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Define#
Define contains four main parts:
- Geometry menu: Read the geometry of the molecules, set up the coordinates of the system, find out the point group symmetry.
- Atomic attributes menu: Select the basis sets for the atoms.
- Initial guess menu: Determine the charge of the molecule and generate the initial guess for the molecular orbitals and their occupation.
- General menu: Select the computational method and set up advanced options such as excited state calculations.
Some general instructions for define:
*(orq) - Closes the current menu and writes the data into control.&- Returns to the previous menu.qq- Quits Define immediately (panic button).
Usually Define offers a default choice for all questions. The default choice can be accepted simply by pressing Enter.
NB! define is case-sensitive.
Starting define#
***********************************************************
* *
* 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<.
Enter
INPUT TITLE OR
ENTER & TO REPEAT DEFINITION OF DEFAULT INPUT FILE
Enter
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
a start-coord
CARTESIAN COORDINATES FOR 12 ATOMS HAVE SUCCESSFULLY
BEEN ADDED.
........
SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=12 SYMMETRY=c1 )
ired
GEOIRED: NBDIM 30 NDEGR: 30 ......
*
ATOMIC ATTRIBUTE DEFINITION MENU ( #atoms=12 #bas=12 #ecp=4 )
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 !)
*
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
eht
Enter
0
Enter
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
*
Examples of define files#
DFT calculation (PB86-D3BJ/def2-SV(P))#
In this example, the BP86 functional (dft/on) and def2-SV(P) basis set (b/all def2-SV(P)) will be used for the calculation. This is the default level of theory for DFT calculations in TURBOMOLE. BP86 functional has a good and stable performance throughout the periodic system, and by default def2 basis sets include ECPs for atoms beyond Kr. Additionally, will be used Grimme's dispersion correction D3BJ (dsp/on/bj). The geometry will be read from the file start-coord. Will be used the redundant internal coordinates (ired) since they typically result in the smallest number of optimization steps. To speed up calculations resolution-of-the-identity (RI) and multipole-accelerated RI-J (MARIJ) approximations will be used (ri/on and marij/on). The molecule's charge is -1. An initial guess of the molecular orbitals will be done by eht* and up to 100 iterations will be done during scf cycle (scf/iter/100**).
start-coord
$coord
-1.95916500780981 -0.42159243893826 0.00000000000000 ir
-1.95916500780981 4.47279824523555 0.00000000000000 i
-6.85355569198362 -0.42159243893826 0.00000000000000 i
-1.95916500780981 -0.42159243893826 -4.89439068417382 i
-1.95916500780981 -0.42159243893826 3.83614404975786 c
-2.45256841929780 -2.26300137375688 4.51014577207379 h
-0.11775648873094 0.07181261661147 4.51014577207379 h
-3.30717015319520 0.92641151591967 4.51014673583412 h
1.87697904194805 -0.42159243893826 0.00000000000000 c
-1.95916500780981 -4.25773648869612 0.00000000000000 c
4.25501040757134 -0.42159243893826 0.00000000000000 o
-1.95916500780981 -6.63576785431941 0.00000000000000 o
$end
define
define <<EOF
a start-coord
ired
*
b
all def2-SV(P)
*
eht
yes
-1
yes
scf
iter
100
ri
on
marij
on
dft
on
dsp
on
bj
*
EOF
comands to run
ridft > JOB.out 2>JOB.err # single point calculation using RI-approximation
jobex -ri -c 45 > FINAL.out 2>FINAL.err # geometry optimization using RI-approximation,
will be don up to 45 steps
DFT calculation (MO6 (hybrid functional) and different basis sets including ECP) with frozen position of several atoms#
In this example, the M06 functional (dft/on/func/m06) and two different basis sets (_b/1 6-31G/ecp/"i" DZP_*) will be used for calculations. For the first atom 6-31G will bu applied and for all I atoms - def-SV(P) with ECP. The geometry will be read from the file start-coord and Cartesian coordinates will be used for further calculations. In addition, the position of the two first atoms will be frozen, that can be done only in Cartesian coordinates. The molecule's charge is 0. An initial guess of the molecular orbitals will be done by eht** and up to 30 default iterations will be done during scf cycle.
start-coord
$coord
0.74398670919525 0.42159243893826 0.00000000000000 n f
2.02272352743997 2.22995142429552 3.13219908774303 i f
2.02265750040888 -3.19517438119679 0.00000000000000 i
2.02272352743997 2.22995142429552 -3.13219909530193 i
$end
define
define <<EOF
a start-coord
*
no
b
1 6-31G*
ecp
"i" DZP
*
eht
yes
0
yes
dft
on
func
m06
*
EOF
NB! In coord file should appear the corresponding "f" marks.
