View source for 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 (CH<sub>4</sub>).<br>

==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 <font color="red">coord</font> file contains now the coordinates in atomic units (Bohr instead of Angstrom)<br>
For the preparation of the job, the <font color="red">define</font> 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<br>
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 <font color="red">basis</font>, <font color="red">control</font> and <font color="red">mos</font>. The <font color="red">basis</font> file contains the exponents and the contraction coefficients of the DZP basis for carbon and hydrogen. The <font color="red">mos</font> file contains the molecular orbitals from the extended Hückel calculation, whereas the <font color="red">control</font> file contains all options for the calculation.<br>

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 <font color="red">-gcart 4</font> denotes the threshold of the cartesian gradient, which we set to 10<sup>-4</sup>, and 
<font color="red">-c 200</font> 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