Glotzilla Unix Executables
Listed below are all of the binaries/executables available in glotzilla (not yet complete). The executables can run from the terminal after installing Glotzilla. Note that many of the binaries that come with unix can be very useful for soft matter research. A short list is provided here. The executables use the pipes and filters approach of unix to create a logical workflow for molcular simulation research.
glotzcc
vis3d
- Displays shapes in an openGL window. Excellent for creating movies of simulation data.
- man page
- examples
mkcrystal
- Places particles on a lattice, the usage is as follows:
- -h --help Prints this help
- -n --numpart=INTEGER Number of particles
- -d --density=DECIMAL Number density of the system
- -s --shape=SHAPE Shape of the crystal (default is cube)
- -S --sc Simple cubic
- -F --fcc Face centered cubic
- -H --hcp Hexagonal close packed
randbox
- Randomly places particles in a box, the usage is as follows:
- -h --help Prints this help
- -n --numpart Number of particles in system [number], (required)
- -m --min Minumum separation between points, (default is 0.0)
- -d --dim Integer number of dimensions (default is 3)
- -r --region xmin,xmax,ymin,ymax,zmin,zmax (no spaces, required)
- -s --seed uint,uint,uint (no spaces)
- -b --boundary p for periodic, h for hard (ex: pph = periodic in xy, hard in z)
- -i --maxiter maximum number of attempts (default is 1e7)
