TURBOMOLE
Program Package for ab initio Electronic
Structure Calculations
Adem Tekin
Yrd. Doc. Dr.
15.06.2012 Istanbul
Attention!!
Input and lsf scripts can be downloaded from:
http://www.be.itu.edu.tr/~adem.tekin/turbomole/filelist.txt
http://www.be.itu.edu.tr/~adem.tekin/turbomole/water.xyz
http://www.be.itu.edu.tr/~adem.tekin/molpro/filelist.txt
http://www.be.itu.edu.tr/~adem.tekin/molpro/ex1.com
Turbomole
15.06.2012
Activate turbomole and molpro in your shell
— Go to your home directory
— Open your bash shell script: vi .bashrc
— Add the following lines for TURBOMOLE:
export TURBODIR=/RS/progs/TURBOMOLE
PATH=$PATH:$TURBODIR/scripts
PATH=$PATH:$TURBODIR/bin/`sysname`
export PARA_ARCH=MPI
— Add the following lines for MOLPRO:
export INTEL_LICENSE_FILE=/RS/progs/intel/licenses/RS/progs/intel/impi/3.1/bin64/mpivars.sh
export molprodir=/RS/progs/molpro/mpp/2009/1-20/x86_64
PATH=$PATH:$molprodir/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/RS/progs/molpro/mpp/2009/120/x86_64/lib
export PARA_ARCH=MPI
— Add the following lines for VESTA:
export PATH=$PATH:/RS/progs/VESTA-x86_64
Turbomole
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— Log
out and log in again then check: export
$TURBODIR
export $molprodir
Outline
— Introduction
— How to create input (define tool)
— Single point calculations at the Hartree-Fock, DFT and RIDFT levels
— Geometry optimization of water dimer at the RIMP2 level
— Geometry optimization of water dimer at the SCS-MP2 level
— Geometry optimization of water dimer at the CP-SCS-MP2 level
Turbomole
15.06.2012
Turbomole
— Developed by Reinhart Ahlrichs (University of Karlsruhe) 1989-2007
— Since 2007 TURBOMOLE GmbH founded by Ahlrichs is responsible
— for more information please visit to:
— http://www.turbomole.com/
— http://www.cosmologic.de
— A forum site is available under http://www.turbo-forum.com
Turbomole
15.06.2012
Turbomole usage philosophy
The usage of TURBOMOLE has been adapted to the way a UNIX user is working:
— Command line driven
— Many different programs, each one specialized for methods and/or properties
— Scripts are used to combine the functionalities and manage workflows
— Input can be changed by text editors
— Output processed by standard UNIX tools (editors, grep, awk, ...)
Turbomole
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Turbomole usage philosophy
Turbomole
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Turbomole modules
Turbomole
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Turbomole modules
DEFINE
interactive input generator which creates the input file control.
UFF
performs a geometry optimization at a force field level.
DSCF
for semi-direct SCF (self-consistent field) and DFT calculations.
GRAD
require a successful DSCF run and calculates the gradient of the energy with respect
to nuclear coordinates.
RIDFT and
RDGRAD
perform DFT calculations – as DSCF and DGRAD – within the RI-J approximation.
MPGRAD
requires a well converged SCF run and performs closed-shell RHF or UHF calculations
yielding single point MP2 energies and, if desired, the corresponding gradient.
RIMP2
calculates MP2 energies and gradients for RHF and UHF wavefunctions significantly
more efficient then MPGRAD.
RICC2
calculates electronic excitation energies, transition moments and properties of excited
states at the CIS, CIS(D), ADC(2) and CC2 level using a closed shell RHF or a UHF
SCF reference function. 15.06.2012
Turbomole
Turbomole modules
RELAX
requires a gradient run – by GRAD, RDGRAD, RIMP2 or MPGRAD and proposes a
new structure based on the gradient and the approximated force constants.
STATPT
performs a structure optimization using the “Trust Radius Image Minimization”
algorithm. It can be used to find minima or transition structure.
FROG
executes one molecular dynamics step.
