Preparing and running a turbomole job
As a simple example, we give a description, how to set up a DFT geometry optimization of the methane molecule (CH4).
Prepare the job
For this purpose, an .xyz file (standart format for structures) with a first guess for the coordinates is required.
xyz file format:
first line : number of atoms second line : comment following lines : atom_symbol x_coordinate y_coordinate z_coordinate
xyz files can either be set up by hand or be exported by several programs:
- molden
- adfinput
- chembiooffice
methane.xyz (coordinates in Angstrom) could look like:
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
In order to use turbomole, the module needs to be loaded
module load turbomole/6.4.0
As a next step the xyz file has to be converted to the file format used by turbomole
x2t methane.xyz > coord
The resulting coord file contains now the coordinates in atomic units (Bohr instead of Angstrom)
For the preparation of the job, the define script needs to be executed:
define
Follow now the instructions on the screen:
IF YOU WANT TO READ DEFAULT-DATA FROM ANOTHER control-TYPE FILE, THEN ENTER ITS LOCATION/NAME OR OTHERWISE HIT >return<.
-> hit return
INPUT TITLE OR ENTER & TO REPEAT DEFINITION OF DEFAULT INPUT FILE
-> hit return
SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=0 SYMMETRY=c1 )
YOU MAY USE ONE OF THE FOLLOWING COMMANDS :
sy <group> <eps> : DEFINE MOLECULAR SYMMETRY (default for eps=3d-1)
desy <eps> : DETERMINE MOLECULAR SYMMETRY AND ADJUST
COORDINATES (default for eps=1d-6)
susy : ADJUST COORDINATES FOR SUBGROUPS
ai : ADD ATOMIC COORDINATES INTERACTIVELY
a <file> : ADD ATOMIC COORDINATES FROM FILE <file>
aa <file> : ADD ATOMIC COORDINATES IN ANGSTROEM UNITS FROM FILE <file>
sub : SUBSTITUTE AN ATOM BY A GROUP OF ATOMS
i : INTERNAL COORDINATE MENU
ired : REDUNDANT INTERNAL COORDINATES
red_info : DISPLAY REDUNDANT INTERNAL COORDINATES
ff : UFF-FORCEFIELD CALCULATION
m : MANIPULATE GEOMETRY
frag : Define Fragments for BSSE calculation
w <file> : WRITE MOLECULAR COORDINATES TO FILE <file>
r <file> : RELOAD ATOMIC AND INTERNAL COORDINATES FROM FILE <file>
name : CHANGE ATOMIC IDENTIFIERS
del : DELETE ATOMS
dis : DISPLAY MOLECULAR GEOMETRY
banal : CARRY OUT BOND ANALYSIS
* : TERMINATE MOLECULAR GEOMETRY SPECIFICATION
AND WRITE GEOMETRY DATA TO CONTROL FILE
IF YOU APPEND A QUESTION MARK TO ANY COMMAND AN EXPLANATION
OF THAT COMMAND MAY BE GIVEN
Read in the coordinate file by typing
a coord
Exit from the menu by typing
*
Then you are asked about the use of internal coordinates
IF YOU DO NOT WANT TO USE INTERNAL COORDINATES ENTER no
type
no
Now the basis set menu is displayed:
ATOMIC ATTRIBUTE DEFINITION MENU ( #atoms=5 #bas=5 #ecp=0 ) b : ASSIGN ATOMIC BASIS SETS bb : b RESTRICTED TO BASIS SET LIBRARY bl : LIST ATOMIC BASIS SETS ASSIGNED bm : MODIFY DEFINITION OF ATOMIC BASIS SET bp : SWITCH BETWEEN 5d/7f AND 6d/10f lib : SELECT BASIS SET LIBRARY ecp : ASSIGN EFFECTIVE CORE POTENTIALS ecpb : ecp RESTRICTED TO BASIS SET LIBRARY ecpi : GENERAL INFORMATION ABOUT EFFECTIVE CORE POTENTIALS ecpl : LIST EFFECTIVE CORE POTENTIALS ASSIGNED ecprm: REMOVE EFFECTIVE CORE POTENTIAL(S) c : ASSIGN NUCLEAR CHARGES (IF DIFFERENT FROM DEFAULTS) cem : ASSIGN NUCLEAR CHARGES FOR EMBEDDING m : ASSIGN ATOMIC MASSES (IF DIFFERENT FROM DEFAULTS) dis : DISPLAY MOLECULAR GEOMETRY dat : DISPLAY ATOMIC ATTRIBUTES YET ESTABLISHED h : EXPLANATION OF ATTRIBUTE DEFINITION SYNTAX * : TERMINATE THIS SECTION AND WRITE DATA OR DATA REFERENCES TO control GOBACK=& (TO GEOMETRY MENU !)
