zum Inhalt springen

Beispiel für das Erstellen eines Inputs für Turbomole

Das folgende Beispiel zeigt das vollständige Erstellen eines Inputs für das Programm Turbomole.

Legen Sie als erstes ein eigenes Verzeichnis für die Rechnung an und rufen Sie es auf.

       mkdir benzoesaeure

       cd benzoesaeure

Danach wird die Koordinatendatei erstellt (zum Beispiel mit GaussView).
Dazu muss zuerst dass Modul gaussian geladen werden:

       module load gaussian09

Jetzt rufen Sie das Programm GaussView auf, um die Molekülgeometrie zu erstellen.

       gview

Stellen Sie  sich das gewünschte Molekül zusammmen und speichern sie die Koordinaten als Gaussian Input Datei (.com) ab. Achten Sie darauf, dass das Häkchen bei "Write Cartesians" aktiviert ist.
In diesen Beispiel wird die Geometrie von Benzoesäure in der Datei benzoesaeure.com gesichert.

Dann wird das Modul turbomole geladen und die Datei benzoesaeure.com mit dem Tool x2t in eine für Turbomole lesbare Form umgewandelt:

       module load turbomole

       x2t benzoesaeure.com >benzoesaeure.coord

Der Inhalt der Datei benzoesaeure.coord hat dann die Form:

$coord
   -0.26436319956551     -0.05787265494975     -0.04546599817499       c
    2.38387764915512     -0.04914395325017     -0.05154237476076       c
    3.70058624636882      2.24780459303870      0.00844492152621       c
    2.36905399486188      4.53602456990881      0.07450507950834       c
   -0.27918685385875      4.52729600049006      0.08057718531305       c
   -1.59589545107245      2.23034735971489      0.02059228897827       c
   -1.26969944867859     -1.81164380180775     -0.09126906680031       h
    3.40053205389316     -1.79625050846901     -0.10198679974106       h
    5.72257690021994      2.25446924136964      0.00380195890401       h
    3.37439022507770      6.28979581125312      0.12030487890745       h
   -3.61788612382083      2.22368290035656      0.02522890212066       h
   -1.74240913068950      7.04182351301367      0.15316778327617       c
   -4.12042131559255      7.03398551482956      0.15862357379990       o
   -0.39882893022235      9.38564871913846      0.21437357497362       o
   -1.38537812683464     10.66974022755881     -0.60350361809977       h
$end

Die Koordinaten werden von einem $coord eingeleitet und von einem $end abgeschlossen.
Die Angabe der Koordinaten erfolgt in atomaren Einheiten im Stil:

X-Koordinate Y-Koordinate Z-Koordinate Elementsymbol

Starten Sie die define-Session (im Folgenden werden alle Ausgaben in einem Kasten dargestellt, alle Eingaben eingerückt in dicktengleicher Schrift):

       define

 define (cheops0) : TURBOMOLE V7.0( 19819 ) 15 Jun 2015 at 15:39:09
 Copyright (C) 2015 TURBOMOLE GmbH, Karlsruhe


    2015-10-15 13:03:07.358

             OPERATING SYSTEM = unix
                    HOST NAME = cheops0
   STANDARD BASIS SET LIBRARY = /opt/rrzk/software/turbomole/7.0/TURBOMOLE/basen/
  ALTERNATE BASIS SET LIBRARY = /opt/rrzk/software/turbomole/7.0/TURBOMOLE/basold/
 LIBRARY FOR RI-J  BASIS SETS = /opt/rrzk/software/turbomole/7.0/TURBOMOLE/jbasen/
 LIBRARY FOR RI-JK BASIS SETS = /opt/rrzk/software/turbomole/7.0/TURBOMOLE/jkbasen/
 LIBRARY FOR RIMP2/RICC2 SETS = /opt/rrzk/software/turbomole/7.0/TURBOMOLE/cbasen/
 LIBRARY FOR RIR12 BASIS SETS = /opt/rrzk/software/turbomole/7.0/TURBOMOLE/cabasen/
 LIBRARY FOR OEP   BASIS SETS = /opt/rrzk/software/turbomole/7.0/TURBOMOLE/xbasen/
            STRUCTURE LIBRARY = /opt/rrzk/software/turbomole/7.0/TURBOMOLE/structures/

