Turbomole

Turbomole is a quantum chemistry software package for ab initio calculations on molecular systems. It is particularly well-suited for large systems and is known for its efficiency in performing Density Functional Theory (DFT) calculations.

Turbomole on Euler¶

On Euler the following versions are available via modules:

Version	Module load command
7.4.1	`module load turbomole/7.4.1`
7.4.1 with SMP	`module load turbomole/7.4.1_smp`
7.2.0	`module load turbomole/7.2.0`
7.2.0 with SMP	`module load turbomole/7.2.0_smp`

Example job¶

This section demonstrates how to set up and run a DFT geometry optimization of methane (CH₄) using Turbomole on Euler.

1. Prepare the Structure¶

Create an .xyz file containing the atomic coordinates. The XYZ format is:

First line: Number of atoms
Second line: Comment (can be blank)
Following lines: atom_symbol x y z (coordinates in Angstrom)

Example methane.xyz:

5

C   0.000000   0.000000   0.000000
H   0.000000   0.000000   1.088718
H   1.226454  -0.000000  -0.562906
H  -0.413227  -0.788935  -0.562906
H  -0.413227   0.788935  -0.562906

You can generate XYZ files manually or export them from programs like molden, adfinput, or chembiooffice.

2. Load Turbomole¶

Load the desired Turbomole module:

module load turbomole/7.4.1

3. Convert coordinates¶

Convert the XYZ file to Turbomole's internal format:

x2t methane.xyz > coord

This creates a coord file with coordinates in atomic units.

4. Initialize the Calculation¶

Start the Turbomole setup:

define

Follow these prompts:

Default Data: Press return
Input Title: Press return
Molecular Geometry: Type a coord, then * to exit
Internal Coordinates: Type no
Basis Set: Type b all DZP, then * to exit
Initial Guess: Type eht, accept all defaults by pressing return as prompted
Method Selection: Type dft, then on, then * twice to exit

5. Adjust calculation parameters¶

Edit the control file to improve convergence:

vi control

- Set $scfiterlimit to 300:

$scfiterlimit        300

- Set $scfconv to 8:

$scfconv    8

Save and exit (:wq).

6. Run the Calculation¶

Submit the job with:

sbatch --time=1:00:00 --wrap="jobex -gcart 4 -c 200"

- -gcart 4: Sets the cartesian gradient threshold to 10⁻⁴ - -c 200: Maximum 200 SCF iterations

7. Running parallel jobs (SMP)¶

For parallel execution, load the SMP module:

module load turbomole/7.4.1_smp

Create a run script (run.tm):

export PARNODES=X
export PARA_ARCH=SMP
export TURBOTMPDIR=$TMPDIR
jobex [Turbomole Parameters] > output.log

Replace X with the number of CPU cores (1–192).

Submit the parallel job:

sbatch -n 1 --cpus-per-task=X --mem-per-cpu=2500 --tmp=2048*X --time=72:00:00 < run.tm

Adjust X as needed for your calculation.