J Schäfer: /* Geometry optimization */

2026-11-13T14:16:27Z

Geometry optimization

← Older revision		Revision as of 16:16, 13 November 2026
Line 223:		Line 223:
	time jobex -dscf -keep 2>&1		time jobex -dscf -keep 2>&1
	</syntaxhighlight>		</syntaxhighlight>
	and submit the modified script to the queueing system on bwForCluster JUSTUS 3 (→[[~~JUSTUS3~~/Jobscripts: Running Your Calculations]] and bwUniCluster (→[[BwUniCluster3.0/Slurm]]) via sbatch.		and submit the modified script to the queueing system on bwForCluster JUSTUS 3 (→[[Justus3/Jobscripts: Running Your Calculations]] and bwUniCluster (→[[BwUniCluster3.0/Slurm]]) via sbatch.
	The Turbomole command ''jobex'' controls the call of all the required Turbomole binaries for the geometry optimization.		The Turbomole command ''jobex'' controls the call of all the required Turbomole binaries for the geometry optimization.
	<br>		<br>

J Schäfer: /* Geometry optimization */

2026-11-13T14:13:31Z

Geometry optimization

← Older revision		Revision as of 16:13, 13 November 2026
Line 223:		Line 223:
	time jobex -dscf -keep 2>&1		time jobex -dscf -keep 2>&1
	</syntaxhighlight>		</syntaxhighlight>
	and submit the modified script to the queueing system on bwForCluster JUSTUS 2 (→[[~~JUSTUS2~~/Jobscripts: Running Your Calculations]] and bwUniCluster (→[[BwUniCluster3.0/Slurm]]) via sbatch.		and submit the modified script to the queueing system on bwForCluster JUSTUS 3 (→[[JUSTUS3/Jobscripts: Running Your Calculations]] and bwUniCluster (→[[BwUniCluster3.0/Slurm]]) via sbatch.
	The Turbomole command ''jobex'' controls the call of all the required Turbomole binaries for the geometry optimization.		The Turbomole command ''jobex'' controls the call of all the required Turbomole binaries for the geometry optimization.
	<br>		<br>

J Schäfer: /* bwForCluster JUSTUS 2 */

2026-11-13T14:07:42Z

bwForCluster JUSTUS 2

← Older revision		Revision as of 16:07, 13 November 2026
Line 46:		Line 46:
	* Turbomole 7.9		* Turbomole 7.9

	== bwForCluster JUSTUS 2 ==		== bwForCluster JUSTUS 3 ==

	* Turbomole 7.5
	* Turbomole 7.4.1
	* Turbomole 7.6.1
	* Turbomole 7.7.1 (standard module)
	* Turbomole 7.8.1 (experimental)
	* Turbomole 8.0
	* Turbomole 8.0.1		* Turbomole 8.0.1

J Schäfer: Created page with "{{Softwarepage|chem/turbomole}} {| width=600px class="wikitable" |- ! Description !! Content |- | module load | chem/turbomole |- | License | [https://www.turbomole.org/turbomole/order-turbomole/ Commerical] |- | Citing | [https://www.turbomole.org/turbomole/turbomole-documentation/ See Turbomole manual] |- | Links | [https://www.turbomole.com Homepage] | [https://www.turbomole.org/turbomole/turbomole-documentation Documentation] |- | User Forum | [https://forum.t..."

2026-11-13T13:46:48Z

Created page with "{{Softwarepage|chem/turbomole}} {| width=600px class="wikitable" |- ! Description !! Content |- | module load | chem/turbomole |- | License | [https://www.turbomole.org/turbomole/order-turbomole/ Commerical] |- | Citing | [https://www.turbomole.org/turbomole/turbomole-documentation/ See Turbomole manual] |- | Links | [https://www.turbomole.com Homepage] | [https://www.turbomole.org/turbomole/turbomole-documentation Documentation] |- | User Forum | [https://forum.t..."

