clear_mat(mat);

  for(i=0; (i<nx); i++) {
    ix=index[i];
    r2=0.0;
    switch (curr->type) {
    case NORMAL:
      for(m=0; (m<DIM); m++) {
        rv[m] = xc[ix][m] - curr->x0[nx0][ix][m] - dcom[m];
        r2   += rv[m]*rv[m];
        if (bTen) {
          for(m2=0; m2<=m; m2++)
            mat[m][m2] += rv[m]*rv[m2];
        }
      }
      break;
    case X:
    case Y:
    case Z:
      r = xc[ix][curr->type-X] - curr->x0[nx0][ix][curr->type-X] - 
                dcom[curr->type-X];
      r2 += r*r;
      break;
    case LATERAL:
      for(m=0; (m<DIM); m++) {
        if (m != curr->axis) {
          r   = xc[ix][m] - curr->x0[nx0][ix][m] - dcom[m];
          r2 += r*r;
        }
      }
      break;
    default:
      gmx_fatal(FARGS,"Error: did not expect option value %d",curr->type);
    }
    g+=r2;
  }
  g/=nx;
  msmul(mat,1.0/nx,mat);

  return g;
}

/* calculate the com of molecules in x and put it into xa */
static void calc_mol_com(int nmol,int *molindex,t_block *mols,t_atoms *atoms,
                         rvec *x,rvec *xa)
{
  int  m,mol,i,d;
  rvec xm;
  real mass,mtot;

  for(m=0; m<nmol; m++) {
    mol = molindex[m];
    clear_rvec(xm);
    mtot = 0;
    for(i=mols->index[mol]; i<mols->index[mol+1]; i++) {
      mass = atoms->atom[i].m;
      for(d=0; d<DIM; d++)
        xm[d] += mass*x[i][d];
      mtot += mass;
    }
    svmul(1/mtot,xm,xa[m]);
  }
}

static real calc_one_mw(t_corr *curr,int ix,int nx0,rvec xc[],real *tm,
                        rvec dcom,bool bTen,matrix mat)
{
  real r2,r,mm;
  rvec rv;
  int  m,m2;
  
  mm=curr->mass[ix];
  if (mm == 0)
    return 0;
  (*tm) += mm;
  r2     = 0.0;
  switch (curr->type) {
  case NORMAL:
    for(m=0; (m<DIM); m++) {
      rv[m] = xc[ix][m] - curr->x0[nx0][ix][m] - dcom[m];
      r2   += mm*rv[m]*rv[m];
      if (bTen) {
        for(m2=0; m2<=m; m2++)
          mat[m][m2] += mm*rv[m]*rv[m2];
      }
    }
    break;
  case X:
  case Y:
  case Z:
    r  = xc[ix][curr->type-X] - curr->x0[nx0][ix][curr->type-X] - 
              dcom[curr->type-X];
    r2 = mm*r*r;
      break;
  case LATERAL:
    for(m=0; (m<DIM); m++) {
      if (m != curr->axis) {
        r   = xc[ix][m] - curr->x0[nx0][ix][m] - dcom[m];
        r2 += mm*r*r;
      }
    }
    break;
  default:
    gmx_fatal(FARGS,"Options got screwed. Did not expect value %d\n",curr->type);
  } /* end switch */
  return r2;
}

/* the normal, mass-weighted mean-squared displacement calcuation */
static real calc1_mw(t_corr *curr,int nx,atom_id index[],int nx0,rvec xc[],
                     rvec dcom,bool bTen,matrix mat,const output_env_t oenv)
{
  int  i;
  real g,tm;

  g=tm=0.0;
  clear_mat(mat);
  for(i=0; (i<nx); i++) 
    g += calc_one_mw(curr,index[i],nx0,xc,&tm,dcom,bTen,mat);
  
  g/=tm;
  if (bTen)
    msmul(mat,1/tm,mat);

  return g;
}

/* prepare the coordinates by removing periodic boundary crossings.
   gnx = the number of atoms/molecules
   index = the indices
   xcur = the current coordinates
   xprev = the previous coordinates
   box = the box matrix */
static void prep_data(bool bMol,int gnx,atom_id index[],
                      rvec xcur[],rvec xprev[],matrix box)
{
    int  i,m,ind;
    rvec hbox;