 
 ***********************************************************
 *                                                         *
 *                       D E F I N E                       *
 *                                                         *
 *         TURBOMOLE'S  INTERACTIVE  INPUT  PROGRAM        *
 *                                                         *
 *  Quantum Chemistry Group       University of Karlsruhe  *
 *                                                         *
 ***********************************************************
 

 DATA WILL BE WRITTEN TO THE NEW FILE control

 IF YOU WANT TO READ DEFAULT-DATA FROM ANOTHER control-TYPE FILE,
 THEN ENTER ITS LOCATION/NAME OR OTHERWISE HIT >return<.

Da keine Vorlage existiert bestätigen Sie die Eingabe mit der Enter-Taste (>return<).

       >return<

 INPUT TITLE OR
 ENTER & TO REPEAT DEFINITION OF DEFAULT INPUT FILE

Als Titel empfiehlt es sich, eine eindeutige Bezeichnung für die Rechnung zu wählen. In diesem Fall wird der Titel aus der Molekülbezeichnung, dem verwendeten Funktional und der Art der Rechnung zusammengesetzt.

       Benzoesaeure_B3-LYP_geom_opt

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

Hier wird die vorgefertigte Koordinatendatei eingelesen:

       a benzoesaeure.coord

 CARTESIAN COORDINATES FOR  15 ATOMS HAVE SUCCESSFULLY
 BEEN ADDED.

 keyword $intdef  missing in file <benzoesaeure.coord>

 DEFINITIONS OF INTERNAL COORDINATES HAVE  N O T  BEEN READ.

 keyword $user-defined bonds missing in file <benzoesaeure.coord>

 SPECIFICATION OF BOND TOPOLOGY HAS  N O T  BEEN READ.

 SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=15    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

Um die Geometrieoptimierung zu beschleunigen werden interne redundante Koordinaten automatisch festgelegt (empfohlen):

       ired

 JUST FOUND ISOLATED RING OF SIZE  6 :
    1    6    5    4    3    2
     GEOIRED: NBDIM      39  NDEGR:      39
      Lowest Eigenvalue of BmBt is:          0.0301259204
     GEOSPY: ATTENTION!
     natural internals not linearly independent?
       Decoupling with "globtry"=    1.08478471555994    
     GEOSPY: ATTENTION!
     natural internals not linearly independent?
       Decoupling with "globtry"=   0.999999999900000    
      Lowest Eigenvalue of projected BBt           0.0301259204 No:    39
      Quotient of Eigenvalues           1.0000000000
     OCCUPATION OF BLOCKS:   39    0    0    0    0

 SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=15    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

In diesem Fall ist keine weitere Eingabe im Geometriemenü erwünscht, es wird mittels eines Sterns (*) beendet:

       *

Das Folgemenü (Basissätze) wird automatisch aufgerufen.

