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Software Introduction
TURBOMOLE | ||||||||||||||
TURBOMOLE consists of a set of programs for carrying out DFT and ab initio electronic structure calculations. One of its unique features is the RI (resolution of identity) technique which uses auxiliary basis sets for main row atoms and transition metals to approximate Coulomb potentials leading to extremely efficient integral evaluation. Note that there are two libraries for the auxiliary basis sets, one for DFT calculations, the other for correlation calculations. The TURBOMOLE package contains a series of programs and a number of scripts. The particular program (or programs) needed will depend on the specific calculation type. A full list of all the programs available is given in the user manual, but the most commonly used are:
The input file for all the programs is control. This is an ascii file that can be generated manually but is normally easier to set up using the interactive input generator called define. define contains four menus as shown below: The geometry main menu
Note that TURBOMOLE comes with a script x2t that converts xyz files to TURBOMOLE coordinates and it is these that must be read into define (if the coordinates are read from a file). The following examples illustrate how define can be used to set up input files for
We will then describe how these calculations can be run and how to interpret the output files. | ||||||||||||||
Examples | ||||||||||||||
Please note that the following examples were carried out with TURBOMOLE version 5.9 on Magellan. For more information on the latest version available from the NSCCS Cluster, users should refer to the TURBOMOLE man page by typing: man runturbo Example 1. SCF single point energy calculation of HF dimer Example 2. RI-MP2 geometry optimisation of HF dimer Note: All explanations are given in red. | ||||||||||||||
| Example 1. SCF single point energy calculation of HF dimer
Step 1: A new directory should be created when using define so that all the input files produced will be in a single location, as the program will only recognise the input files by their generic names. Step 2: The geometry can be input interactively into define or read in from the coord file. In this case, a coord file is created by converting a geometry from an xyz file using the x2t script: x2t hf_dimer.xyz > coord Click here to download the xyz file. Step 3: A series of menus will appear in define for modifying/setting up the coord file (containing the geometry information), the basis file (containing the basis set information), the mos file (containing the initial guess molecular orbitals and occupation numbers), and finally the control file (containing the keywords). Once these input files are created, users can then select the correct programs or series of programs to run the desired job. Here is an example of what is output to the screen when define is run. A coord file is already available for use and is located in the same directory. Type define at the prompt.
define(magellan) : TURBOMOLE V5-9-1 30 Apr 2007 at 02:43:04
Copyright (C) 2007 University of Karlsruhe
2007-10-25 11:38:46.568
OPERATING SYSTEM = unix
HOST NAME = magellan
STANDARD BASIS SET LIBRARY = /usr/local/Chem-Apps/turbomole5.9/basen/
ALTERNATE BASIS SET LIBRARY = /usr/local/Chem-Apps/turbomole5.9/basold/
LIBRARY FOR RI-J BASIS SETS = /usr/local/Chem-Apps/turbomole5.9/jbasen/
LIBRARY FOR RI-JK BASIS SETS = /usr/local/Chem-Apps/turbomole5.9/jkbasen/
LIBRARY FOR RIMP2/RICC2 SETS = /usr/local/Chem-Apps/turbomole5.9/cbasen/
STRUCTURE LIBRARY = /usr/local/Chem-Apps/turbomole5.9/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<.
Hit return here.
INPUT TITLE OR
ENTER & TO REPEAT DEFINITION OF DEFAULT INPUT FILE
HF Dimer Specify title for input file.
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 coord Specify that atomic coordinates will be read from existing coord file.
CARTESIAN COORDINATES FOR 4 ATOMS HAVE SUCCESSFULLY
BEEN ADDED.
keyword $intdef missing in file <coord>
DEFINITIONS OF INTERNAL COORDINATES HAVE N O T BEEN READ.
keyword $user-defined bonds missing in file <coord>
SPECIFICATION OF BOND TOPOLOGY HAS N O T BEEN READ.
SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=4 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
desy First of all, determine the molecular symmetry.
molecule is planar
2 symmetry operations found :
given set of 4 coordinate triples separated
into 4 bin(s) for a given accuracy of 0.5000D-06
no atom resides at center of mass
found x-fold axis : 0.334826 0.942280 0.000000
symmetry axes are incompatible with bin 2
thrsym = 1.000000000000000E-006
RESULTING SCHOENFLIES SYMBOL = cs
symmetry group of the molecule : cs
the group has the following generators :
c1(z)
mirror plane sigma(xy)
2 symmetry operations found
THE MOLECULAR GEOMETRY WILL BE SYMMETRIZED !
SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=4 SYMMETRY=cs )
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
ired Specify that redundant internal coordinates are to be generated.
hydrob: WARNING!
NEW BOND 1 2 IS VERY LONG
GEOSPY: NBDIM: 5 NDEGR: 5
Lowest Eigenvalue of BmBt is: 0.1290233451
GEOSPY: ATTENTION!
natural internals not linearly independent?
Decoupling with "globtry"= 0.999999999900000
Lowest Eigenvalue of projected BBt 0.1290233451 No: 5
Quotient of Eigenvalues 1.0000000000
OCCUPATION OF BLOCKS: 5 0 0 0 0
SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=4 SYMMETRY=cs )
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
* No more geometry options needed, type * to terminate molecular geometry specification.
GEOMETRY DATA WILL BE WRITTEN TO FILE coord
file cannot be opened
SUPPLYING BASIS SETS TO 4 ATOMS Enter basis set menu.
#
# 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)
# (4s)/[2s] {31}
# HF(equiv) energy is -0.49927840571 a.u. (virial = 2.00000000184)
# H. Horn, Aug. 91
#
# BASIS SET LIBRARY FOR FLUORINE
# 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(2P) = -99.409349 a.u. (C. Froese Fischer, 1977)
########################################################################
# Roothaan parameters for F(2P) in symmetry I:
# a = 24/25 b = 24/25
########################################################################
#
f def-SV(P)
f def2-SVP
f def2-SV(P)
# ROHF(equiv) energy is -99.27968957052 a.u. (virial = 2.00000000002)
# UHF(noneq) energy is -99.28405120061 a.u. (virial = 2.00004903429)
# (7s4p1d)/[3s2p1d] {511/31/1}
==============================================================================
NOTE: Improved basis sets are available for H-Rn ("def2-bases").
For further information type "bi".
==============================================================================
ATOMIC ATTRIBUTE DEFINITION MENU ( #atoms=4 #bas=4 #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 !)
bb all TZVPP To assign TZVPP basis set s to all atoms.
SUPPLYING BASIS SETS TO 4 ATOMS
#
# 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 TZVPP
h def-TZVPP
h def2-TZVPP
# SCF(equiv) energy is -0.49980983223 a.u. (virial = 2.00000022225)
# TZ + cc-pVTZ polarization functions
# (5s2p1d)/[3s2p1d] {311/11/1}
#
# BASIS SET LIBRARY FOR FLUORINE
# 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(2P) = -99.409349 a.u. (C. Froese Fischer, 1977)
########################################################################
# Roothaan parameters for F(2P) in symmetry I:
# a = 24/25 b = 24/25
########################################################################
#
f TZVPP
f def-TZVPP
f def2-TZVP
f def2-TZVPP
# ROHF(equiv) energy is -99.40536759038 a.u. (virial = 1.99999999938)
# UHF(noneq) energy is -99.41179850040 a.u. (virial = 2.00003675791)
# note that def2-TZVP and def2-TZVPP are identical
# (11s6p2d1f)/[5s3p2d1f] {62111/411/11/1}
ATOMIC ATTRIBUTE DEFINITION MENU ( #atoms=4 #bas=4 #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 !)
bl To list basis sets specified for atoms.
------------------------------------------------------------------------
LIST OF BASIS SETS DEFINED YET
------------------------------------------------------------------------
INDEX | BASIS SET NICKNAME
------------------------------------------------------------------------
1 | h TZVPP
2 | f TZVPP
------------------------------------------------------------------------
NOTE THAT YOU MAY USE bm #<i> IF YOU WANT TO MODIFY THE
BASIS SET WITH THE INDEX <i> BY MEANS OF THE bm COMMAND
TO CONTINUE, ENTER <return> Hit return here.
ATOMIC ATTRIBUTE DEFINITION MENU ( #atoms=4 #bas=4 #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 !)
* Type * to terminate atomic attribute definition.