    /* Remove periodicity */
    for(m=0; (m<DIM); m++)
        hbox[m]=0.5*box[m][m];
    
    for(i=0; (i<gnx); i++) {
        if (bMol)
            ind = i;
        else
            ind = index[i];

        for(m=DIM-1; m>=0; m--) 
        {
            while(xcur[ind][m]-xprev[ind][m] <= -hbox[m])
                rvec_inc(xcur[ind],box[m]);
            while(xcur[ind][m]-xprev[ind][m] >  hbox[m])
                rvec_dec(xcur[ind],box[m]);
        }      
    }
}

/* calculate the center of mass for a group 
   gnx = the number of atoms/molecules
   index = the indices
   xcur = the current coordinates
   xprev = the previous coordinates
   box = the box matrix
   atoms = atom data (for mass)
   com(output) = center of mass  */
static void calc_com(bool bMol, int gnx, atom_id index[], 
                     rvec xcur[],rvec xprev[],matrix box, t_atoms *atoms,
                     rvec com)
{
    int  i,m,ind;
    real mass;
    double tmass;
    dvec sx;

    clear_dvec(sx);
    tmass = 0;
    mass = 1;

    prep_data(bMol, gnx, index, xcur, xprev, box);
    for(i=0; (i<gnx); i++) 
    {
        if (bMol)
            ind = i;
        else
            ind = index[i];


        mass = atoms->atom[ind].m;
        for(m=0; m<DIM; m++)
            sx[m] += mass*xcur[ind][m];
        tmass += mass;
    }
    for(m=0; m<DIM; m++)
        com[m] = sx[m]/tmass;
}


static real calc1_mol(t_corr *curr,int nx,atom_id index[],int nx0,rvec xc[],
                      rvec dcom,bool bTen,matrix mat, const output_env_t oenv)
{
  int  i;
  real g,tm,gtot,tt;

  tt = curr->time[in_data(curr,nx0)];
  gtot = 0;
  tm = 0;
  clear_mat(mat);
  for(i=0; (i<nx); i++) {
    g = calc_one_mw(curr,i,nx0,xc,&tm,dcom,bTen,mat);
    /* We don't need to normalize as the mass was set to 1 */
    gtot += g;
    if (tt >= curr->beginfit && (curr->endfit < 0 || tt <= curr->endfit))
      gmx_stats_add_point(curr->lsq[nx0][i],tt,g,0,0);
  }
  msmul(mat,1.0/nx,mat);

  return gtot/nx;
}

void printmol(t_corr *curr,const char *fn,
              const char *fn_pdb,int *molindex,t_topology *top,
              rvec *x,int ePBC,matrix box, const output_env_t oenv)
{
#define NDIST 100
  FILE  *out;
  gmx_stats_t lsq1;
  int   i,j;
  real  a,b,D,Dav,D2av,VarD,sqrtD,sqrtD_max,scale;
  t_pdbinfo *pdbinfo=NULL;
  int   *mol2a=NULL;

  out=xvgropen(fn,"Diffusion Coefficients / Molecule","Molecule","D",oenv);
  
  if (fn_pdb) {
    if (top->atoms.pdbinfo == NULL)
      snew(top->atoms.pdbinfo,top->atoms.nr);
    pdbinfo = top->atoms.pdbinfo;
    mol2a = top->mols.index;
  }

  Dav = D2av = 0;
  sqrtD_max = 0;
  for(i=0; (i<curr->nmol); i++) {
    lsq1 = gmx_stats_init();
    for(j=0; (j<curr->nrestart); j++) {
      real xx,yy,dx,dy;
      
      while(gmx_stats_get_point(curr->lsq[j][i],&xx,&yy,&dx,&dy) == estatsOK)
          gmx_stats_add_point(lsq1,xx,yy,dx,dy);
    }
    gmx_stats_get_ab(lsq1,elsqWEIGHT_NONE,&a,&b,NULL,NULL,NULL,NULL);
    gmx_stats_done(lsq1);
    sfree(lsq1);
    D     = a*FACTOR/curr->dim_factor;
    if (D < 0)
      D   = 0;
    Dav  += D;
    D2av += sqr(D);
    fprintf(out,"%10d  %10g\n",i,D);
    if (pdbinfo) {
      sqrtD = sqrt(D);
      if (sqrtD > sqrtD_max)
        sqrtD_max = sqrtD;
      for(j=mol2a[molindex[i]]; j<mol2a[molindex[i]+1]; j++)
        pdbinfo[j].bfac = sqrtD;
    }
  }
  ffclose(out);
  do_view(oenv,fn,"-graphtype bar");
  
