Evaluation of weighted Voronoi decompositions of physicochemical ensembles

Foam Data Key:

The data are organized into two main trees with the same structure, 1000 balls and 100 balls. Within these folders lies six subfolders:

1. PBC Overlap 0.0r

2. NonPBC Overlap 0.0r

3. PBC Overlap 0.5r

4. NonPBC Overlap 0.5r

5. PBC Overlap 1.0r

6. NonPBC Overlap 1.0r

Within each subfolder lies the data for each setting across different CV and Density values. These range as follows:

CV Values (11)      = [0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 1.00]

Density Values (10) = [0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50]

Each combination has 20 different iterations bringing the total number of subfolders to 11 x 10 x 20 = 2200. (Note: in ensembles with no overlap, some combinations of low CV and high density are missing due to their difficulty to generate).

The subfolders are named with the settings used to create the ensembles they house. These naming settings are, in order, as follows:

1. Mean - The average ball size in the grouping of balls

2. CV - The coefficient of variation of the set of balls

3. Number of Balls - The number of balls in the ensemble (note that if the ensemble has periodic boundary conditions, the number of balls in the actual ball file will be 27x this number)

4. Density - How tightly packed the balls are. Density = Volume of balls / Volume of the box that contains them

5. Number - File number for repeated runs with the same settings

Example:

1.0_0.2_1000_0.5_3 = Mean: 1.0, CV: 0.2, # of Balls: 1000, Density: 0.5, Iteration: 3

Each subfolder has the following files in the following structure:

> aw

> aw_verts.txt - The vertices from the additively weighted Voronoi diagram. 

> aw_logs.csv - The complete logs of the additively weighted Voronoi diagram

> pow

> pow_verts.txt - The vertices from the power Voronoi diagram. 

> pow_logs.csv - The complete logs of the power Voronoi diagram

> balls.pdb - A pdb file with the location, radius, and grouping of the balls in the foam. This works as a viewable file in molecular visualization software like PyMOL. 

> balls.txt - A text file with the locations and radii of the balls for more precise calculation than the pdb.

> retaining_box.off - This is an object file that shows the box that the balls were constructed using. The volume os the box is used in the density calculation. Note: depending on if the ensemble has a periodic boundary, the balls in the central grouping may hang outside of the box, but in either case their centers will lie inside the box. 

> set_balls.pml - This file is a PyMOL script file that sets the radii of the balls in viewer.