AOFORCE
require a well converged SCF or DFT run and performs an analytic calculation
of force constants, vibrational frequencies and IR intensities.
ESCF
requires a well converged SCF or DFT run and calculates time dependent and dielectric
properties.
EGRAD
computes gradients and first-order properties of excited states.
MPSHIFT
computes NMR chemical shieldingns for all atoms of the molecules at the SCF, DFT
or MP2 level.
FREEH
calculates thermodynamic functions from molecular data in a control file: an
AOFORCE or a NUMFORCE run is a necessary prerequisite.
Turbomole
15.06.2012
How to create the input
— Build
define has some limited features to build a structure from scratch, but that
is neither convenient nor intuitive, except for some small cases.
→ Use an external builder (molden, ECCE, Hyperchem, Insight, Arguslab,
MAPS, Accelrys DS Visualizer, ...there are many!) and convert the structure
to xyz format.
— Convert
Use the TURBOMOLE script x2t to convert xyz files to TURBOMOLE
coordinates:
x2t struct.xyz > coord
Turbomole
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Define
define is an interactive input generator which creates the input file control:
—
Supports most basis sets in use, especially the only fully atom optimized consistent basis sets of
SVP, TZV, and QZV quality available for the atoms H–Rn (including lanthanides and actinides
up to Lawrencium for SVP and TZV)
— Determines the molecular symmetry
—
Determines the internal coordinates, allowing efficient geometry optimization
— Allows to perform a geometry optimization at a force field level to pre-optimize the geometry
and to calculate a Cartesian Hessian matrix
—
Sets the keywords necessary for single point calculations and geometry optimizations for a variety
of methods
—
Manipulate geometries of molecules
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Define
There are four major menus in define:
•Molecular Geometry Menu
•Atomic Attribute Definition Menu
•Occupation number & Molecular Orbital Definition Menu
•General Menu
Navigation within define:
1.
To finish the menu and proceed to the next one, enter:
*
2.
To go back to the previous menu, enter:
&
3.
If you are in one of the four main menus, hitting <Enter> will just print out the menu
you are in
4.
To quit define immediately (and prematurely), enter:
Turbomole
qq
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Define
To call define just type define in the shell : $define
— First you will be asked whether you want to define a new system or not
— If not press the ENTER button
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Define
Then you will be asked for a n input title:
— either give a name
— or press the ENTER button to proceed
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Define – molecular geometry menu
Turbomole
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Define – atomic attribute definition menu
Suppose we created the coord file via: x2t struct.xyz > coord
Select only these for
a geometry
optimization based
on cartesian coordinates
a coord
desy
ired
to load the geometry
to detect the symmetry, if you expect a higher symmetry, repeat
with increased tolerance desy 0.1
to use internal redundant coordinates
Then pressing * will lead us to the Atomic Attribute Definition Menu
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Define – atomic attribute definition menu
The default basis set is def-SV(P)
You can assign the same basis set for all atoms in the system by:
b all aug-cc-pVTZ
(Dunning’s basis set)
If you want to use a different basis set for any atomic species (let’s say for hydrogen):
b “h” aug-cc-pVDZ
bl
use to see the current basis set assignments
TURBOMOLE has a new set of basis sets abbreviated by def2:
def2-SV(P), def2-SVP, def2-TZVP, def2-TZVPP, def2-QZVP, def2-QZVPP
bi
(At least
Turbomole
information about improved TURBOMOLE basis sets
you must use def2-TZVP for 15.06.2012
a quantative analysis)
Define – atomic attribute definition menu
SV(P) or def-SV(P)
for routine SCF or DFT. Quality is about 6-31G*.
TZVP or def-TZVP
for accurate SCF or DFT. Quality is slightly better than 6-311G**.
TZVPP or def-TZVPP for MP2 or close to basis set limit SCF or DFT. Comparable
to 6-311G(2df).
QZVP and QZVPP for highly correlated treatments; quadruple zeta + 3d2f1g
or 4d2f1g (beyond Ne), 3p2d1f for H.