BASIS SETS WILL BE WRITTEN TO FILE basis BY DEFAULT
ATOMIC COORDINATES ATOM SHELLS CHARGE PSEUDO MASS
1.02698794 2.89019118 0.00000000 h 6 1. 0 1.008
0.65161882 -3.82657134 0.00000000 f 11 9. 0 18.998
-2.33022558 -5.23852119 0.00000000 h 6 1. 0 1.008
0.65161882 6.17490135 0.00000000 f 11 9. 0 18.998
we will work with the 1s 3p 5d 7f 9g basis set
SYMMETRY HAS BEEN CHANGED
there are 2 real representations : a' a"
OCCUPATION NUMBER & MOLECULAR ORBITAL DEFINITION MENU
CHOOSE COMMAND
infsao : OUTPUT SAO INFORMATION
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
& : 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 To use extended Huckel guess for initial molecular orbitals and occupation numbers.
PROVIDING EHT AOS FOR THE FOLLOWING SET OF ATOMS :
1 h 3 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 /usr/local/Chem-Apps/turbomole5.9/basen/h .
PROVIDING EHT AOS FOR THE FOLLOWING SET OF ATOMS :
2 f 4 f
for the 9 electrons of the actual atom you have
to provide at least basis functions for the AO's : 2s 1p 0d 0f
reading orbital data 2P(DZ) from file /usr/local/Chem-Apps/turbomole5.9/basen/f .
sao summary :
irrep number of sao's referring to
old basis new basis
a' 10 62
a" 2 28
CALCULATING COMPLETE OVERLAP MATRIX
EFFECTIVE NUMBER OF NON-VANISHING CARTESIAN
OVERLAP MATRIX ELEMENTS : 4420
DO YOU WANT THE DEFAULT PARAMETERS FOR THE EXTENDED HUECKEL CALCULATION ?
DEFAULT=y HELP=?
Hit return to use the default value.
JUST SETTING UP HUECKEL MATRIX !
HUECKEL EQUATIONS ARE BEING SOLVED
ENTER THE MOLECULAR CHARGE (DEFAULT=0)
Hit return to use the default value.
NUMBER OF ELECTRONS IN YOUR MOLECULE IS 20
AUTOMATIC OCCUPATION NUMBER ASSIGNMENT ESTABLISHED !
FOUND CLOSED SHELL SYSTEM !
HOMO/LUMO-SEPARATION : 0.285350
ORBITAL SYMMETRY ENERGY DEFAULT
(SHELL) TYPE OCCUPATION
7 7a' -0.71635 2
8 1a" -0.71635 2
9 2a" -0.71635 2
10 8a' -0.71635 2
11 9a' -0.43100 0
12 10a' -0.42905 0
DO YOU ACCEPT THIS OCCUPATION ? DEFAULT=y
Hit return to accept the default occupation.
projection quality sqrt{sum[1-<i|i>]}/korb irrep a' : 0.88D-02
projection quality sqrt{sum[1-<i|i>]}/korb irrep a" : 0.24D-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/cc2: OPTIONS AND DATA GROUPS FOR MP2, CC2, ETC.
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
scf Type scf to select SCF calculation.
ENTER SCF-OPTION TO BE MODIFIED
conv : ACCURACY OF SCF-ENERGY $scfconv
thi : INTEGRAL STORAGE CRITERIA $thize $thime
ints : INTEGRAL STORAGE ALLOCATION $scfintunit
iter : MAXIMUM NUMBER OF ITERATIONS $scfiterlimit
diis : DIIS CONVERGENCE ACCELERATION $scfdiis
damp : OPTIONS FOR DAMPING $scfdamp
shift: SHIFTING OF ORBITALS $scforbitalshift
order: ORDERING OF ORBITALS $scforbitalorder
fermi: THERMAL SMEARING OF OCC. NUMBERS $fermi
pdiag: PREDIAGONALIZATION $prediag
You can change the SCF parameters here. In this case, hit return to use the defaults.
GENERAL MENU : SELECT YOUR TOPIC
scf : SELECT NON-DEFAULT SCF PARAMETER
mp2/cc2: OPTIONS AND DATA GROUPS FOR MP2, CC2, ETC.
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
* Type * to terminate define session.
***********************************************************
* *
* 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 : 0.17 seconds
total wall-time : 1 minutes and 17 seconds
------------------------------------------------------------------------
**** define : all done ****
2007-10-25 11:40:03.581
define ended normally A number of files will be produced.
| ||||||||||||||
Input | ||||||||||||||
The following files are produced by define.