 GEOMETRY DATA WILL BE WRITTEN TO FILE coord


 SUPPLYING BASIS SETS TO   15 ATOMS
 #                                                                      
 #                   BASIS SET LIBRARY FOR CARBON                       
 #            ECPs, HONDO-BASIS SETS FROM basen AND                     
 #     FULLY OPTIMIZED BASIS SETS FROM newbas MERGED 02/6/93            
 #                                                                      
 #         abbreviation hondo refers to the version 7.0 of HONDO        
 #                                                                      
 ########################################################################
 #       HF limit : E(3P) = -37.688619 a.u. (C. Froese Fischer, 1977)   
 ########################################################################
 #       Roothaan parameters for C(3P) in symmetry I:                   
 #        a = 3/4      b = 3/2                                          
 ########################################################################
 #                                                                      
 c def-SV(P)                                                            
 c def2-SVP                                                             
 c dhf-SVP                                                              
 c dhf-SVP-2c                                                           
 c def2-SV(P)                                                           
 c dhf-SV(P)                                                            
 c dhf-SV(P)-2c                                                         
 # c (7s4p1d)/[3s2p1d] {511/31/1}                                       
 # ROHF(equiv) energy is -37.64114337919 a.u.  (virial theorem = 2.000000
 # UHF(noneq)  energy is -37.64522986135 a.u.  (virial theorem = 2.000084
 #                                                                      
 #                    BASIS SET LIBRARY FOR HYDROGEN                    
 #            ECPs, HONDO-BASIS SETS FROM basen AND                     
 #     FULLY OPTIMIZED BASIS SETS FROM newbas MERGED 02/6/93            
 #                                                                      
 #         abbreviation hondo refers to the version 7.0 of HONDO        
 #                                                                      
 ########################################################################
 #       HF limit : E(2S) = -0.5 a.u.                                   
 ########################################################################
 #       Roothaan parameters for H(2S):                                 
 #        a = 0      b = 0                                              
 ########################################################################
 #                                                                      
 h def-SV(P)                                                            
 h def2-SV(P)                                                           
 h dhf-SV(P)                                                            
 h dhf-SV(P)-2c                                                         
 # HF(equiv) energy is -0.49927840571 a.u.  (virial theorem = 2.000000001
 # (4s)/[2s] {31}                                                       
 # H. Horn, Aug. 91                                                     
 #                                                                      
 #                       BASIS SET LIBRARY FOR OXYGEN                   
 #            ECPs, HONDO-BASIS SETS FROM basen AND                     
 #     FULLY OPTIMIZED BASIS SETS FROM newbas MERGED 02/6/93            
 #                                                                      
 #         abbreviation hondo refers to the version 7.0 of HONDO        
 #                                                                      
 #                                                                      
 ########################################################################
 #       HF limit : E(3P) = -74.809398 a.u. (C. Froese Fischer, 1977)   
 ########################################################################
 #       Roothaan parameters for O(3P) in symmetry I:                   
 #        a = 15/16      b = 9/8                                        
 ########################################################################
 #                                                                      
 o def-SV(P)                                                            
 o def2-SVP                                                             
 o dhf-SVP                                                              
 o dhf-SVP-2c                                                           
 o def2-SV(P)                                                           
 o dhf-SV(P)                                                            
 o dhf-SV(P)-2c                                                         
 # o (7s4p1d)/[3s2p1d] {511/31/1}                                       
 # ROHF(equiv) energy is -74.71374601625 a.u.  (virial theorem = 2.000000
 # UHF(noneq)  energy is -74.72010092377 a.u.  (virial theorem = 2.000106
 
 ==============================================================================
 NOTE: Improved basis sets are available for H-Rn ("def2-bases").
 For further information type "bi".
 ==============================================================================

 ATOMIC ATTRIBUTE DEFINITION MENU  ( #atoms=15    #bas=15    #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 !)

Um einen Basissatz aus den in /opt/rrzk/software/turbomole/7.0/TURBOMOLE/basen/ verfügbaren auszuwählen, wird das dazugehörige Untermenü mit

       b

aufgerufen.

 ENTER A SET OF ATOMS TO WHICH YOU WANT TO ASSIGN BASIS SETS
 ( ATOMIC SET : all none <index list> <identifier> )
 TO OUTPUT ATOMIC SET SYNTAX ENTER A QUESTION MARK  ?
 E.G.  all dz            (DZ BASIS FOR ALL ATOMS)
       all sto-3g hondo  (SCALED STO-3G)
       1,2,4-6 dzp       (DZP BASIS FOR ATOMS 1,2,4,5,6)
       "c" tz            (TZ BASIS FOR ALL CARBON ATOMS)
 ANY DISPLAY COMMAND  dis  MAY BE ENTERED OR YOU MAY
 HIT >return< TO QUIT (GOING BACK TO MAIN MENU)

Für dieses Rechnung wird für alle Atome (all) die Basis STO-3G verwendet:

