Locally Developed Scripts and Tools


The command mkpearson provides an interface to the Pearson database of intermetallic phases. The coding was mainly done by Marek Mihalkovic. You must put
into your path to use this. Some examples are:
mkpearson -h to view options
mkpearson -ch fe-c -pea cF116 to list binary and higher alloy structures containing Fe and C, with Pearson type cF116.
mkpearson 1234 -pcell -ch2ch a-b -mdsys -vasp to prepare VASP relaxation run for primitive cell of database entry #1234, swapping chemical species a for b.


MGTOOLS is a suite of programs for visualizing, analyzing and manipulating the structures in the Pearson database and the outputs of VASP runs. The coding was mainly done by Marek Mihalkovic. You must put
into your path to use the tools. Most programs give help using the -h option. Some examples are:
outcars to summarize contents of VASP OUTCAR files.
vrename run1 to save files from VASP run, giving them filename extension .run1.
cont2xyz > XYZ.cont to create file XYZ.cont from VASP CONTCAR file.
xmfig XYZ.cont -para h k l -z a b to view structure XYZ.cont along direction h k l in height interval z=a-b.
gofr -x XYZ.cont plots radial distribution function g(r).
pdiag -ch al-co -r to calculate and view convex hull of cohesive energies in the Al-Co alloy system. Option -r forces entry of data from recent runs.
doscar DOSCAR.* plots electronic DOS from runs with any filename extension. Option -efs shifts Fermi energy to 0.


Various other locally developed programs are located in /home/Tools/bin such as:
qvasp to submit VASP job via PBS. Takes options -q queue to submit to queue; -l resources to request specific resources.
vint_Q[S[xyz]] to integrate VASP CHG or CHGCAR data (including collinear or noncollinear spins) over atomic Voronoi cells.
pbsjobs to collect and summarize PBS job data from qstat.