The basis, coord and mos files are straightforward to interpret. The control file is more complicated and is shown below with explanations. control $title Title specification. HF Dimer $operating system unix Operating system. $symmetry cs Symmetry specification. $redundant file=coord To read redundant coordinates from file coord. $coord file=coord To read in coordinates from file coord. $user-defined bonds file=coord To read in user-defined bonds from file coord. $atoms Atomic specification. h 1,3 \ Atom type, Atom labels, \ backslash is required. basis =h TZVPP Specifying basis set to be used for H. f 2,4 \ Atom type, Atom labels, \ backslash is required. basis =f TZVPP Specifying basis set to be used for F. $pople AO Spherical harmonics to be used for basis functions. $basis file=basis To read in basis sets from file basis. $rundimensions Size specification of the run. dim(fock,dens)=5463 Dimension for Fock densities. natoms=4 Number of atoms. nshell=34 Number of shells. nbf(CAO)=102 Number of Cartesian basis functions. nbf(AO)=90 Number of SCF basis functions. dim(trafo[SAO<-->AO/CAO])=126 Dimension for basis functions. rhfshells=1 Restricted Hartree-Fock. $scfmo file=mos Reading orbital data $scfmo from file mos. $closed shells RHF MO occupations. a' 1-8 ( 2 ) a" 1-2 ( 2 ) $scfiterlimit 30 Maximum number of SCF iterations. $scfconv 7 SCF convergence. $thize 0.10000000E-04 Threshold size. $thime 5 Threshold time. $scfdamp start=0.500 step=0.050 min=0.100 Damping oscillations in SCF iterations. $scfdump MOs to be saved after each iteration in formatted form on file mos. $scfintunit Scratch file for two-electron integrals in semi-direct calculations. unit=30 size=0 file=twoint $scfdiis start=0.5 Default setting of define for the onset of DIIS acceleration of SCF convergence. $scforbitalshift automatic=.1 Automatic virtual shell shift switched on to help convergence. $drvopt Derivative options. cartesian on Evaluate derivatives with respect to nuclear coordinates. basis off Do not evaluate derivatives with respect to basis set components and/or contraction coefficients. global off Do not evaluate gradient with respect to a uniform scale factor for all basis set exponents. hessian on Evaluate second derivatives with respect to nuclear coordinates. dipole on Evaluate derivatives of dipole moment with respect to nuclear coordinates. nuclear polarizability Calculate nuclear contribution to electrostatic polarisability. $interconversion off Conversion to internals is switched off. qconv=1.d-7 Convergence criterion for internals -> cartesians. maxiter=25 Maximum number of iterations for the iterative conversion procedure. $optimize Optimisation specifications. internal on Optimise molecular geometries in internal coordinates as specified in $intdef. redundant on Read in redundant coordinates from $coord. cartesian off Not to optimise geometry in the space of cartesian coordinates. global off Not to optimise a global scaling factor for all basis set exponents. basis off logarithm Do not optimise basis set exponents. $coordinateupdate Coordinate update specifications. dqmax=0.3 Maximum allowed total change for update of coordinates. interpolate on Calculate geometry update by inter/extrapolation of geometries of the last 2 cycles. statistics 5 Provide a statistics output for the last 5 cycles. $forceupdate Force update specifications. ahlrichs numgeo=0 mingeo=3 maxgeo=4 modus=<g|dq> dynamic fail=0.3 threig=0.005 reseig=0.005 thrbig=3.0 scale=1.00 damping=0.0 $forceinit on Force initialisation. diag=default Provide a diagonal force constant matrix. $energy file=energy Output energy to file energy. $grad file=gradient Output gradient to file gradient. $forceapprox file=forceapprox Approximate force constant, save file as forceapprox. $lock off Set by define, not needed. $last step define $end Input files (gzipped) can be downloaded as follow: | ||||||||||||||
Output | ||||||||||||||
Step 4: To run a single point energy calculation, the program dscf needs to be used. On Magellan, this can be done by typing: $CHEM/runturbo dscf No input files need to be specified as TURBOMOLE will automatically read in the four input files generated by define. A number of files will be produced - dscf.out, energy and statistics. Please note that the starting files control and mos are updated after the completion of the calculation, ready to be used in further calculations. Therefore if you would like to keep the original starting files, make sure they are copied into a different directory. energy - contains a summary of the energy calculated. statistics - contains the statistics from the SCF calculation. dscf.out
operating system is UNIX !