$coord
0.74398670919525 0.42159243893826 0.00000000000000 n f
2.02272352743997 2.22995142429552 3.13219908774303 i f
comands to run
dft > JOB.out 2>JOB.err # single point calculation
jobex -c 45 > FINAL.out 2>FINAL.err # geometry optimization, will be done up to 45 steps
HF & optimization with frozen internal coordinated#
In this example, HF and minix basis set will be used for calculations. Some internal coordinates will be frozen (i/idef/f tors 1 2 3 4/f bend 1 2 3/f stre 1 2) during geometry optimization. To speed up calculations RI-approximations will be used.
coord file
$coord
1.27839972889714 0.80710203135546 0.00041573974923 c
1.42630859331810 2.88253155131977 0.00372276048178 h
3.06528696563114 -0.57632867600746 -0.00069919866917 o
-1.91446264796512 -0.31879679861781 0.00039684248791 o
-2.98773260513752 1.98632893279876 -0.00701088395301 h
$end
define
define <<EOF
a start-coord
i
idef
f tors 1 2 3 4
f bend 1 2 3
f stre 1 2
ired
*
bb all minix
*
eht
yes
0
yes
ri
on
*
EOF
NB! In coord file should appear a corresponding part with list of defined internal coordinates:
$intdef
# definitions of internal coordinates
1 f 1.0000000000000 tors 1 2 3 4 val= -0.04664
2 f 1.0000000000000 bend 1 2 3 val= 26.89863
3 f 1.0000000000000 stre 1 2 val= 2.08070
comands to run
dscf > JOB.out 2>JOB.err # single point calculation
jobex -ri > FINAL.out 2>FINAL.err # geometry optimization
(RI-approximation will be used if it is specified in control file)
RI-MP2 calculation#
In this example, calculations will be performed at the MP2/def2-TZVP level of theory (b/all def2-TZVP and cc/ricc2/mp2/geoopt model=mp2), inner core electrons will be freezed and conergence criteria increaced (_mp2/freeze//cbas/b/all def2-TZVP//denconv/0.1E-07_*). The symmetry of the molecule is determined and will be utilized (desy). To speed up calculations RI-approximations will be used (ricc2). The molecule's charge is 0. An initial guess of the molecular orbitals will be done by eht* and up to 70 iterations will be done during scf cycle.
coord file
$coord
0.00000000000000 -0.00000000000000 0.00000000000000 c
-1.18649579051912 1.18649579051912 1.18649579051912 h
1.18649579051912 -1.18649579051912 1.18649579051912 h
-1.18649579051912 -1.18649579051912 -1.18649579051912 h
1.18649579051912 1.18649579051912 -1.18649579051912 h
$end
define
define <<EOF
a start-coord
desy
ired
*
b
all def2-TZVP
*
eht
yes
0
yes
scf
iter
70
mp2
freeze
*
cbas
b
all def2-TZVP
*
denconv
0.1E-07
*
cc
ricc2
mp2
geoopt model=mp2
*
*
*
EOF
comands to run
jobex -ri -level mp2 > FINAL.out 2>FINAL.err
CC2 calculation#
In this example, calculations will be performed at the cc22/def2-TZVP level of theory (b/all def2-TZVP and cc/ricc2/cc2/geoopt model=cc2), inner core electrons will be freezed and conergence criteria increaced (_mp2/freeze//cbas/b/all def2-TZVP//denconv/0.1E-07_*). The symmetry of the molecule is determined and will be utilized (desy). To speed up calculations RI-approximations will be used (ricc2). The molecule's charge is 0. An initial guess of the molecular orbitals will be done by eht* and up to 70 iterations will be done during scf cycle.
coord file
$coord
0.00000000000000 -0.00000000000000 0.00000000000000 c
-1.18649579051912 1.18649579051912 1.18649579051912 h
1.18649579051912 -1.18649579051912 1.18649579051912 h
-1.18649579051912 -1.18649579051912 -1.18649579051912 h
1.18649579051912 1.18649579051912 -1.18649579051912 h
$end
define
define <<EOF
a start-coord
desy
ired
*
b
all def2-TZVP
*
eht
yes
0
yes
scf
iter
70
cc
freeze
*
cbas
b
all def2-TZVP
*
denconv
0.1E-07
ricc2
cc2
geoopt model=cc2
*
*
*
EOF
comands to run
jobex -ri -level cc2 > FINAL.out 2>FINAL.err