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.
Given a shell the usage is:
nohup jobex &
This command invokes structure optimization using the default program statpt. Structure optimizations using program relax can be performed using -relax flag:
nohup jobex -relax &
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 &):
converge total energy up to
10(-<integer>) Hartree (default: 6)
converge maximum norm of cartesian gradient up to
10(-<integer>) atomic units (default: 3)
perform up to integer cycles (default: 100)
begin with a direct SCF step
begin with a gradient step
begin with a force relaxation step
use the relax program for force relaxation
perform transition state search
define the optimization level, level=scf, mp2, cc2, uff, or rirpa (default is scf).
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
in connection with ’-level cc2’, the RI-JK versions of HF and CPHF are switched on
perform excited state geometry optimization using egrad
employ programs from directory <path>
load scripts from directory <path>
a molecular dynamics (MD) run (using frog instead of relax)
commands for MD run are contained in this file (default: mdmaster).
option to execute a shell script before the frog step
keep program output from all optimization steps
shows a short description of the commands above
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.