Turbomole
15.06.2012
Define – occupation number & orbital
definition menu
This menu serves for the definition of occupation numbers (and thereby the charge of the
molecule) and the start orbitals for the SCF calculations. For well-behaved molecules,
The procedure is very easy. Just choose the option:
eht
to perform an extended Huckel calculation.
Turbomole
15.06.2012
Define – occupation number & orbital
definition menu
— If you do not want them type n
— You can accept the default parameters by typing y, then you will be
asked for the charge of the system (default is 0)
Turbomole
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Define – occupation number & orbital
definition menu
— to accept the current occupation type y, then you will enter to the GENERAL MENU
Turbomole
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Define – general menu
Here, you can choose additional parameters for your calculation.
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Define – general menu - scf
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Define – general menu – mp2
— Do not forget to freeze (frozen core approximation)
— Do not forget to add cbas basis: the basis set selected in atomic attribute definition menu
— You can change memory (default is 60 MB)
— You can change convergence, use 0.1E-07
Turbomole
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Define – general menu – cc2
— CC2 is an approximated coupled cluster singles and doubles (CCSD) model
— The CC2 total energy is of second-order Moller-Plesset perturbation theory (MP2) quality
— The scaling of CC2 is N5 whereas the scaling of CCSD is N6, where N is the number of orbitals
— Similar to MP2 submenu
Turbomole
— Use always ri option
— Spin component scaled (SCS) MP2 is hidden in the ricc2 submenu
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For more info about CC2 check Chem. Phys. Lett. 243 409 (1995)
Define – general menu – cc2 – ricc2
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Define – general menu – dft
— switch on DFT
— select functional
— select gridsize
Type on to switch on DFT
(default functional is b-p)
(default gridsize is m3)
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Define – general menu – dft
Turbomole
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S22 test of interaction energies [JCP 132
(2010) 144104]
Mean Absolute Deviation
Turbomole
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Empirical Dispersion Correction for DFT
Calculations
— DFT functionals fails for intermolecular interaction energy calculations
(They do not result any binding between two monomers)
— This is due to insufficient treatment of electron correlation
(which is so important to describe dispersion forces)
— Stefan Grimme suggested dispersion correction to ordinary DFT energies
— When using the dispersion correction, the total energy is given by
— Edisp is an empirical dispersion correction given by
Turbomole
Nat is the number of atoms
C6ij denotes the dispersion coefficient for atom pair ij
15.06.2012on the selected DF
s6 global scaling factor depends
R is the interatomic distance between i and j
Define – general menu – dft
Turbomole offers grids 1 (coarse) to 7 (nest), and the multiple
grids m3 to m5. The latter employ a coarser grid during SCF
iterations, and grid 3 to grid 5 in the final SCF iteration and the
gradient evaluation. Default is grid m3, for clusters with more
than 50 atoms use m4.
Turbomole
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Define – general menu – RI-J (resolution
of identity)
— In the RI approximation two-electron integrals are approximated by three-center expansions
— RI procedure is recommended for non-hybrid functionals (which speeds up calculations
by a factor of 10 at least)
Turbomole
— activate ri with on
— assign jbas
15.06.2012
— then call jobex script with –ri option (jobex -ri)
Define – general menu – MARI-J
— RI-J calculations can be done even more effciently with the Multipole Accelerated
RI-J (MARI-J ) option, especially for larger molecules.
— Just rely on the defaults.
Turbomole
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Define – general menu – stp – transition
state search
— Stationary points are places on the potential energy surface (PES) with a zero gradient.
— Two types of stationary points are of special importance to chemists. These are minima
(reactants, products, intermediates) and first-order saddle points (transition states)
— The type of stationary point optimization depends on the value of irtvec. By default
irtvec is set to 0, which implies a structure minimization. A value irtvec > 0 implies a
transition state optimization using the eigenvalue-following TRIM (Trust Radius Image
Minimization) algorithm .