       all sto-3g hondo

 SUPPLYING BASIS SETS TO   15 ATOMS
 #                                                                      
 #                   BASIS SET LIBRARY FOR CARBON                       
 #            ECPs, HONDO-BASIS SETS FROM basen AND                     
 #     FULLY OPTIMIZED BASIS SETS FROM newbas MERGED 02/6/93            
 #                                                                      
 #         abbreviation hondo refers to the version 7.0 of HONDO        
 #                                                                      
 ########################################################################
 #       HF limit : E(3P) = -37.688619 a.u. (C. Froese Fischer, 1977)   
 ########################################################################
 #       Roothaan parameters for C(3P) in symmetry I:                   
 #        a = 3/4      b = 3/2                                          
 ########################################################################
 #                                                                      
 c sto-3g hondo                                                         
 # ROHF(equiv) energy is -37.19839253884 a.u.  (virial theorem = 2.019521
 # UHF(noneq)  energy is -37.19839253884 a.u.  (virial theorem = 2.019521
 # note the shared exponents for the sp-basis set                       
 # scale factors :                                                      
 # 1s  5.67  2sp  1.72                                                  
 # WJ Hehre, RF Stewart, JA Pople JCP 51,2657 (1969)                    
 # WJ Hehre, R Ditchfield, RF Stewart, JA Pople JCP 52,2769 (1970)      
 #                                                                      
 #                    BASIS SET LIBRARY FOR HYDROGEN                    
 #            ECPs, HONDO-BASIS SETS FROM basen AND                     
 #     FULLY OPTIMIZED BASIS SETS FROM newbas MERGED 02/6/93            
 #                                                                      
 #         abbreviation hondo refers to the version 7.0 of HONDO        
 #                                                                      
 ########################################################################
 #       HF limit : E(2S) = -0.5 a.u.                                   
 ########################################################################
 #       Roothaan parameters for H(2S):                                 
 #        a = 0      b = 0                                              
 ########################################################################
 #                                                                      
 h sto-3g hondo                                                         
 # h 3s/1s                                                              
 # HF(equiv) energy is -0.46658184606 a.u.  (virial theorem = 2.628935862
 #                                                                      
 # sto-3g basis set from hondo basis set library                        
 # default contraction   -.466582                                       
 #                                                                      
 #                                                                      
 #                       BASIS SET LIBRARY FOR OXYGEN                   
 #            ECPs, HONDO-BASIS SETS FROM basen AND                     
 #     FULLY OPTIMIZED BASIS SETS FROM newbas MERGED 02/6/93            
 #                                                                      
 #         abbreviation hondo refers to the version 7.0 of HONDO        
 #                                                                      
 #                                                                      
 ########################################################################
 #       HF limit : E(3P) = -74.809398 a.u. (C. Froese Fischer, 1977)   
 ########################################################################
 #       Roothaan parameters for O(3P) in symmetry I:                   
 #        a = 15/16      b = 9/8                                        
 ########################################################################
 #                                                                      
 o sto-3g hondo                                                         
 # ROHF(equiv) energy is -73.80415025596 a.u.  (virial theorem = 1.995133
 # UHF(noneq)  energy is -73.80415025596 a.u.  (virial theorem = 1.995133
 # note the shared exponents for the sp-basis set                       
 # scale factors :                                                      
 # 1s  7.66  2sp  2.25                                                  
 # WJ Hehre, RF Stewart, JA Pople JCP 51,2657 (1969)                    
 # WJ Hehre, R Ditchfield, RF Stewart, JA Pople JCP 52,2769 (1970)      

 ATOMIC ATTRIBUTE DEFINITION MENU  ( #atoms=15    #bas=15    #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 !)

Damit ist die Eingabe der Basis beendet und Sie können zum nächsten Menü wechseln:

       *

 BASIS SETS WILL BE WRITTEN TO FILE basis BY DEFAULT


              ATOMIC COORDINATES              ATOM SHELLS CHARGE PSEUDO MASS
    -0.26436320   -0.05787265   -0.04546600    c      3      6.     0 12.011
     2.38387765   -0.04914395   -0.05154237    c      3      6.     0 12.011
     3.70058625    2.24780459    0.00844492    c      3      6.     0 12.011
     2.36905399    4.53602457    0.07450508    c      3      6.     0 12.011
    -0.27918685    4.52729600    0.08057719    c      3      6.     0 12.011
    -1.59589545    2.23034736    0.02059229    c      3      6.     0 12.011
    -1.26969945   -1.81164380   -0.09126907    h      1      1.     0  1.008
     3.40053205   -1.79625051   -0.10198680    h      1      1.     0  1.008
     5.72257690    2.25446924    0.00380196    h      1      1.     0  1.008
     3.37439023    6.28979581    0.12030488    h      1      1.     0  1.008
    -3.61788612    2.22368290    0.02522890    h      1      1.     0  1.008
    -1.74240913    7.04182351    0.15316778    c      3      6.     0 12.011
    -4.12042132    7.03398551    0.15862357    o      3      8.     0 15.999
    -0.39882893    9.38564872    0.21437357    o      3      8.     0 15.999
    -1.38537813   10.66974023   -0.60350362    h      1      1.     0  1.008
 

