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
cont2xyz > XYZ.cont to create file XYZ.cont from VASP
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
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
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.