  /* Compute variance, stddev and error */
  Dav  /= curr->nmol;
  D2av /= curr->nmol;
  VarD  = D2av - sqr(Dav);
  printf("<D> = %.4f Std. Dev. = %.4f Error = %.4f\n",
         Dav,sqrt(VarD),sqrt(VarD/curr->nmol));

  if (fn_pdb && x) {
    scale = 1;
    while (scale*sqrtD_max > 10)
      scale *= 0.1;
    while (scale*sqrtD_max < 0.1)
      scale *= 10;
    for(i=0; i<top->atoms.nr; i++)
      pdbinfo[i].bfac *= scale;
    write_sto_conf(fn_pdb,"molecular MSD",&top->atoms,x,NULL,ePBC,box);
  }
}

/* this is the main loop for the correlation type functions 
 * fx and nx are file pointers to things like read_first_x and
 * read_next_x
 */
int corr_loop(t_corr *curr,const char *fn,t_topology *top,int ePBC,
              bool bMol,int gnx[],atom_id *index[],
              t_calc_func *calc1,bool bTen, int *gnx_com, atom_id *index_com[],
              real dt, real t_pdb,rvec **x_pdb,matrix box_pdb, 
              const output_env_t oenv)
{
  rvec         *x[2]; /* the coordinates to read */
  rvec         *xa[2]; /* the coordinates to calculate displacements for */
  rvec         com={0};
  real         t,t_prev=0;
  int          natoms,i,j,cur=0,maxframes=0;
  t_trxstatus *status;
#define        prev (1-cur)
  matrix       box;
  bool         bFirst;
  gmx_rmpbc_t  gpbc=NULL;

  natoms = read_first_x(oenv,&status,fn,&curr->t0,&(x[cur]),box);
#ifdef DEBUG
  fprintf(stderr,"Read %d atoms for first frame\n",natoms);
#endif
  if ((gnx_com!=NULL) && natoms < top->atoms.nr) {
    fprintf(stderr,"WARNING: The trajectory only contains part of the system (%d of %d atoms) and therefore the COM motion of only this part of the system will be removed\n",natoms,top->atoms.nr);
  }

  snew(x[prev],natoms);

  if (bMol) {
    curr->ncoords = curr->nmol;
    snew(xa[0],curr->ncoords);
    snew(xa[1],curr->ncoords);
  } else {
    curr->ncoords = natoms;
    xa[0] = x[0];
    xa[1] = x[1];
  }

  bFirst = TRUE;
  t=curr->t0;
  if (x_pdb)
    *x_pdb = NULL;

  if (bMol)
    gpbc = gmx_rmpbc_init(&top->idef,ePBC,natoms,box);

  /* the loop over all frames */
  do 
  {
    if (x_pdb && ((bFirst && t_pdb < t) || 
                  (!bFirst && 
                   t_pdb > t - 0.5*(t - t_prev) && 
                   t_pdb < t + 0.5*(t - t_prev)))) 
    {
        if (*x_pdb == NULL)
            snew(*x_pdb,natoms);
        for(i=0; i<natoms; i++)
            copy_rvec(x[cur][i],(*x_pdb)[i]);
        copy_mat(box,box_pdb);
    }
      