hostname is magellan
dscf(magellan) : TURBOMOLE V5-9-1 30 Apr 2007 at 02:43:04
Copyright (C) 2007 University of Karlsruhe
2007-10-25 13:51:37.795
d s c f - program
idea & directorship : reinhart ahlrichs
program development : marco haeser
michael baer
dft version : oliver treutler
quantum chemistry group
universitaet karlsruhe
germany
References
Density Functional:
O. Treutler and R. Ahlrichs
Efficient Molecular Numerical Integration Schemes
J. chem. Phys. 102: 346 (1995)
Parallel Version:
Performance of parallel TURBOMOLE for Density
Functional Calculations
M. v.Arnim and R. Ahlrichs
J. comp. Chem. 19: 1746 (1998)
Job title as specified.
*************************************************************************
HF Dimer
*************************************************************************
ht3@magellan:~/softintro/turbomole/ex1/after> cat *.out
operating system is UNIX !
hostname is magellan
dscf(magellan) : TURBOMOLE V5-9-1 30 Apr 2007 at 02:43:04
Copyright (C) 2007 University of Karlsruhe
2007-10-25 13:51:37.795
DSCF program is used.
d s c f - program
idea & directorship : reinhart ahlrichs
program development : marco haeser
michael baer
dft version : oliver treutler
quantum chemistry group
universitaet karlsruhe
germany
References
Density Functional:
O. Treutler and R. Ahlrichs
Efficient Molecular Numerical Integration Schemes
J. chem. Phys. 102: 346 (1995)
Parallel Version:
Performance of parallel TURBOMOLE for Density
Functional Calculations
M. v.Arnim and R. Ahlrichs
J. comp. Chem. 19: 1746 (1998)
*************************************************************************
HF Dimer
*************************************************************************
Coordinates of molecules.
+--------------------------------------------------+
| Atomic coordinate, charge and isotop information |
+--------------------------------------------------+
atomic coordinates atom shells charge pseudo isotop
1.02698794 2.89019118 0.00000000 h 6 1.000 0 0
0.65161882 -3.82657134 0.00000000 f 11 9.000 0 0
-2.33022558 -5.23852119 0.00000000 h 6 1.000 0 0
0.65161882 6.17490135 0.00000000 f 11 9.000 0 0
center of nuclear mass : 0.58595851 1.05585038 0.00000000
center of nuclear charge: 0.52129505 0.93933200 0.00000000
Basis set used.
+--------------------------------------------------+
| basis set information |
+--------------------------------------------------+
we will work with the 1s 3p 5d 7f 9g ... basis set
...i.e. with spherical basis functions...
type atoms prim cont basis
---------------------------------------------------------------------------
h 2 16 14 TZVPP [3s2p1d|5s2p1d]
f 2 46 31 TZVPP [5s3p2d1f|11s6p2d1f]
---------------------------------------------------------------------------
total: 4 124 90
---------------------------------------------------------------------------
total number of primitive shells : 28
total number of contracted shells : 34
total number of cartesian basis functions : 102
total number of SCF-basis functions : 90
Threshold specification.
integral neglect threshold : 0.33E-10
integral storage threshold THIZE : 0.10E-04
integral storage threshold THIME : 5
Symmetry specified - as determined by define.
symmetry group of the molecule : cs
the group has the following generators :
c1(z)
mirror plane sigma(xy)
2 symmetry operations found
there are 2 real representations : a' a"
maximum number of shells which are related by symmetry : 1
Molecular orbitals occupation.
mo occupation :
irrep mo's occupied
a' 62 8
a" 28 2
number of basis functions : 90
number of occupied orbitals : 10
------------------------
nuclear repulsion energy : 15.7634426152
------------------------
-----------------
-S,T+V- integrals
-----------------
1e-integrals will be neglected if expon. factor < 0.327643E-11
Difference densities algorithm switched on.