New page

{{Softwarepage|chem/turbomole}}

{| width=600px class="wikitable"
|-
! Description !! Content
|-
| module load
| chem/turbomole
|-
| License
| [https://www.turbomole.org/turbomole/order-turbomole/ Commerical]
|-
| Citing
| [https://www.turbomole.org/turbomole/turbomole-documentation/ See Turbomole manual]
|-
| Links
| [https://www.turbomole.com Homepage] | [https://www.turbomole.org/turbomole/turbomole-documentation Documentation]
|-
| User Forum
| [https://forum.turbomole.org/ external]
|}
= Description =
'''Turbomole''' is a general purpose ''quantum chemistry'' software package for ''ab initio'' electronic structure calculations and provides:
* ground state calculations for methods such as Hartree-Fock, DFT, MP2, and CCSD(T);
* excited state calculations at different levels such as full RPA, TDDFT, CIS(D), CC2, and ADC(2);
* geometry optimizations, transition state searches, molecular dynamics calculations;
* property and spectra calculations such as IR, UV/VIS, Raman, and CD;
* approximations like resolution-of-the-identity (RI) to speed-up the calculations without introducing uncontrollable or unknown errors; as well as
* parallel versions for all kind of jobs.
For more information on Turbmole's features please visit [https://www.turbomole.org/turbomole/turbomole-features/ https://www.turbomole.org/turbomole/turbomole-features/].
 
 

= Versions and Availability =

On the command line interface (CLI) of a particular bwHPC cluster a list of all available Turbomole versions can be inquired as followed
<pre>
$ module avail chem/turbomole
</pre>

A current list of the versions available on the bwUniCluster and bwForClusters can be found here:
https://www.bwhpc.de/software.php

== bwUniCluster 3.0 ==

* Turbomole 7.9

== bwForCluster JUSTUS 2 ==

* Turbomole 7.5
* Turbomole 7.4.1
* Turbomole 7.6.1
* Turbomole 7.7.1 (standard module)
* Turbomole 7.8.1 (experimental)
* Turbomole 8.0
* Turbomole 8.0.1

== Parallel computing ==
The Turbomole ''Module'' subsumes all available parallel computing variants of Turbomole's binaries. Turbomole defines the following parallel computing variants:
* SMP = Shared-memory parallel computing based on OpenMP and Fork() with the latter using separated address spaces.
* MPI = Message passing interface protocol based parallel computing
However, only one of the parallel variants or the sequential variant can be loaded at once and most Turbomole's binaries support only 1 or 2 of the parallelization variants. Like for Turbomole installations without the ''Module'' system of the bwHPC clusters, the variants have to be triggered by the environment variable $PARA_ARCH.
 
 

= Usage =
== Before loading the Module ==
Before loading the Turbomole ''Module'', the parallel computing variant has to be defined via the environment variable $PARA_ARCH, using the abbreviations SMP or MPI, e.g.:
<pre>
$ export PARA_ARCH=MPI
</pre>
will [[#Loading the Module|later load]] the '''MPI binary variants'''. If the variable $PARA_ARCH is not defined or empty, the sequential binary variants will be active once the Turbomole Module is loaded.
 

== Loading the Module ==
You can load the default version of ''Turbomole'' with the command:
<pre>
$ module load chem/turbomole
</pre>
The Turbomole ''Module'' does not depend on any other ''Module'', but on the variable $PARA_ARCH. Moreover, Turbomole provides its own libraries regarding ''OpenMP'', ''Fork()'', and ''MPI'' based parallelization.
If you wish to load a specific (older) version you can do so by executing, e.g.:
<pre>
$ module load chem/turbomole/8.0
</pre>
to load the version 8.0.
 

== Switching between different parallel variants ==
To switch between the different parallel variants provided by the Turbomole ''Module'', simply define the new parallel variant via $PARA_ARCH and load the ''Module'' again. Note that for switching between the parallel variants unloading of the Turbomole ''Module'' is not required. For instance to change to the MPI variant, execute:
<pre>
$ export PARA_ARCH=MPI
$ module load chem/turbomole
</pre>
 
