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11.03.2015
The Codes
Orca general purpose QC code
Free (download from http://cec.mpg.de/forum/)
Developed by F.Neese et al. in C++
Precompiled binaries (no sources)
Gabedit
Free (download from
https://sites.google.com/site/allouchear/Home/gabedit/download)
Developed by A.-R. Allouche
Sources and Binaries available
Both codes available for Mac, Linux & Windows
Good combination for research & teaching
Page 2
Learning Outcome
Page 3
Gabedit
Assuming you have the gabedit executable in your $PATH
Please open a terminal:
mkdir qc_lab
cd qc_lab
gabedit
Have a look around
Open the structure
editor
Page 4
Editing Structures
Press the pen tool to add atoms
Press the periodic-table button
to change the atom (C is standard)
Press the button below that to
toggle adding hydrogens
Pre-optimizing self-drawn structures
Important for speedup of real calculations
Avoid for transition metals, lanthanides & actinides
Two methods available: MM or semiempirical calculations
Press M button or right-click in drawing window
Choose Molecular Mechanics
Optimization
Page 5
Page 6
Drawing Formaldehyde
Please try to draw formaldehyde
Menu-Edit-Delete Molecule
Add Carbon
Choose Oxygen from periodic table
Replace one hydrogen
Click on the bond to make double bond
Pre optimize using MM
The result should look like this
Close the drawing window (Menu-Close)
(saving possible not necessary here)
Page 7
Press Ok
Page 9
Running Orca
Input files can be saved (File menu)
QC codes can be run by Gabedit
Set up run commands in
Settings-Preferences on the
Commands tab
Page 11
Interlude
Congratulations, you have hopefully just run your Orca calculation
A few considerations:
Gabedit is useful for drawing simple structures
many alternatives exist (have a look at Avogadro)
Good to remember basic input file structure
Excellent for visualizing results
The input file can be changed in gabedit
A simple text editor might be easier to use ...
We will visualize the results
Then an editor will be used to set up some more advanced calculations
Page 12
Looking at Results
During a run you can
Look at the output file
Update it
Look at geometry convergence
Visualize MO's & Densities
from the first step of the calculation
Get data from remote calculations
After the calculation has finished, press the
visualize button
Page 13
Visualizing Orbitals
In the visualization window
click M or right-click
Choose Orbitals
from the menu
Choose Orca output file
Read the NoName.out file
An MO selection should appear
Select an orbital
The right part shows its
participating AOs
Change cut-off value here
Click Ok
Page 14
Visualising Orbitals
Orbitals are calculated in a cube
Select position here
Select size here
Select quality here
Standard choices are ok
Press Ok
After the calculation is finished you can
Change the iso-value
0.1 should be a good choice
Get a proposition for a certain size
Press Ok
Page 15
Page 16
Page 17
Page 18
Orca List of
DFT functionals
Available functionals
Double hybrids are available
(MP2 calculation will be performed!)
DFT tries to use the RI approach
automatically (NORI to witch of)
Dispersion correction with
keywords vdw10 or vdw10bj
Page 19
Page 20
TZVPP
QZVPP
r(CO) =
r(CO) =
r(CO) =
t =
t =
t =
r(CO) =
r(CO) =
r(CO) =
t =
t =
t =
r(CO) =
r(CO) =
r(CO) =
t =
t =
t =
r(CO) =
r(CO) =
r(CO) =
t =
t =
t =
r(CO) =
r(CO) =
r(CO) =
t =
t =
t =
Exp
r(CO)
=
120.5
pm
Further Remarks
Page 23
Properties
Vibrational frequencies are available for HF, MP2, GGA and hybrid GGA
functionals through:
!Opt Freq
Speedup through much memory, give per core with the extra line:
%maxcore 1000
Page 24
Solvent Effects
Solvent effects on structures and frequencies through COSMO
Treatment differs for MP2 from Turbomole, different results possible
Two ways to specify,
in command line: ! COSMO(solvent)
As input block:
! COSMO
%cosmo
epsilon 78
end
Page 25
Relativity
Two ways to include scalar relativistic effects (no SO!):
For elements heavier than Kr one can include ECPs with:
!
BP
def2-SVP
def2-SVP/J
ECP{def2-SVP,def2-SVP/J}
printbasis
where printbasis prints the basis, in order to check that ECP and basis set fit
Manually define ECPs for certain elements:
!
ECP{TZVP=Hf-Hg}
!
ECP{TZVP=[Ag,Pt,Au]}
All electron ZORA or DKH2 calculations:
!
BP86
ZORA
def2-SVP
def2-SVP/J
TIGHTSCF
printbasis
!
BP86
DKH2
def2-SVP
def2-SVP/J
TIGHTSCF
printbasis
Very important: ZORA/DKH2 and basis set definitions have to be on the
same line!
Defining a special basis set requires:
U
0.0
0.0
1.0
newgto
"ZORA-def2-TZVP"
end
Page 26
Constraints
Useful for optimisations
Freeze parts of the molecule
during optimisation:
%geom
Constraints
{
B
0
1
1.25
C
}
{
A
2
0
3
120.0
C
}
end
end
Page 27
Hydrogen Optimisation
A simple example
One hydrogen is moved
Page 28
Constrained Scans
Scan energy along bond expansion, optimise all steps:
!
RKS
BP
SV(P)
TightSCF
Opt
%geom
Scan
B
0
1
=
1.35,
1.10,
12
#
scan
C-O
distance
end
end
*
int
0
1
C
0
0
0
0.0000
0.000
0.00
O
1
0
0
1.3500
0.000
0.00
H
1
2
0
1.1075
122.016
0.00
H
1
2
3
1.1075
122.016
180.00
*
Page 29
An Advanced Example
Reminder: static vs. dynamic correlation
For static correlation Orca offers CASSCF or MRCI calculations
Try this example, rotation of the double bond in ethylene:
! RHF SV(P) SV/C SmallPrint NoPop NoMOPrint
%casscf nel = 2
norb = 2
mult = 1,3
nroots = 2,1
TrafoStep RI
switchstep nr
end
%paras R= 1.3385
Alpha=0,180,37
end
* int 0 1
C 0 0 0 0 0 0
C 1 0 0 {R} 0 0
H 1 2 0 1.07 120 0
H 1 2 3 1.07 120 180
H 2 1 3 1.07 120 {Alpha}
H 2 1 3 1.07 120 {Alpha+180}
*
Page 30
An Advanced Example
With UHF the lowest singlet and triplet look like this:
Things to note around 0:
Singlet energy too high
Triplet energy too low
Around 90:
Singlet convergence issues
Orca reuses orbitals from
previous runs
Page 31
Energy extrapolation
We would like to know energies at the basis set limit
Computationally not feasible
Extrapolation procedures exist for e.g. Dunning's and ANO basis sets
Orca uses for HF:
Page 34
The End
Have fun with Orca
Thank you for your attention!
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