This program will generate random tetrahedral packings in a cubic lattice. It attempts to find high density packings. It is only in its first generation of development, however, so it has some ways to go before it is complete.

To run with defaults, type python main.py

to see the options, add the -h flag:

Options: -h, --help show this help message and exit -t N_T, --n_tet=N_T number of trials per output cluster -c NC, --n_clusters=N_C number of output clusters in set -b N_B, --n_buffer=N_B number of trial (buffer) clusters -l L_T, --l_trial=L_T number of tetrahedrons per trial -s RANDOM_SEED, --random_seed=RANDOM_SEED random seed -o N_O, --n_opt_steps=N_O # optimization steps

The output will go into a local directory that contains the options in the directory name. Within the directory, you will find a list of pdb files. These files contain methane like molecules, with the hydrogens given as vertices. To convert to the citrine format, there is a pdb_to_cit.py utility in this directory. There are also a variety of scripts for generating UCSF Chimera figures, which I will cover (later), once they are in a more stable form.

The following naming conventions apply to the output file:

clust-X-trial-Y-n-Z.XTAL_LOC.pdb

X: the cluster number (goes from 0 to n_cluster-1) Y: the trial number (goes from 0 to n_tet-1)

Each trial consists of a series of l_trial attempts to place tetrahedra a given cluster. As the packing becomes more dense, they are not always successful.

Z: the number of tetrahedra in the pdb file (up to Y*l_trial+1 maximum).

XTAL_LOC: The label for the crystal copy.

Since the symmetry is a simple rectangular prism displacement, each extension indicates the nature of the displacement relative to the central crystallographic unit with extension x0y0z0.

The dimensions of the crystal are listed in the headers.
For example xpymz0 means x is displaced by +DX y is displaced by -DY, and z is unchanged, where DX,DY,DZ are the prism dimensions.