    /* check whether we've reached a restart point */
    if (bRmod(t,curr->t0,dt)) {
      curr->nrestart++;
  
      srenew(curr->x0,curr->nrestart);
      snew(curr->x0[curr->nrestart-1],curr->ncoords);
      srenew(curr->com,curr->nrestart);
      srenew(curr->n_offs,curr->nrestart);
      srenew(curr->lsq,curr->nrestart);
      snew(curr->lsq[curr->nrestart-1],curr->nmol);
      for(i=0;i<curr->nmol;i++)
          curr->lsq[curr->nrestart-1][i]  = gmx_stats_init();

      if (debug)
        fprintf(debug,"Extended data structures because of new restart %d\n",
                curr->nrestart);
    }
    /* create or extend the frame-based arrays */
    if (curr->nframes >= maxframes-1) {
      if (maxframes==0) {
        for(i=0; (i<curr->ngrp); i++) {
          curr->ndata[i] = NULL;
          curr->data[i]  = NULL;
          if (bTen)
            curr->datam[i] = NULL;
        }
        curr->time = NULL;
      }
      maxframes+=10;
      for(i=0; (i<curr->ngrp); i++) {
        srenew(curr->ndata[i],maxframes);
        srenew(curr->data[i],maxframes);
        if (bTen)
          srenew(curr->datam[i],maxframes);
        for(j=maxframes-10; j<maxframes; j++) {
          curr->ndata[i][j]=0;
          curr->data[i][j]=0;
          if (bTen)
            clear_mat(curr->datam[i][j]);
        }
      }
      srenew(curr->time,maxframes);
    }

    /* set the time */
    curr->time[curr->nframes] = t - curr->t0;

    /* for the first frame, the previous frame is a copy of the first frame */
    if (bFirst) {
      memcpy(xa[prev],xa[cur],curr->ncoords*sizeof(xa[prev][0]));
      bFirst = FALSE;
    }

    /* make the molecules whole */
    if (bMol)
      gmx_rmpbc(gpbc,natoms,box,x[cur]);

    /* first remove the periodic boundary condition crossings */
    for(i=0;i<curr->ngrp;i++)
    {
        prep_data(bMol, gnx[i], index[i], xa[cur], xa[prev], box);
    }

    /* calculate the center of mass */
    if (gnx_com)
    {
        prep_data(bMol, gnx_com[0], index_com[0], xa[cur], xa[prev], box);
        calc_com(bMol, gnx_com[0], index_com[0], xa[cur], xa[prev], box,
                 &top->atoms, com);
    }

    /* calculate the molecules' centers of masses and put them into xa */
    if (bMol)
        calc_mol_com(gnx[0],index[0],&top->mols,&top->atoms, x[cur],xa[cur]);
    
    /* loop over all groups in index file */
    for(i=0; (i<curr->ngrp); i++) 
    {
      /* calculate something useful, like mean square displacements */
      calc_corr(curr,i,gnx[i],index[i],xa[cur], (gnx_com!=NULL),com,
                calc1,bTen,oenv);
    }
    cur=prev;
    t_prev = t;
    
    curr->nframes++;
  } while (read_next_x(oenv,status,&t,natoms,x[cur],box));
  fprintf(stderr,"\nUsed %d restart points spaced %g %s over %g %s\n\n", 
          curr->nrestart, 
          output_env_conv_time(oenv,dt), output_env_get_time_unit(oenv),
          output_env_conv_time(oenv,curr->time[curr->nframes-1]), 
          output_env_get_time_unit(oenv) );
  
  if (bMol)
    gmx_rmpbc_done(gpbc);

  close_trj(status);

  return natoms;
}
 
static void index_atom2mol(int *n,int *index,t_block *mols)
{
  int nat,i,nmol,mol,j;

  nat = *n;
  i = 0;
  nmol = 0;
  mol = 0;
  while (i < nat) {
    while (index[i] > mols->index[mol]) {
      mol++;
      if (mol >= mols->nr)
        gmx_fatal(FARGS,"Atom index out of range: %d",index[i]+1);
    }
    for(j=mols->index[mol]; j<mols->index[mol+1]; j++) {
      if (i >= nat || index[i] != j)
        gmx_fatal(FARGS,"The index group does not consist of whole molecules");
      i++;
    }
    index[nmol++] = mol;
  }

  fprintf(stderr,"Split group of %d atoms into %d molecules\n",nat,nmol);
  