 we will work with the  1s 3p 5d  7f  9g basis set


 there are 1 real representations :   a  

 OCCUPATION NUMBER & MOLECULAR ORBITAL DEFINITION MENU

 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

Für die erste Schätzung der Molekülorbitale wird der extended Hueckel guess empfohlen:

       eht

 PROVIDING EHT AOS FOR THE FOLLOWING SET OF ATOMS :
     1 c            2 c            3 c            4 c            5 c      
     6 c           12 c      
 for the   6 electrons of the actual atom you have
 to provide at least basis functions for the AO's :   2s  1p  0d  0f


 reading orbital data 3P(DZ)  from file /opt/rrzk/software/turbomole/7.0/TURBOMOLE/basen/c .

 

 PROVIDING EHT AOS FOR THE FOLLOWING SET OF ATOMS :
     7 h            8 h            9 h           10 h           11 h      
    15 h      
 for the   1 electrons of the actual atom you have
 to provide at least basis functions for the AO's :   1s  0p  0d  0f


 reading orbital data 2S(DZ)  from file /opt/rrzk/software/turbomole/7.0/TURBOMOLE/basen/h .

 

 PROVIDING EHT AOS FOR THE FOLLOWING SET OF ATOMS :
    13 o           14 o      
 for the   8 electrons of the actual atom you have
 to provide at least basis functions for the AO's :   2s  1p  0d  0f


 reading orbital data 3P(DZ)  from file /opt/rrzk/software/turbomole/7.0/TURBOMOLE/basen/o .

 

    sao summary :
   irrep      number of sao's referring to
                old basis    new basis
    a              51           51

 CALCULATING COMPLETE OVERLAP MATRIX


 EFFECTIVE NUMBER OF NON-VANISHING CARTESIAN
 OVERLAP MATRIX ELEMENTS   :    5193


 DO YOU WANT THE DEFAULT PARAMETERS FOR THE EXTENDED HUECKEL CALCULATION ?
 DEFAULT=y   HELP=?

       >return<

 JUST SETTING UP HUECKEL MATRIX !


 HUECKEL EQUATIONS ARE BEING SOLVED


 ENTER THE MOLECULAR CHARGE  (DEFAULT=0)

Für ein ungeladenes Molekül ist hier die Eingabe >return< , bei einem geladenen Molekül tragen Sie hier die Ladung ein.

       >return<

 NUMBER OF ELECTRONS IN YOUR MOLECULE IS   64


 AUTOMATIC OCCUPATION NUMBER ASSIGNMENT ESTABLISHED !
 FOUND CLOSED SHELL SYSTEM !
 HOMO/LUMO-SEPARATION :  0.096264
 ORBITAL  SYMMETRY      ENERGY     DEFAULT
 (SHELL)    TYPE                 OCCUPATION
    29    29a          -0.48582      2
    30    30a          -0.48180      2
    31    31a          -0.43236      2
    32    32a          -0.42351      2
    33    33a          -0.32724      0
    34    34a          -0.26786      0
    35    35a          -0.21028      0

 DO YOU ACCEPT THIS OCCUPATION ?  DEFAULT=y

       >return<

 projection quality sqrt{sum[1-<i|i>]}/korb irrep a    :  0.19D-01

 PROVIDING  'derivative'  DEFAULT PARAMETERS ...

 PROVIDING FORCE RELAXATION DEFAULT PARAMETERS ...

 FILE SPACE LOCKING WILL BE DISABLED BY DEFAULT !