— Transition state search is invoked by
jobex –trans
Turbomole
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Vibrational normal modes
— After having performed a single point energy calculation or a geometry optimization,
just start the program aoforce (analytic force constant calculation):
aoforce > force.out
— All details will be written to force.out
— The keyword $vibrational spectrum in the control file contains a list of the modes:
— NumForce enables numerical force constant calculations for all levels of theory with a
gradient implemented. To run NumForce just issue the command
NumForce –ri –level mp2 -central
Turbomole
15.06.2012
Structure optimizations using the jobex script
— The shell script Jobex controls and executes automatic optimizations of molecular
geometry parameters.
— It will cycle through the direct SCF, gradient and force relaxation programs and stop if
either the maximum number of cycles is reached or the convergence criteria are fulfilled.
— Jobex has many options:
-energy integer
-gcart integer
-c integer
-dscf
-grad
-statpt
-relax
-trans
-level level
-ri
-ex
-md
Turbomole
converge total energy up to 10-integer Hartree (default:6)
converge maximum norm of cartesian gradient up to 10-integer a.u. (def:3)
perform up to integer cycles (default:20)
begin with a direct SCF step
begin with a gradient step
begin with a force relaxation step
use the RELAX program for force relaxation
perform transition state search
define the optimization level, level=scf, mp2, cc2 or uff
use RI modules
perform excited state geometry optimization using EGRAD
a molecular dynmaics run
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Turbomole output
— There will be an output written to file job.start.
— The convergence is signalled by the file converged; otherwise, you should find the file
not.converged within your working directory.
— If Jobex finds a file named stop or STOP in the working directory, Jobex will stop after the
present step has terminated. You can create stop by the command touch stop.
— The output of the last complete cycle is written to file job.last, while the output of the
running cycle is collected within the file job.<cycle>, where <cycle> is the index of the
cycle.
— Look at the file gradient: it contains all geometries and gradients at each step of
optimization:
grep cycle gradient
— To see the final geometry call
t2x –c > final.xyz
t2x > final_all.xyz (to see all trajectory)
— At the command line, use dist, bend or tors to get bond lengths, angles, dihedral angles
Turbomole
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Keywords in the control file
— The file control is the input file for TURBOMOLE.
— Keywords start with a ‘$’, e.g. $title.
Turbomole
$title
NO2 c2v UKS SVP
$operating system unix
$symmetry c2v
$coord file=coord
$intdef file=coord
$atoms
n 1 \
basis =n def-SVP
o 2-3 \
basis =o def-SVP
…
$energy file=energy
$grad file=grad
$forceapprox file=force
$lock off
$dft
functional b-p
gridsize m3
$last step define 15.06.2012
$end
Submitting Turbomole jobs on UHEM
— single job submission
#!/bin/bash
#BSUB -m karadeniz_temp1
#BSUB -a intelmpi
#BSUB -J triazine
#BSUB -o triazine.out
#BSUB -e triazine.err
#BSUB -q workshop
#BSUB -P workshop
#BSUB -R "span[ptile=1]"
#BSUB -n 1
# ege or anadolu
# bu kismi degistirmeyin !!!
# isinizi tanimlayacak bir isim
# bu kismi degistirmeyin !!!
# bu kismi degistirmeyin !!!
# kuyruk ismi
# proje ismi
# bu kismi degistirmeyin !!!
# kullanilacak olan islemci sayisi
echo 'Starting time:'
date
jobex -ri -level cc2 -energy 7 -gcart 4 -c 1000
echo 'Ending time:'
date
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Submitting Turbomole jobs on UHEM
— parallel job submission
#!/bin/bash
#BSUB -m karadeniz_temp1
#BSUB -m "b074 b075"
#BSUB -a intelmpi
#BSUB -J triazine
#BSUB -o triazine.out
#BSUB -e triazine.err
#BSUB -q workshop
#BSUB -P workshop
#BSUB -R "span[ptile=8]"