  *n = nmol;
}
                            
void do_corr(const char *trx_file, const char *ndx_file, const char *msd_file, 
             const char *mol_file, const char *pdb_file,real t_pdb,
             int nrgrp, t_topology *top,int ePBC,
             bool bTen,bool bMW,bool bRmCOMM,
             int type,real dim_factor,int axis,
             real dt,real beginfit,real endfit,const output_env_t oenv)
{
  t_corr       *msd;
  int          *gnx; /* the selected groups' sizes */
  atom_id      **index; /* selected groups' indices */
  char         **grpname; 
  int          i,i0,i1,j,N,nat_trx;
  real         *DD,*SigmaD,a,a2,b,r,chi2;
  rvec         *x;
  matrix       box;
  int          *gnx_com=NULL; /* the COM removal group size  */
  atom_id      **index_com=NULL; /* the COM removal group atom indices */
  char         **grpname_com=NULL; /* the COM removal group name */

  snew(gnx,nrgrp);
  snew(index,nrgrp);
  snew(grpname,nrgrp);
   
  fprintf(stderr, "\nSelect a group to calculate mean squared displacement for:\n");
  get_index(&top->atoms,ndx_file,nrgrp,gnx,index,grpname);

  if (bRmCOMM)
  {
      snew(gnx_com,1);
      snew(index_com,1);
      snew(grpname_com,1);

      fprintf(stderr, "\nNow select a group for center of mass removal:\n");
      get_index(&top->atoms, ndx_file, 1, gnx_com, index_com, grpname_com);
  }
  
  if (mol_file)
    index_atom2mol(&gnx[0],index[0],&top->mols);

  msd = init_corr(nrgrp,type,axis,dim_factor,
                  mol_file==NULL ? 0 : gnx[0],bTen,bMW,dt,top,
                  beginfit,endfit);
  
  nat_trx =
    corr_loop(msd,trx_file,top,ePBC,mol_file ? gnx[0] : 0,gnx,index,
              (mol_file!=NULL) ? calc1_mol : (bMW ? calc1_mw : calc1_norm),
              bTen, gnx_com, index_com, dt,t_pdb,
              pdb_file ? &x : NULL,box,oenv);

  /* Correct for the number of points */
  for(j=0; (j<msd->ngrp); j++) {
    for(i=0; (i<msd->nframes); i++) {
      msd->data[j][i] /= msd->ndata[j][i];
      if (bTen)
        msmul(msd->datam[j][i],1.0/msd->ndata[j][i],msd->datam[j][i]);
    }
  }

  if (mol_file) {
    if (pdb_file && x == NULL) {
      fprintf(stderr,"\nNo frame found need time tpdb = %g ps\n"
              "Can not write %s\n\n",t_pdb,pdb_file);
    }
    i = top->atoms.nr;
    top->atoms.nr = nat_trx;
    printmol(msd,mol_file,pdb_file,index[0],top,x,ePBC,box,oenv);
    top->atoms.nr = i;
  }

  DD     = NULL;
  SigmaD = NULL;

  if (beginfit == -1) {
    i0 = (int)(0.1*(msd->nframes - 1) + 0.5);
    beginfit = msd->time[i0];
  } else
  for(i0=0; i0<msd->nframes && msd->time[i0]<beginfit; i0++) 
    ;

  if (endfit == -1) {
    i1 = (int)(0.9*(msd->nframes - 1) + 0.5) + 1;
    endfit = msd->time[i1-1];
  } else
    for(i1=i0; i1<msd->nframes && msd->time[i1]<=endfit; i1++)
                      ;
  fprintf(stdout,"Fitting from %g to %g %s\n\n",beginfit,endfit,
                 output_env_get_time_unit(oenv));