The maximal number of linear combinations of
difference densities is 20 .
automatic virtual orbital shift switched on
shift if e(lumo)-e(homo) < 0.10000000
DIIS switched on: error vector is FDS-SDF
Max. Iterations for DIIS is : 5
DIIS matrix (see manual)
Scaling factor of diagonals : 1.200
threshold for scaling factor : 0.000
SCF specifications.
scf convergence criterion : increment of total energy < .1000000D-06
and increment of one-electron energy < .1000000D-03
Output files (gzipped) can be downloaded as follow: dscf.out | energy | statistics | control (updated) | mos (updated) | ||||||||||||||
| Example 2. RI-MP2 geometry optimisation of HF dimer
In order to carry out the RI-MP2 optimisation of the HF dimer, we use the same steps as in Example 1 to obtain the initial input files. However, before running the dscf calculation, we need to make some modifications to the input files. These can be done with rimp2prep which is a post-processing tool used to set up RI-MP2 calculations. Steps 1-3: Carry out as in Example 1 to obtain the input files. Step 4: Copy the input files created in Step 3 to a new directory. Run the post-processor rimp2prep in this new directory where the basis, coord, control and mos input files are located. Here is an example of what is output to the screen when rimp2prep is run: Type rimp2prep at the prompt.
operating system is UNIX !
hostname is magellan
rimp2prep(magellan) : TURBOMOLE V5-9-1 30 Apr 2007 at 02:43:04
Copyright (C) 2007 University of Karlsruhe
2007-10-25 13:56:43.196
r i m p 2 p r e p
by F. Weigend
quantum chemistry group
university karlsruhe
germany
WHICH KIND OF CALCULATION WOULD YOU LIKE TO PERFORM:
MP2-ENERGY ONLY (e) OR ENERGY AND GRADIENT (g) ?
DEFAULT: ENERGY AND GRADIENT
g To request MP2 energy and gradient calculation to be performed.
*************************************************************************
HF Dimer
*************************************************************************
+--------------------------------------------------+
| Atomic coordinate, charge and isotop information |
+--------------------------------------------------+
atomic coordinates atom shells charge pseudo isotop
1.02698794 2.89019118 0.00000000 h 6 1.000 0 0
0.65161882 -3.82657134 0.00000000 f 11 9.000 0 0
-2.33022558 -5.23852119 0.00000000 h 6 1.000 0 0
0.65161882 6.17490135 0.00000000 f 11 9.000 0 0
center of nuclear mass : 0.58595851 1.05585038 0.00000000
center of nuclear charge: 0.52129505 0.93933200 0.00000000
+--------------------------------------------------+
| basis set information |
+--------------------------------------------------+
we will work with the 1s 3p 5d 7f 9g ... basis set
...i.e. with spherical basis functions...
type atoms prim cont basis
---------------------------------------------------------------------------
h 2 16 14 TZVPP [3s2p1d|5s2p1d]
f 2 46 31 TZVPP [5s3p2d1f|11s6p2d1f]
---------------------------------------------------------------------------
total: 4 124 90
---------------------------------------------------------------------------
total number of primitive shells : 28
total number of contracted shells : 34
total number of cartesian basis functions : 102
total number of SCF-basis functions : 90
symmetry group of the molecule : cs
the group has the following generators :
c1(z)
mirror plane sigma(xy)
2 symmetry operations found
there are 2 real representations : a' a"
maximum number of shells which are related by symmetry : 1
mo occupation :
irrep mo's occupied
a' 62 8
a" 28 2
number of basis functions : 90
number of occupied orbitals : 10
------------------------------------------------------
FREEZING OF ORBITALS
------------------------------------------------------
reading orbital data $scfmo from file mos .
orbital characterization : expanded
Orbitals with eigenvalues smaller than -3.000 will be
treated as inert with respect to electronic correlations,
that is, they constitute the frozen cores:
ORBITAL SYMMETRY ENERGY OCCUPATION STATUS
1 1a' -26.37740 2.000 frozen
2 2a' -26.37740 2.000 frozen
3 3a' -1.55952 2.000 active
4 4a' -1.55949 2.000 active
5 5a' -0.72658 2.000 active
present status of $freeze:
implicit core= 2 virt= 0
frozen core / frozen virtual assignment menu:
s <list> : list information about shells in <list>
p <list> : print mo coefficients of shells in <list>
f <list> : choose shells in <list> to become frozen shells
a <list> : choose shells in <list> to become active shells
fp <val> : set new freezing point for core orbitals to <val>
ver (off): switch verbose mode on (off)
exp (off): enforce explicit (old) format for $freeze
core <n> : set number of frozen core orbitals to <n>
* / end : write $freeze to file and leave the menu
& : go back - leaving $freeze unchanged...