 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
 pnocc  : OPTIONS AND DATA GROUPS FOR pnoccsd
 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
 rirpa  : RIRPA Parameters
 senex  : seminumeric exchange parameters
 hybno  : hybrid Noga/Diag parameters
 dsp    : DFT dispersion correction
 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

Um eine Rechenmethode zu benutzen, wählen Sie sie in diesem Menü aus (Ausnahme: SCF ist standardmässig aktiviert). In diesem Beispiel wird die Dichtefunktionaltheorie (dft) verwendet.

       dft

STATUS OF DFT_OPTIONS:
 DFT is NOT used
   functional b-p
     gridsize m3

 ENTER DFT-OPTION TO BE MODIFIED

 func    : TO CHANGE TYPE OF FUNCTIONAL
 grid    : TO CHANGE GRIDSIZE
  on:   TO SWITCH ON  DFT
 Just <ENTER>, q or '*' terminate this menu.

Die Auswahl des Funktionals geschieht mit der Eingabe

       func

 SURVEY OF AVAILABLE EXCHANGE-CORRELATION ENERGY FUNCTIONALS

 FUNCTIONAL      | TYPE | EXCHANGE       | CORRELATION    | REFERENCES
 ---------------------------------------------------------------------
 slater-dirac-   | LDA  | S              |                | 1,2
 exchange        |      |                |                |
 s-vwn           | LDA  | S              | VWN(V)         | 1-3
 vwn             | LDA  |                | VWN(V)         | 3
 s-vwn_Gaussian  | LDA  | S              | VWN(III)       | 1-3
 pwlda           | LDA  | S              | PW             | 1,2,4
 becke-exchange  | GGA  | S+B88          |                | 1,2,5
 b-lyp           | GGA  | S+B88          | LYP            | 1,2,6
 b-vwn           | GGA  | S+B88          | VWN(V)         | 1-3,5
 lyp             | GGA  |                | LYP            | 6
 b-p             | GGA  | S+B88          | VWN(V)+P86     | 1-3,5,7
 pbe             | GGA  | S+PBE(X)       | PW+PBE(C)      | 1,2,4,8
 tpss            | MGGA | S+TPSS(X)      | PW+TPSS(C)     | 1,2,4,14
 bh-lyp          | HYB  | 0.5(S+B88)     | LYP            | 1,2,5,6,9
                 |      | +0.5HF         |                |
 b3-lyp          | HYB  | 0.8S+0.72B88   | 0.19VWN(V)     | 1-3,5,6,10
                 |      | +0.2HF         | +0.81LYP       |
 b3-lyp_Gaussian | HYB  | 0.8S+0.72B88   | 0.19VWN(III)   | 1-3,5,6,10
                 |      | +0.2HF         | +0.81LYP       |
 pbe0            | HYB  | 0.75(S+PBE(X)) | PW+PBE(C)      | 1,2,4,8,11
                 |      | +0.25HF        |                |
 tpssh           | HYB  | 0.9(S+TPSS(X)) | PW+TPSS(C)     | 1,2,4,14,15
                 |      | +0.1HF         |                |
 m06             | HYB  |                |  +0.27HF       | 20        
 m06-2x          | HYB  |                |  +0.54HF       | 20        
 lhf             | ODFT | E-EXX          |                | 12,13
 oep             | ODFT | EXX            |                | 18
 b97-d           | GGA  | B97 refit      | B97 refit      | 16
 pbeh-3c         | GGA  | PBE0 refit     |  PBE0 refit    | 21
 b2-plyp         | DHYB |0.47(SB88)+0.53HF|0.73LYP+0.27PT2| 17


