voro++/zeo++

zeo++
---------

(1) The radii of atoms are tabulated in networkinfo.cc. If needed, you could define new atom types and assign atomic radii of your choice here.

(2) Box/unit cell vectors: a is aligned with the x-axis and b is in the xy-plane.

(3) The format of the output of the stochastic ray tracing option:
      x y z dx dy dz magnitude
      Here, magnitude = sqrt(dx*dx + dy*dy + dz*dz) and, for a given ray shooted into the free volume region, it provides a measure of the norm of that ray . I think, x y z are the coordinates of the starting point of the ray (not sure!). I think, the way to understand the output is as follows: A given ray starts from (x,y,z) and extends by dx, dy, and dz units along the x-, y-, and z-axes, respectively.

(4) Pore diameters:
     First value: D_i (Diameter of the largest included sphere).
     The largest included sphere points to the location of the largest cavity in the system and D_i measures the size of this cavity.

     Second value: D_f (Diameter of the largest free sphere).
      The largest free sphere corresponds to the largest spherical probe that can diffuse through the structure and D_f measures a minimum restricting aperture on a diffusion path.

     Third value: D_if (Diameter of the largest included sphere along free sphere path).
     D_if is a measure of the size of the largest cavity along free sphere path/diffusion path.

(5) The distance grid option is possible. The energy grid option is not available.
      Distance grid:
      A grid representation of the system is used.  Each grid point is assigned a distance to the surface of the nearest atom. The radius of the largest included sphere is then equal to the maximum value over all grid points. The clusters of neighboring grid points with the assigned distance values above a threshold corresponding to the probe radius are identified and connected to calculate the largest free sphere.

The energy grid option, in principle, can be used to estimate the net activation energy for diffusion of a probe through the system.

 (6) Voronoi netowrk:
        - Voro++ is used
        - voronoi cell associated with each atom is computed individually
        - the collection of edges and vertices/nodes of individual voronoi cell is stored
        - for each edge and vertix of the voronoi cell of an atom, the minimum distance to the atom is also stored. This distance is the distance to the surface of the central atom if its radius is specified (otherwise it is the distance to the center of the atom).

(7) To visualize the network:
      -  cd zeovis
      -  open ZeoVis.tcl and change the path to the network executable. 
      -  vmd -e ZeoVis.tcl
      -  You will be asked to provide the filename of your input file (i.e., the structure file). After providing the input filename, nothing will be displayed on the graphical window of vmd. Do not worry!
      - to show all atoms: show atom all
      - to show all nodes: show node all
      - to show the voronoi cell of an given atom (say, with index 4): show vorcel 4
      - to undo : undo
      - to show unit cell : show unitcell