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).
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