#BSUB -n 16
# submit the job to the b074 and b075 nodes
# bu kismi degistirmeyin !!!
# isinizi tanimlayacak bir isim
# bu kismi degistirmeyin !!!
# bu kismi degistirmeyin !!!
# kuyruk ismi
# proje ismi
# bu kismi degistirmeyin !!!
# kullanilacak olan islemci sayisi
export HOSTS_FILE=/AKDENIZ/HOME005/users/tekin/hostsfile
export PARNODES=16
echo 'Starting time:'
date
jobex -ri -level cc2 -energy 7 -gcart 4 -c 1000
echo 'Ending time:'
date
Turbomole
15.06.2012
check availability of nodes with bhosts command
b074
b074
b074
b074
b074
b074
b074
b074
b075
b075
b075
b075
b075
b075
b075
b075
Turbomole examples
— Single point calculations at the Hartree-Fock, DFT and RIDFT
levels
— Geometry optimization at the RIMP2 level
— Geometry optimization at the SCS-MP2 level
— Geometry optimization at the CP-SCS-MP2 level
Turbomole
15.06.2012
Single point calculations – Hartree Fock, DFT
and RIDFT energy calculation of benzene
1.
2.
3.
4.
Create an empty directory, e.g., hf_def2_tzvp_benzene
Call define
Hit <enter>
Give a title:
benzene, HF calculation
5. Load benzene from the structure library ($TURBODIR/structures)
a !benzene
6. define will scan through the structure library and ask you if you want to take the proposed
molecule
Turbomole
15.06.2012
Single point calculations – Hartree Fock, DFT
and RIDFT energy calculation of benzene
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
Just say y to accept the structure
Switch on the symmetry detection be entering:
desy
Next step is to provide internal coordinates. (That is not needed for single point calculations.)
ired
Now we are done with this menu and proceed to the next one by entering
*
This is the atomic attributes menu. Choose your basis set:
b all def2-TZVP
Now we are done with this menu and proceed to the next one by entering
*
Determine the starting molecular orbitals with an extended Huckel guess:
eht
Then you will be asked a lot of questions. Just accept the defaults.
Now you are in general menu.
The default method is Hartree-Fock (HF) calculation, and therefore we do not have to
change anything here. Simply enter:
*
To run a HF single point energy calculation,
call
Turbomole
15.06.2012
dscf > dscf.out
Single point calculations – Hartree Fock, DFT
and
RIDFT
energy
calculation
of
benzene
18. After the run, look in the output (dscf.out) and/or the energy file. The energy file should give:
$energy
SCF
1 -230.7848712224
$end
SCFKIN
230.6217054044
SCFPOT
-461.4065766268
19. Look in the output (dscf.out) for the dipole and quadrupole moments and whatever you like
to know.
20. Get more details about the orbitals, the HOMO-LUMO gap and occupation:
eiger
21. Let’s run a DFT calculation just after the HF calculation .
22. Call define and just accept all the defaults, then you will be in general menu.
23. Choose dft
24. Choose on to switch on DFT (Now you have chosen the default functional (b-p) and
gridsize m3)
25. Quit from define with *
26. Run dscf again.
27. Look again to the energy file:
$energy
SCF
1 -230.7848712224
Turbomole
2 -232.3365711535
$end
SCFKIN
230.6217054044
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231.4048783475
SCFPOT
-461.4065766268
-463.7414495010
Single point calculations – Hartree Fock,
DFT and RIDFT energy calculation of
benzene
28. Now, let’s switch on RI approximation following previous steps enter to the general menu
29. enter ri and then on.
30. Run ridft program:
ridft > ridft.out
$energy
SCF
1 -230.7848712224
2 -232.3365711535
3 -232.3368258829
$end
Turbomole
SCFKIN
230.6217054044
231.4048783475
231.4106397547
15.06.2012
SCFPOT
-461.4065766268
-463.7414495010
-463.7474656376
Do not be confused with auxiliary basis
1. Coulomb-Fitting ($jbas). Basis sets declared in this data-group are needed for RI-DFT
calculations, where only the Coulomb part of the Fock operator is approximated. They can
be kept rather small.