<list> = list of mo-shell indices (like 1-5,7-8,11)
enter command
* Type * to accept the default core assignments.
freezing orbitals :
frozen occupied orbitals:
1 a' -26.377403 H
2 a' -26.377401 H
number of non-frozen orbitals : 88
number of non-frozen occupied orbitals : 8
------------------------------------------------------
SPECIFICATION OF AUXBASIS-SETS:
------------------------------------------------------
Hit <ENTER> to accept the the default auxiliary basis for each atom.
ENTER NAME OF AUXILIARY BASIS FOR h DEFAULT:
h TZVPP
(DO NOT FORGET ELEMENT SPECIFICATION)
ENTER NAME OF AUXILIARY BASIS FOR f DEFAULT:
f TZVPP
(DO NOT FORGET ELEMENT SPECIFICATION)
...trying to read auxbasis-sets just specified...
we will work with the 1s 3p 5d 7f 9g 11h 13i auxiliary basis set
...i.e. with spherical basis functions...
type atoms prim cont basis
---------------------------------------------------------------------------
h 2 30 30 TZVPP [4s3p2d1f|4s3p2d1f]
f 2 81 76 TZVPP [8s6p4d3f1g|8s6p5d3f1g]
---------------------------------------------------------------------------
total: 4 222 212
---------------------------------------------------------------------------
total number of primitive shells : 33
total number of contracted shells : 64
total number of cartesian basis functions : 260
total number of SCF-basis functions : 212
------------------------------------------------------
MEMORY REQUIREMENTS:
------------------------------------------------------
Memory for RIMP2 is currently set to: 200 MB
DO YOU WANT TO CHANGE MEMORY FOR RIMP2 ?
Just <ENTER>, q or '*' terminate this menu.
y Type y to change memory.
Please enter the amount of memory (in MB) which should be used by RIMP2.
1000 Type 1000 to change memory to 1Gb.
Memory for RIMP2 is currently set to: 1000 MB
DO YOU WANT TO CHANGE MEMORY FOR RIMP2 ?
Just <ENTER>, q or '*' terminate this menu.
Hit <ENTER> to terminate the menu.
------------------------------------------------------
DISC SPACE REQUIREMENTS:
------------------------------------------------------
TOTAL AMOUNT OF DISC SPACE (kB): 4101
IN DETAIL (kB):
auxbai : 1061
auxboi : 133
auxxiv : 1658
other files (size ~ n**2) : 1249
Warning is given if the original SCF calculation was not performed using $denconv,
| ||||||||||||||
Input | ||||||||||||||
The preparation of the input files is now complete. An auxbasis file is created to use the corresponding auxiliary basis for the RI-MP2 calculation. Note that it is recommended in the User Manual to use a converged SCF calculation with the one-electron density convergence threshold set to $denconv 1.d-7 or less for RI-MP2 calculations. The control file has been modified to set up the RI-MP2 calculation. Input files (gzipped) can be downloaded as follow: basis | control (modified by rimp2prep) | coord | mos | auxbasis | ||||||||||||||
Output | ||||||||||||||
Step 5: Before we can carry out our geometry optimisation, we need to run a dscf calculation again using: $CHEM/runturbo dscf This will produce a similar output file to the one shown in Example 1, but will set up the RI-MP2 calculation. Step 6: Now, we make use of the script jobex to run the geometry optimisation calculation. In this case, we use the following command: $CHEM/runturbo jobex -keep -ri -level mp2 -c 50 -keep tells the program to keep a file for each of the cycles. -ri -level mp2 tells the program to run the RI at MP2 level. -c 50 tells the program to change the maximum number of optimisation cycles from the default to 50 cycles. Each cycle of jobex will run a dscf calculation, followed by a rimp2 calculation and a relax calculation. The job then checks to see if the geometry has converged using test_relax. If the geometry has not converged, it will repeat the cycle until convergence is reached. When the geometry has converged, a file called converged will be produced. The starting and final geometries will be stored in job.1 and job.last, respectively. job.1 also contains the dscf output, rimp2 output and relax output for the initial cycle, and job.last the same information for the last step (but without the relax output as the geometry has converged). Information from each of the intermediate cycles is stored in files called job.2, job.3, etc. The energy will be given in the energy file. Selected final output files (gzipped) can be downloaded as follow: job.1 | job.last | energy | converged | statistics |