 REFERENCES:
 [1] Dirac, P.A.M., Proc. Royal Soc. (London) A 123 (1929), 714.
 [2] Slater, J.C., Phys. Rev. 81 (1951), 385.
 [3] Vosko, S.H., Wilk, L., Nusair, M., Can. J. Phys. 58 (1980), 1200.
 [4] Perdew, J.P., Wang, Y., Phys. Rev. B 45 (1992), 13244.
 [5] Becke, A.D., Phys. Rev. A 38 (1988), 3098.
 [6] Lee, C., Yang, W., Parr, R.G., Phys. Rev. B 37 (1988), 785.
 [7] Perdew, J.P., Phys. Rev. B 33 (1986), 8822.
 [8] Perdew, J.P., Burke, K., Ernzerhof, M., Phys. Rev. Lett. 77 (1996), 3865.
 [9] Becke, A.D., J. Chem. Phys. 98 (1993), 1372.
[10] Becke, A.D., J. Chem. Phys. 98 (1993), 5648.
[11] Perdew, J.P., Ernzerhof, M., Burke, K., J. Chem. Phys. 105 (1996), 9982.
[12] Della Sala, F., Goerling, A., J. Chem. Phys. 115 (2001), 5718.
[13] Della Sala, F., Goerling, A., J. Chem. Phys. 116 (2002), 5374.
[14] Tao, J., Perdew, J.P., Staroverov, V.N., Scuseria, G.E, Phys. Rev. Lett.
     91 (2003), 146401.
[15] Staroverov, V.N., Scuseria, G.E, Tao, J., Perdew, J.P., J. Chem. Phys.
     119 (2003), 12129.
[16] Grimme, S., J. Comput. Chem. 27, (2006), 1787
     (add $disp for dispersion correction)
[17] Grimme, S., J. Chem. Phys. 124, (2006), 034108
[18] Hesselmann, A., Goetz, A.W., Della Sala, F., Goerling, A.,
     J. Chem. Phys. 127 (2007), 054102
[20] Y. Zhao, D. G. Truhlar, Theor. Chem. Acc., 120, (2008), 215
[21] S. Grimme et al 2015, to be published

Und

       b3-lyp

 ENTER DFT-OPTION TO BE MODIFIED

 func    : TO CHANGE TYPE OF FUNCTIONAL
 grid    : TO CHANGE GRIDSIZE
  on:   TO SWITCH ON  DFT
 Just <ENTER>, q or '*' terminate this menu.

Natürlich muss die Methode auch aktiviert werden:

       on

STATUS OF DFT_OPTIONS:
 DFT is used
   functional b3-lyp
     gridsize m3

 ENTER DFT-OPTION TO BE MODIFIED

 func    : TO CHANGE TYPE OF FUNCTIONAL
 grid    : TO CHANGE GRIDSIZE
  off:  TO SWITCH OFF DFT
 Just <ENTER>, q or '*' terminate this menu.

       >return<

 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
 pnocc  : OPTIONS AND DATA GROUPS FOR pnoccsd
 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
 rirpa  : RIRPA Parameters
 senex  : seminumeric exchange parameters
 hybno  : hybrid Noga/Diag parameters
 dsp    : DFT dispersion correction
 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

Nachdem alle benötigten Eingaben getätigt wurden, wird die Define-Session mit einem Stern beendet:

       *

 ***********************************************************
 *                                                         *
 *                       e n d   o f                       *
 *                       D E F I N E                       *
 *                                                         *
 *         TURBOMOLE'S  INTERACTIVE  INPUT  PROGRAM        *
 *                                                         *
 *  Quantum Chemistry Group       University of Karlsruhe  *
 *                                                         *
 ***********************************************************


    ------------------------------------------------------------------------
         total  cpu-time :   0.37 seconds
         total wall-time : 49 minutes and 15 seconds
    ------------------------------------------------------------------------


   ****  define : all done  ****


    2015-10-15 13:52:22.346

 define ended normally

 Im Arbeitsordner befinden sich nun sechs Dateien (überprüfbar mit dem Befehl ls):

  • basis : enthält die Basissätze für alle vorkommenden Atome
  • benzoesaure.com : Koordinatendatei aus GaussView
  • benzoesaure.coord : enthält die Startgeometrie des Moleküls
  • control : enthält alle Befehle an Turbomole (diese Datei wird während der Rechnung verändert)
  • coord : enthält die aktuelle Geometrie (diese Datei wird während der Rechnung verändert)
  • mos : enthält die aktuelle Molekülorbitale (diese Datei wird während der Rechnung verändert)

Da drei der Dateien während einer Turbomole Rechnung verändert werden, empfehlen wir Ihnen ein Backup der Inputdateien zu erstellen.

       mkdir input

       cp * input/.

Die Anzahl der Dateien kann sich erhöhen, wenn eine andere Rechnung durchgeführt wird (beispielsweise UHF, frozen core Orbitals und andere).

Kontakt
Bei Fragen und für eine individuelle Beratung wenden Sie sich bitte an:
RRZK-Helpdesk