new_contents: #!/usr/bin/env python
  "Plot the concentration field rho(x,y) in the course of time"
  from __future__ import print_function, division
  
  import argparse
  
  parser = argparse.ArgumentParser(description=__doc__)
  parser.add_argument('file', type=str, help='H5MD datafile')
  parser.add_argument('--species', type=int, default=1)
  parser.add_argument('--interval', type=int, default=20)
  args = parser.parse_args()
  
  import numpy as np
  import h5py
  import matplotlib.pyplot as plt
  import matplotlib.animation as animation
  
  f = plt.figure()
  c = None
  
  with h5py.File(args.file, 'r') as a: 
  
      rho_xy = a['fields/rho_xy/value']
      traj = a['particles/dimer/position/value'][:]
      edges = a['particles/dimer/box/edges'][:]
      traj += a['particles/dimer/image/value'][:]*edges.reshape((1,1,-1))
  
      x = np.arange(rho_xy.shape[1]+1)
      y = np.arange(rho_xy.shape[2]+1)
      X, Y = np.meshgrid(x, y)
  
      def update_plot(i):
          global c
          plt.title(str(i))
          l = plt.pcolormesh(X, Y, rho_xy[i*args.interval,:,:,args.species].T)
          if c is None:
              c = plt.colorbar()
          plt.plot(traj[:i*args.interval,0,0],traj[:i*args.interval,0,1], c='r', lw=4)
          plt.plot(traj[:i*args.interval,1,0],traj[:i*args.interval,1,1], c='k', lw=4)
          return l
  
      ani = animation.FuncAnimation(f, update_plot, rho_xy.shape[0]//args.interval, interval=100, repeat=False)
  
      plt.show()
  
subject: add analysis code time_rhoxy.py