UPU

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DESCRIPTION

UPU = Universal POSCAR Utilities

UPU is a command-line tool for viewing and modifying POSCAR/CONTCAR files and extracting information of those structure files.

As the program is a rather private project of the only developer Dr. M. Jahnátek (Univ.Vienna [1]), it is not documented elsewhere.

SYNTAX

UPU is programmed in C language and uses a C-like syntax.

Script mode:

upu '{command1;command2}' POSCAR|CONTCAR

Interactive mode:

upu POSCAR|CONTCAR

(or just "upu" command). You are redirected to the UPU sub-shell. The output of inserted commands is directly listed into the UPU shell. Press <ESC><ESC> or type quit command to return to BASH shell.

Note: C-like syntax also means that UPU starts to count atoms and atomic layers from 0, i.e. the 5^th atom in the POSCAR/POTCAR has the label 4. Take care of avoiding errors based on wrong numbering.

USAGE

Example #1 (level 1)

upu '{cartesian;ls;save;export xsf}' /path/to/CONTCAR

The command proceeds the following steps: reads a CONTCAR file, switches easily from the default direct coordinates to Cartesian, prints this half-edited version of CONTCAR to the the stdout, saves it the modification (output file "CONTCAR"), exports and saves the supercell to the XCrysDen format (output file "CONTCAR.xsf") and quits to BASH shell.

Example #2 (level 2)

upu '{cartesian ;\
      measure distance a 0 a 1 ;\
      measure angle a 0 a 1 a 2 ;\
      measure dihedral a 0 a 1 a 2 a 3
      }' /path/to/CONTCAR

The command reads in a stucture-*CAR file, and measures the distance between atoms # 1 and 2, the bond angle between the atoms # 1-2-3 and the dihedral angle on the atoms # 1-2-3-4.

Each measurement has a one-line numerical output, thus it is easy to be parsed. So if the output of the upu command is redirected into a file ("upu '{commands}' CONTCAR > data.dat"), you can easily parse the variable in a BASH-script using e.g

tail -3 data.dat > temp.dat
for i in `seq 1 3` ; do
 var[$i]=`awk -v line=$i '(NR==line){print $1}' temp.dat`
done

LIST OF COMMANDS

Listed alphabetically:

aassoct	attempt to specify atom types automatically by reading OUTCAR file in the current directory (no parameters needed)
assoct element1 [element2] [...]	associate the previously unspecified atom types with the user input (e.g. "assoct Pt N H")
bye	exit
cartesian
cell
cmd
commandline
cmd
curl
direct
deassoct
exchange
exit	exit
export
extract
fractional
identify
kpoints
kpoints@ls
kpoints@save
kpoints@set
la	list atoms
label
layers@alook
layers@buckling
layers@create
layers@delete
layers@join
layers@look
layers@ls
layers@measure
layers@order
layers@shift
list	list the POSCAR/CONTCAR file
load file	load (=open) the file (usually POSCAR/CONTCAR) to buffer
loud
ls	lists the POSCAR/CONTCAR file
measure
open [file]	open (=load) the file (usually POSCAR/CONTCAR) to buffer o
origin
pbc	apply periodic boundary conditions (PBS) - all atoms with coordinates sticking out of the supercell will be moved inside; use with caution
prefix [number]	change the prefix factor (2nd line in POSCAR) to a specified number
pretty
quiet	enter quiet mode - reduce UPU messages to minimum
quit	exit
redo
replicate
rotate
save [file]	save the current state of the buffer (structure) to a file
scale
script
seldyn
select
selection
sense
strain
undo
unselect
update
arbitrary command	do arbitrary things

INSTALLATION

Although UPU is a freeware, you will not find it easily in internet. The compressed packages are located at the author's homepage (binary (5.9MB)).

The preferred way of installation is the following:

wget -nv http://homepage.univie.ac.at/michal.jahnatek/upu/upu-1.4.0-linux-bundle.tar.bz2
mkdir ~/bin/upu ; tar -C ~/bin/upu -xjf upu-1.4.0-linux-bundle.tar.bz2

Do not forget to update your $PATH shell variable, e.g.:

 printf '\nexport PATH=$PATH:~/bin/upu\n' >> ~/.bashrc