Assign a DZP (double-zeta with polarization functions) basis set to the atoms
b all DZP
Exit the menu
*
Another menu is displayed which allows you to choose the method for the first guess of the molecular orbitals
CHOOSE COMMAND infsao : OUTPUT SAO INFORMATION atb : Switch for writing MOs in ASCII or binary format eht : PROVIDE MOS && OCCUPATION NUMBERS FROM EXTENDED HUECKEL GUESS use <file> : SUPPLY MO INFORMATION USING DATA FROM <file> man : MANUAL SPECIFICATION OF OCCUPATION NUMBERS hcore : HAMILTON CORE GUESS FOR MOS flip : FLIP SPIN OF A SELECTED ATOM & : MOVE BACK TO THE ATOMIC ATTRIBUTES MENU THE COMMANDS use OR eht OR * OR q(uit) TERMINATE THIS MENU !!! FOR EXPLANATIONS APPEND A QUESTION MARK (?) TO ANY COMMAND
Perform an extended Hückel calculation by typing
eht
Follow the instructions on the screen
DO YOU WANT THE DEFAULT PARAMETERS FOR THE EXTENDED HUECKEL CALCULATION ? DEFAULT=y HELP=?
Accept the default parameters by hiting return
ENTER THE MOLECULAR CHARGE (DEFAULT=0)
Since the methane molecule is neutral, accept the default charge by hiting return
DO YOU ACCEPT THIS OCCUPATION ? DEFAULT=y
When no warning is poping up, accept the default occupation numbers by hiting return
Now you are almost done with the preparation of the turbomole job. In the next menu, you are asked to choose a method for the calculation
GENERAL MENU : SELECT YOUR TOPIC
scf : SELECT NON-DEFAULT SCF PARAMETER
mp2 : OPTIONS AND DATA GROUPS FOR rimp2 and mpgrad
cc : OPTIONS AND DATA GROUPS FOR ricc2
ex : EXCITED STATE AND RESPONSE OPTIONS
prop : SELECT TOOLS FOR SCF-ORBITAL ANALYSIS
drv : SELECT NON-DEFAULT INPUT PARAMETER FOR EVALUATION
OF ANALYTICAL ENERGY DERIVATIVES
(GRADIENTS, FORCE CONSTANTS)
rex : SELECT OPTIONS FOR GEOMETRY UPDATES USING RELAX
stp : SELECT NON-DEFAULT STRUCTURE OPTIMIZATION PARAMETER
e : DEFINE EXTERNAL ELECTROSTATIC FIELD
dft : DFT Parameters
ri : RI Parameters
rijk : RI-JK-HF Parameters
trunc : USE TRUNCATED AUXBASIS DURING ITERATIONS
marij : MULTIPOLE ACCELERATED RI-J
dis : DISPLAY MOLECULAR GEOMETRY
list : LIST OF CONTROL FILE
& : GO BACK TO OCCUPATION/ORBITAL ASSIGNMENT MENU
* or q : END OF DEFINE SESSION
enter the DFT menu by typing
dft
DFT needs to be activated
func : TO CHANGE TYPE OF FUNCTIONAL grid : TO CHANGE GRIDSIZE on: TO SWITCH ON DFT Just <ENTER>, q or '*' terminate this menu.
type
on
exit the menu by typing
*
terminate the define script by typing
*
The script produced three files named basis, control and mos. The basis file contains the exponents and the contraction coefficients of the DZP basis for carbon and hydrogen. The mos file contains the molecular orbitals from the extended Hückel calculation, whereas the control file contains all options for the calculation.
Open the control file by typing
vic
Change the value of $scfiterlimit from 30 to 300
$scfiterlimit 300
Change the value of $scfconv from 6 to 8
$scfconv 8
Save and exit the file by typing
:wq
And hit return.
Run the job
Because this is a quite small job, a time limit of one hour should be sufficient at all. The job is now executed by
sbatch --time=1:00:00 --wrap="jobex -gcart 4 -c 200"
Here -gcart 4 denotes the threshold of the cartesian gradient, which we set to 10-4, and -c 200 sets the maximum number of iterations in the SCF to 200.
Parallel jobs (SMP)
For running parallel jobs in Turobmole, one has to load a different module:
module load turbomole/6.4.0_smp
It is convenient to create a small runscript (run.tm) for parallel Turbomole jobs to set the necessary environment variables:
run.tm:
export PARNODES=X export PARA_ARCH=SMP export TURBOTMPDIR=$TMPDIR jobex [Turbomole Parameter] > output.log)
Here X denotes a number between 1 and 192. It is important that when submitting a job, the -n option of bsub needs to be set to X too.
sbatch -n 1 --cpus-per-task=X --mem-per-cpu=2500 --tmp=2048*X --time=72:00:00 < run.tm