  N = i1-i0;
  if (N <= 2) {
    fprintf(stdout,"Not enough points for fitting (%d).\n"
            "Can not determine the diffusion constant.\n",N);
  } else {
    snew(DD,msd->ngrp);
    snew(SigmaD,msd->ngrp);
    for(j=0; j<msd->ngrp; j++) {
      if (N >= 4) {
        lsq_y_ax_b(N/2,&(msd->time[i0]),&(msd->data[j][i0]),&a,&b,&r,&chi2);
        lsq_y_ax_b(N/2,&(msd->time[i0+N/2]),&(msd->data[j][i0+N/2]),&a2,&b,&r,&chi2);
        SigmaD[j] = fabs(a-a2);
      } else
        SigmaD[j] = 0;
      lsq_y_ax_b(N,&(msd->time[i0]),&(msd->data[j][i0]),&(DD[j]),&b,&r,&chi2);
      DD[j]     *= FACTOR/msd->dim_factor;
      SigmaD[j] *= FACTOR/msd->dim_factor;
      if (DD[j] > 0.01 && DD[j] < 1e4)
          fprintf(stdout,"D[%10s] %.4f (+/- %.4f) 1e-5 cm^2/s\n",
                  grpname[j],DD[j],SigmaD[j]);
      else
          fprintf(stdout,"D[%10s] %.4g (+/- %.4g) 1e-5 cm^2/s\n",
                  grpname[j],DD[j], SigmaD[j]);
    }
  }
  /* Print mean square displacement */
  corr_print(msd,bTen,msd_file,
             "Mean Square Displacement",
             "MSD (nm\\S2\\N)",
             msd->time[msd->nframes-1],beginfit,endfit,DD,SigmaD,grpname,oenv);
}

int gmx_msd(int argc,char *argv[])
{
  const char *desc[] = {
    "g_msd computes the mean square displacement (MSD) of atoms from",
    "a set of initial positions. This provides an easy way to compute",
    "the diffusion constant using the Einstein relation.",
    "The time between the reference points for the MSD calculation",
    "is set with [TT]-trestart[tt].",
    "The diffusion constant is calculated by least squares fitting a",
    "straight line (D*t + c) through the MSD(t) from [TT]-beginfit[tt] to",
    "[TT]-endfit[tt] (note that t is time from the reference positions,",
    "not simulation time). An error estimate given, which is the difference",
    "of the diffusion coefficients obtained from fits over the two halves",
    "of the fit interval.[PAR]",
    "There are three, mutually exclusive, options to determine different",
    "types of mean square displacement: [TT]-type[tt], [TT]-lateral[tt]",
    "and [TT]-ten[tt]. Option [TT]-ten[tt] writes the full MSD tensor for",
    "each group, the order in the output is: trace xx yy zz yx zx zy.[PAR]",
    "If [TT]-mol[tt] is set, g_msd plots the MSD for individual molecules: ",
    "for each individual molecule a diffusion constant is computed for ",
    "its center of mass. The chosen index group will be split into ",
    "molecules.[PAR]",
    "The default way to calculate a MSD is by using mass-weighted averages.",
    "This can be turned off with [TT]-nomw[tt].[PAR]",
    "With the option [TT]-rmcomm[tt], the center of mass motion of a ",
    "specific group can be removed. For trajectories produced with ",
    "GROMACS this is usually not necessary, ",
    "as mdrun usually already removes the center of mass motion.",
    "When you use this option be sure that the whole system is stored",
    "in the trajectory file.[PAR]",
    "The diffusion coefficient is determined by linear regression of the MSD,",
    "where, unlike for the normal output of D, the times are weighted",
    "according to the number of reference points, i.e. short times have",
    "a higher weight. Also when [TT]-beginfit[tt]=-1,fitting starts at 10%",
    "and when [TT]-endfit[tt]=-1, fitting goes to 90%.",
    "Using this option one also gets an accurate error estimate",
    "based on the statistics between individual molecules.",
    "Note that this diffusion coefficient and error estimate are only",
    "accurate when the MSD is completely linear between",
    "[TT]-beginfit[tt] and [TT]-endfit[tt].[PAR]",
    "Option [TT]-pdb[tt] writes a pdb file with the coordinates of the frame",
    "at time [TT]-tpdb[tt] with in the B-factor field the square root of",
    "the diffusion coefficient of the molecule.",
    "This option implies option [TT]-mol[tt]."
  };
  static const char *normtype[]= { NULL,"no","x","y","z",NULL };
  static const char *axtitle[] = { NULL,"no","x","y","z",NULL };
  static int  ngroup     = 1;
  static real dt         = 10; 
  static real t_pdb      = 0; 
  static real beginfit   = -1; 
  static real endfit     = -1; 
  static bool bTen       = FALSE;
  static bool bMW        = TRUE;
  static bool bRmCOMM    = FALSE;
  t_pargs pa[] = {
    { "-type",    FALSE, etENUM, {normtype},
      "Compute diffusion coefficient in one direction" },
    { "-lateral", FALSE, etENUM, {axtitle}, 
      "Calculate the lateral diffusion in a plane perpendicular to" },
    { "-ten",      FALSE, etBOOL, {&bTen},
      "Calculate the full tensor" },
    { "-ngroup",  FALSE, etINT,  {&ngroup},
      "Number of groups to calculate MSD for" },
    { "-mw",      FALSE, etBOOL, {&bMW},
      "Mass weighted MSD" },
    { "-rmcomm",      FALSE, etBOOL, {&bRmCOMM},
      "Remove center of mass motion" },
    { "-tpdb",FALSE, etTIME, {&t_pdb},
      "The frame to use for option -pdb (%t)" },
    { "-trestart",FALSE, etTIME, {&dt},
      "Time between restarting points in trajectory (%t)" },
    { "-beginfit",FALSE, etTIME, {&beginfit},
      "Start time for fitting the MSD (%t), -1 is 10%" },
    { "-endfit",FALSE, etTIME, {&endfit},
      "End time for fitting the MSD (%t), -1 is 90%" }
  };

