5.1 Structure Optimizations using the Jobex Script

In its normal mode of operation, the shell script jobex controls and executes automatic optimizations of molecular geo­metry parameters. It will cycle through the direct SCF, gradient and force relaxation programs and stop if either the maximum number of cycles is reached or the convergence criteria (change in the total energy, maximum norm of the gradient) are fulfilled. By default, the executable programs are taken from the load modules library within the TURBOMOLE directory.

5.1.1 Options

Given a shell the usage is:

This command invokes structure optimization using the default program statpt. Structure optimizations using program relax can be performed using -relax flag:

nohup means that the command is immune to hangups, logouts, and quits. & runs a background command. jobex accepts the following arguments controlling the level of calculation, convergence criteria and many more (for example nohup jobex -gcart 4 &):

-energy integer

converge total energy up to
\(10^{(-<\mathrm{integer}>)}\) Hartree (default: 6)

-gcart integer

converge maximum element of Cartesian gradient up to
\(10^{(-<\mathrm{integer}>)}\) atomic units (default: 3)

-grms integer

converge root mean square of Crtesian gradient up to
\(10^{(-<\mathrm{integer}>)}\) atomic units (default: 4). Note that statpt applies a criterion of \(5 \cdot 10^{-4}\) by default and the statpt data group of the control file overwrites all options for the energy and the gradient.

-c integer

perform up to integer cycles (default: 100)

begin with a direct SCF step

-grad

begin with a gradient step

-statpt

begin with a force relaxation step

-relax

use the relax program for force relaxation

-trans

perform transition state search

-level level

define the optimization level, level=scf, mp2, cc2, uff, rirpa or xtb (default is scf).

-ri

use RI modules ridft and rdgrad (fast Coulomb approximation) instead of dscf and grad as well as rimp2 instead of mpgrad; obligatory option if -level rirpa

-rijk

in connection with ’-level cc2’, the RI-JK versions of HF and CPHF are switched on

-ex

perform excited state geometry optimization using egrad 

-l <path>

employ programs from directory <path>

-ls <path>

load scripts from directory <path>

-md

a molecular dynamics (MD) run (using frog instead of relax)

-mdfile file

commands for MD run are contained in this file (default: mdmaster).

-mdscript file

option to execute a shell script before the frog step

-keep

keep program output from all optimization steps

-help

shows a short description of the commands above

5.1.2 Output

There will be an output written to file job.start which informs you about the current options. The convergence is signalled by the file converged; otherwise, you should find the file not.converged within your working directory. If jobex finds a file named stop or STOP in the working directory, jobex will stop after the present step has terminated. You can create stop by the command touch stop.

The output of the last complete cycle is written to file job.last, while the output of the running cycle is collected within the file job.<cycle>, where <cycle> is the index of the cycle. The convergence criteria and their current values are written out at the bottom of the job.last file.