Scripting capabilities of tetr

Since tetr uses the Text User Interface (TUI), it can easily be used in scripts as a general UNIX routine. This can be done by using a file with the tetr commands in the right order.

To illustrate the idea, let us consider a simple problem in which it is necessary to calculate a potential energy surface of a water molecule in which a single atom #2 (one of its hydrogens) is moved by small steps of $\sqrt{2}/10$ $\textrm{Å}$ along the $x=y$ direction in the cell. The VASP code is used. The initial geometry is contained in the file POSCAR.cm, given below:

made by tetr; -> species: O H

1.00000000000000

5.00000000000000 0.00000000000000D+000 0.00000000000000D+000

0.00000000000000D+000 5.00000000000000 0.00000000000000D+000

0.00000000000000D+000 0.00000000000000D+000 5.00000000000000

1 2

Selective dynamics

Direct

0.000000000000 0.000000000000 -0.013266064393 T T T

0.152276020145 0.000000000000 0.105285414074 T T T

-0.152276020145 0.000000000000 0.105285414074 T T T

All other VASP files are the same for this calculation. Then, the following tetr commands will do a single step:

3

POSCAR.cm

O

H

M

Mv

2 2

4

0.1 0.1 0.0

S

3

POSCAR.1

Q

Q

Collect all these commands in a file inp_for_tetr. Now, if tetr is executed with this input file read in from the standart input, e.g.

 tetr < inp_for_script > out

, then the following will happen: first of all, the VASP input file POSCAR.cm will be read in, then a chain M$\rightarrow$Mv commands is executed, and the atom #2 is moved by a vector (0.1,0.1,0.0). Finally, the new geometry is saved in a file POSCAR.1, after which tetr is stopped. The following sch script will then run the required calculation for 10 steps:

#!/bin/csh

cp POSCAR.cm POSCAR.ref

foreach step ( 1 2 3 4 5 6 7 8 9 10 )

   tetr < inp_for_script > out

   mv POSCAR.1 POSCAR

   vasp

   mv OUTCAR OUTCAR.$step

   mv CONTCAR POSCAR.cm

end

mv POSCAR.ref POSCAR.cm

At the end of the calculation, the current directory will contain ten OUTCAR.1,...,OUTCAR.10 files for each point of the calculation.