  t_filenm fnm[] = { 
    { efTRX, NULL, NULL,  ffREAD },
    { efTPS, NULL, NULL,  ffREAD }, 
    { efNDX, NULL, NULL,  ffOPTRD },
    { efXVG, NULL, "msd", ffWRITE },
    { efXVG, "-mol", "diff_mol",ffOPTWR },
    { efPDB, "-pdb", "diff_mol", ffOPTWR }
  };
#define NFILE asize(fnm)

  t_topology  top;
  int         ePBC;
  matrix      box;
  char        title[256];
  const char  *trx_file, *tps_file, *ndx_file, *msd_file, *mol_file, *pdb_file;
  rvec        *xdum;
  bool        bTop;
  int         axis,type;
  real        dim_factor;
  output_env_t oenv;

  CopyRight(stderr,argv[0]);

  parse_common_args(&argc,argv,
                    PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT | PCA_BE_NICE,
                    NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
  trx_file = ftp2fn_null(efTRX,NFILE,fnm);
  tps_file = ftp2fn_null(efTPS,NFILE,fnm);
  ndx_file = ftp2fn_null(efNDX,NFILE,fnm);
  msd_file = ftp2fn_null(efXVG,NFILE,fnm);
  pdb_file = opt2fn_null("-pdb",NFILE,fnm);
  if (pdb_file)
    mol_file = opt2fn("-mol",NFILE,fnm);
  else
    mol_file = opt2fn_null("-mol",NFILE,fnm);
  
  if (ngroup < 1)
    gmx_fatal(FARGS,"Must have at least 1 group (now %d)",ngroup);
  if (mol_file && ngroup > 1)
    gmx_fatal(FARGS,"With molecular msd can only have 1 group (now %d)",
              ngroup);


  if (mol_file) {
    bMW  = TRUE;
    fprintf(stderr,"Calculating diffusion coefficients for molecules.\n");
  }

  if (normtype[0][0]!='n') {
    type = normtype[0][0] - 'x' + X; /* See defines above */
    dim_factor = 2.0;
  }
  else {
    type       = NORMAL;
    dim_factor = 6.0;
  }
  if ((type==NORMAL) && (axtitle[0][0]!='n')) {
    type=LATERAL;
    dim_factor = 4.0;
    axis = (axtitle[0][0] - 'x'); /* See defines above */
  }
  else
    axis = 0;

  if (bTen && type != NORMAL)
    gmx_fatal(FARGS,"Can only calculate the full tensor for 3D msd");

  bTop = read_tps_conf(tps_file,title,&top,&ePBC,&xdum,NULL,box,bMW||bRmCOMM); 
  if (mol_file && !bTop)
    gmx_fatal(FARGS,
              "Could not read a topology from %s. Try a tpr file instead.",
              tps_file);
    
  do_corr(trx_file,ndx_file,msd_file,mol_file,pdb_file,t_pdb,ngroup,
          &top,ePBC,bTen,bMW,bRmCOMM,type,dim_factor,axis,dt,beginfit,endfit,
          oenv);
  
  view_all(oenv,NFILE, fnm);
  
  thanx(stderr);
  
  return 0;
}