2. Coulomb- and Exchange-Fitting ($jkbas). If additionally the exchange part of the Fock
operator needs to be approximated (RI-SCF calculations), a larger fitting basis is needed.
It also can be used for RI-DFT runs (if the accuracy of the $jbas auxiliary basis is not
satisfactory for you).
3. Correlation-Fitting ($cbas). These basis sets are needed for RI-MP2 and RI-CC2
calculations. They contain basis functions with high angular momentum.
Turbomole
15.06.2012
Geometry optimizations – RIMP2, SCS-MP2 and CPSCS-MP2 calculations of water dimer
1. Open a new directory, e.g., rimp2_avdz_water
2. Create water.xyz file. Here are the coordinates:
6
O
H
H
O
H
H
Turbomole
0.0640488861
-0.0275603110
-0.8291328873
-0.0539423286
0.3402097464
0.3402097464
-1.5542001572
-0.6109761929
-1.8994223998
1.4751039841
1.8881478835
1.8881478835
3. Convert xyz file to turbomole coord file:
x2t water.xyz > coord
4. Call define
5. Hit <Enter>
6. Give a title
7. Read the coordinates:
a coord
15.06.2012
8. desy
9. ired
0.0000000000
0.0000000000
0.0000000000
0.0000000000
0.7547208224
-0.7547208224
Geometry optimizations – RIMP2, SCS-MP2 and
CP-SCS-MP2 calculations of water dimer
10. Type * to go to the next menu
11. Choose basis set:
b all aug-cc-pVDZ
12. Type * to go to the next menu
13. Activate eht and accept the defaults
14. Now you are in the general menu
15. First select scf
16. Change scf option conv and then type 8 and go back to the general menu by pressing to ENTE
17. Now, select mp2
18. Activate freeze and go back to the mp2 submenu by pressing to *
19. Activate cbas: Automatically the auxiliary basis set will be loaded.
20. Press * to go back to the mp2 submenu.
21. Select the denconv and enter 0.1E-07.
22. Press * to go back to the mp2 submenu.
23. Press * to quit define.
24. Run the jobex script with the following parameters:
jobex -ri -level mp2 -energy 7 -gcart 4 -c 1000
25. Check the convergence by grep cycle gradient
26. After the convergence convert the turbomole geometry to xyz:
t2x –c > rimp2_opt.xyz or t2x > final_all_trajectory.xyz
Geometry optimizations – RIMP2, SCS-MP2 and
CP-SCS-MP2 calculations of water dimer
1. Open a new folder, e.g., scsmp2_avdz_water
2. Copy the rimp2 xyz output here:
cp ../rimp2_avdz_water/rimp2_opt.xyz .
3. Convert the xyz file to turbomole file:
x2t rimp2_opt.xyz > coord
4. Call define
5. a coord
6. desy
7. ired
8. *
9. b all aug-cc-pVDZ
10. *
11. Activate eht and accept the defaults
12. Now you are in the general menu
13. First select scf
14. Change scf option conv and then type 8 and go back to the general menu by pressing to ENTE
15. Now, select cc2
16. Activate freeze and go back to the cc2 submenu by pressing to *
17. Activate cbas: Automatically the auxiliary basis set will be loaded.
18. Press * to go back to the cc2 submenu.
19. Select the denconv and enter 0.1E-07.
Geometry optimizations – RIMP2, SCS-MP2 and
CP-SCS-MP2 calculations of water dimer
20. Press * to go back to the cc2 submenu.
21. Activate ricc2
22. Switch on scs correction by typing scs
23. Choose geoopt model:
geoopt mp2
24. *
25. *
26. *
27. vi control to check the ricc2 entries:
$ricc2
mp2 energy only
geoopt model=mp2
scs
cos= 1.20000
state=(x)
css= 0.33333
28. If there is nothing after mp2, enter “energy only” by hand
29. Run the jobex script with the following parameters:
jobex -ri -level cc2 -energy 7 -gcart 4 -c 1000
30. Check the convergence by grep cycle gradient
31. After the convergence convert the turbomole geometry to xyz:
t2x –c > scsmp2_opt.xyz or t2x > final_all_trajectory.xyz
Geometry optimizations – RIMP2, SCS-MP2 and
CP-SCS-MP2 calculations of water dimer
1. Open a new folder, e.g., cp_scsmp2_avdz_water
2. Copy the scsmp2 xyz output here:
cp ../scsmp2_avdz_water/scsmp2_opt.xyz .