== Turbomole binaries ==
The '''Turbomole''' software package consists of a set of stand-alone program binaries providing different features and parallelization support:
{| width=750px class="wikitable"
|- style=text-align:left"
! Binary !! Features !! OpenMP !! Fork !! MPI
|- style="vertical-align:top;"
| define
| Interactive input generator
| no
| no
| no
|- style="vertical-align:top;"
| dscf
| Energy calculations
| yes
| yes
| yes
|- style="vertical-align:top;"
| grad
| Gradient calculations
| yes
| yes
| yes
|- style="vertical-align:top;"
| ridft
| Energy calc. with fast Coulomb approximation
| no
| yes
| yes
|- style="vertical-align:top;"
| rdgrad
| Gradient calc. with fast Coulomb approximation
| yes
| yes
| yes
|- style="vertical-align:top;"
| ricc2
| Electronic excitation energies, transition moments and properties of excited states
| yes
| no
| yes
|- style="vertical-align:top;"
| statpt
| Hessian and coordinate update for stationary point search
| no
| no
| no
|- style="vertical-align:top;"
| aoforce
| Analytic calculation of force constants, vibrational frequencies and IR intensities
| yes
| yes
| yes
|- style="vertical-align:top;"
| escf
| Calc. of time dependent and dielectric properties
| yes
| yes
| yes
|- style="vertical-align:top;"
| egrad
| gradients and first-order properties of excited states
| yes
| no
| yes
|- style="vertical-align:top;"
| odft
| Orbital-dependent energy calc.
| yes
| no
| no
|}
For the complete set of binaries and more detailed description of their features read [https://www.turbomole.org/turbomole/turbomole-documentation/ here].
 

== Turbomole tools ==
Turbomole's tool set contains scripts and binaries that help to prepare, execute workflows (such as geometry optimisation) and postprocess results.
{| width=750px class="wikitable"
|- style="text-align:left"
! Script !! Type !! Description
|- style="vertical-align:top;"
| x2t
| Preparation
| Converts XYZ coordinates into ''Turbomole'' coordinates.
|- style="vertical-align:top;"
| sdg
| Preparation
| Shows data group from ''control'' file: for example$ sdg coordshows current Turbomole coordinates used.
|- style="vertical-align:top;"
| jobex
| Optimization workflow
| Shell script that controls and executes automatic optimizations of molecular geometry parameters.

|- style="vertical-align:top;"
| tm2molden
| Postprocessing
| Creates a molden format input file for the [[Molden]] program.
|- style="vertical-align:top;"
| eiger
| Postprocessing
| Script front-end of program ''eigerf'' to display HOMO-LUMO gap and MO eigenvalues.
|}
For the complete set of tools and more detailed description of their features read [http://www.turbomole-gmbh.com/manuals/version_6_5/Documentation_html/node9.html here].
 
== Disk Usage ==
By default, scratch files of Turbomole binaries are placed in the directory of Turbomole binary execution. Please do not run your Turbomole calculations in your $HOME or $WORK directory.
 
 
= Examples =
== Single node jobs ==
=== Template provided by Turbomole Module ===
The Turbomole ''Module'' provides a simple job script example of Cubane (C8H8) that runs an energy relaxation via MPI parallel ''dscf'' using 2 cores on a single node and its local file system. To simply run the example do the following steps:
<pre>
$ module load chem/turbomole
$ mkdir -vp ~/Turbomole-example/
$ cd ~/Turbomole-example/
$ cp -r $TURBOMOLE_EXA_DIR/* ~/Turbomole-example/
$ sbatch bwHPC_turbomole_single-node_tmpdir_example.sh
</pre>
The last step submits the job example script bwHPC_turbomole_single-node_example.sh to the queueing system. Once started on a compute node, all calculations will be done under a unique directory on the local file system of that particular compute node. You have to explicitely request local disk space on Justus.
 

=== Geometry optimization ===
To do a geometry optimization of the [[#Single node job template provided by Turbomole Module|previous job example]], modify bwHPC_turbomole_single-node_tmpdir_example.sh by replacing the following line
<syntaxhighlight lang="bash">
time dscf > dscf.out 2>&1
</syntaxhighlight>
with
<syntaxhighlight lang="bash">
time jobex -dscf -keep 2>&1
</syntaxhighlight>
and submit the modified script to the queueing system on bwForCluster JUSTUS 2 (→[[JUSTUS2/Jobscripts: Running Your Calculations]] and bwUniCluster (→[[BwUniCluster3.0/Slurm]]) via sbatch.
The Turbomole command ''jobex'' controls the call of all the required Turbomole binaries for the geometry optimization.
 
 

= Turbomole-Specific Environment Variables =
To see a list of all Turbomole environments set by the 'module load'-command do the following:
<pre>
module show chem/turbomole 2>&1 | grep -E '(setenv|prepend-path)'
</pre>

= Version-Specific Information =
For specific information about the Turbomole version (e.g., 7.5) to be loaded do the following:
<pre>
module help chem/turbomole/7.5
</pre>

----

Justus3/Software/Turbomole - Revision history

J Schäfer: /* Geometry optimization */

J Schäfer: /* Geometry optimization */

J Schäfer: /* bwForCluster JUSTUS 2 */