3. Convert the xyz file to turbomole file:
x2t scsmp2_opt.xyz > coord
4. Call define
5. a coord
6. desy
7. ired
8. frag
Turbomole
9. Switch frag on by typing on
15.06.2012
Geometry optimizations – RIMP2, SCS-MP2 and
CP-SCS-MP2 calculations of water dimer
Turbomole
15.06.2012
Two times press <ENTER> button to see the fragment numbers. At most you can define
three fragments.
Geometry optimizations – RIMP2, SCS-MP2 and
CP-SCS-MP2 calculations of water dimer
—First three atoms belong to the first water molecule and the last three atoms belong to the
Second water molecule. You can assign them like below:
Turbomole
15.06.2012
Geometry optimizations – RIMP2, SCS-MP2 and
CP-SCS-MP2 calculations of water dimer
10. Enter to leave the frag menu
11. *
12. b all aug-cc-pVDZ
13. *
14. Activate eht and accept the defaults
15. Now you are in the general menu
16. First select scf
17. Change scf option conv and then type 8 and go back to the general menu by pressing to ENTE
18. Now, select cc2
19. Activate freeze and go back to the cc2 submenu by pressing to *
20. Activate cbas: Automatically the auxiliary basis set will be loaded.
21. Press * to go back to the cc2 submenu.
22. Select the denconv and enter 0.1E-07.
20. Press * to go back to the cc2 submenu.
21. Activate ricc2
22. Switch on scs correction by typing scs
23. Choose geoopt model:
geoopt mp2
24. *
Turbomole
15.06.2012
25. *
26. *
Geometry optimizations – RIMP2, SCS-MP2
and CP-SCS-MP2 calculations of water
dimer
27. vi control to check the ricc2 entries:
$ricc2
mp2 energy only
geoopt model=mp2
scs
cos= 1.20000
state=(x)
css= 0.33333
28. If there is nothing after mp2, enter “energy only” by hand
29. Run the jobex script with the following parameters:
jobbsse -ri -level mp2 –opt
30. Check the convergence by grep cycle gradient
31. After the convergence convert the turbomole geometry to xyz:
t2x –c > cp_scsmp2_opt.xyz or t2x > final_all_trajectory.xyz
Turbomole
15.06.2012
Geometry optimizations – Comparison of RIMP2, SCS-MP2
and CP-SCS-MP2 water dimer geometries
RIMP2
Turbomole
SCS-MP2
15.06.2012
CP-SCS-MP2
COSMO – Dealing with solvation effects
1. Open a new folder, e.g., cosmo_benzene
2. Load benzene from the structure library with
a !benzene
3. desy
4. ired
5. *
6. b all def-TZVP
7. *
8. eht and many times <Enter>
9. Switch on dft and ri
10. Exit from define with *
11. cosmoprep
Turbomole
15.06.2012
http://www.gaussian.com/
g_tech/g_ur/k_scrf.htm
Water: ε=78.3553
Acetonitrile: ε=35.688
Methanol: ε=32.613
Ethanol: ε=24.852
IsoQuinoline: ε=11.00
Quinoline: ε=9.16
Chloroform: ε=4.7113
DiethylEther: ε=4.2400
Dichloromethane: ε=8.93
DiChloroEthane: ε=10.125
CarbonTetraChloride: ε=2.2280
Benzene: ε=2.2706
Toluene: ε=2.3741
COSMO – Dealing with solvation effects
Turbomole
15.06.2012
COSMO – Dealing with solvation effects
12. r all o
if you have atoms
like “mg”
r “mg” b
13. *
14. <Enter>
15. jobex –ri > jobex.out
Turbomole
15.06.2012