This post will tell you how to visualize the normal mode frequencies from ORCA calculations.
I used the standalone program orca_pltvib, to get the trajectory files for animations of different normal modes. Step by step procedure to get the above figure are given here
orca_pltvib filename.out all
Open the filename.out.v0026 file using Jmol
Open Jmol console
Start the animation by typing animation on or from gui
Type vector on
You will see the displacement vectors along with the molecule
Export figure as JPEG or POVRAY as you wish
You can also see the each step of optimization by opening filename.trj with JMol
If anyone wants to know how to start using JMol on Mac go to the below site to get basic information on using JMol
Obtain molden inputfile by using orca_2mkl by using this command ” orca_2mkl filename -molden”
Now convert the .molden file to AIM .wfn format using molden2aim conversion program which can be obtained from the below link http://people.smu.edu/wzou/program/
input file for NCI plot program should have .nci extension and it looks as follows
1 ! no of .wfn files
filename.wfn !file name
INTERMOLECULAR ! Keywords
Extract the nciplot using “tar -zxvf nciplot-3.0.tar.gz” command
Go to src file and “make” will generate nciplot executable
nciplot input.nci generates .cube files,.vmd files and .dat files
Plotting filename.dat files give you nice plot of reduced density vs density
Open .vmd files with VMD program suites to visualize the NCI and render the image files using snapshot tool. You will get some nice figures like the one given in this paper.
This worked for me, if you have any problems please let me know 🙂
Hi, In this post I will be giving an example of how to assign basis functions to an element in ORCA . MG3S basis set from Truhler’s group is not preset in the ORCA . To do benzene optimization calculation using MG3S basis set , the input file format is as follows
! RI-MP2 3-21G FROZENCORE SP PMODEL AUTOAUX RIJCOSX
!printbasis
%id "DIMER"
%basis</pre>
NewGTO C
S 6
1 4.563240000000E+03 1.966650000000E-03
2 6.820240000000E+02 1.523060000000E-02
3 1.549730000000E+02 7.612690000000E-02
4 4.445530000000E+01 2.608010000000E-01
5 1.302900000000E+01 6.164620000000E-01
6 1.827730000000E+00 2.210060000000E-01
S 3
1 2.096420000000E+01 1.146600000000E-01
2 4.803310000000E+00 9.199990000000E-01
3 1.459330000000E+00 -3.030680000000E-03
S 1
1 4.834560000000E-01 1.000000000000E+00
S 1
1 1.455850000000E-01 1.000000000000E+00
S 1
1 4.380000000000E-02 1.000000000000E+00
P 3
1 2.096420000000E+01 4.024870000000E-02
2 4.803310000000E+00 2.375940000000E-01
3 1.459330000000E+00 8.158540000000E-01
P 1
1 4.834560000000E-01 1.000000000000E+00
P 1
1 1.455850000000E-01 1.000000000000E+00
P 1
1 4.380000000000E-02 1.000000000000E+00
D 1
1 1.252000000000E+00 1.000000000000E+00
D 1
1 3.130000000000E-01 1.000000000000E+00
F 1
1 8.000000000000E-01 1.000000000000E+00
end;
NewGTO H
S 3
1 3.386500000000E+01 2.549380000000E-02
2 5.094790000000E+00 1.903730000000E-01
3 1.158790000000E+00 8.521610000000E-01
S 1
1 3.258400000000E-01 1.000000000000E+00
S 1
1 1.027410000000E-01 1.000000000000E+00
S 1
1 3.600000000000E-02 1.000000000000E+00
P 1
1 1.500000000000E+00 1.000000000000E+00
P 1
1 3.750000000000E-01 1.000000000000E+00
end;
NewGTO O
S 6
1 8.588500000000E+03 1.895150000000E-03
2 1.297230000000E+03 1.438590000000E-02
3 2.992960000000E+02 7.073200000000E-02
4 8.737710000000E+01 2.400010000000E-01
5 2.567890000000E+01 5.947970000000E-01
6 3.740040000000E+00 2.808020000000E-01
S 3
1 4.211750000000E+01 1.138890000000E-01
2 9.628370000000E+00 9.208110000000E-01
3 2.853320000000E+00 -3.274470000000E-03
S 1
1 9.056610000000E-01 1.000000000000E+00
S 1
1 2.556110000000E-01 1.000000000000E+00
S 1
1 8.450000000000E-02 1.000000000000E+00
P 3
1 4.211750000000E+01 3.651140000000E-02
2 9.628370000000E+00 2.371530000000E-01
3 2.853320000000E+00 8.197020000000E-01
P 1
1 9.056610000000E-01 1.000000000000E+00
P 1
1 2.556110000000E-01 1.000000000000E+00
P 1
1 8.450000000000E-02 1.000000000000E+00
D 1
1 2.584000000000E+00 1.000000000000E+00
D 1
1 6.460000000000E-01 1.000000000000E+00
F 1
1 1.400000000000E+00 1.000000000000E+00
end;
end
%method
gridx 3,3,3
intaccx 5,5,5
end
* xyz 0 1
C 0.001622 0.000000 0.003743
C 0.002422 -0.000000 1.425784
C 1.251527 0.000000 2.111650
C 2.470594 -0.000000 1.372516
C 2.440029 -0.000000 -0.052180
C 1.179512 -0.000000 -0.710431
C -1.197903 0.000000 2.188293
C -1.168352 0.000000 3.565465
C 0.063580 -0.000000 4.275789
C 1.282105 0.000000 3.536959
C 2.531749 -0.000000 4.223137
C 2.562314 -0.000000 5.647825
C 1.331200 -0.000000 6.359552
C 0.123752 0.000000 5.696552
C 3.750816 -0.000000 3.483999
C 3.720234 -0.000000 2.058686
C 4.938777 0.000000 1.319881
C 6.170701 0.000000 2.030210
C 6.200241 0.000000 3.407381
C 4.999905 -0.000000 4.169884
C 3.822822 -0.000000 6.306097
C 5.000724 -0.000000 5.591923
C 3.671152 -0.000000 -0.763889
C 4.878588 -0.000000 -0.100884
H -0.949762 0.000000 -0.515973
H 5.806804 -0.000000 -0.660929
H -2.147023 0.000000 1.664457
H 7.096482 0.000000 1.466150
H 1.158608 0.000000 -1.794311
H 3.645548 -0.000000 -1.847668
H 7.149372 0.000000 3.931203
H -2.094145 0.000000 4.129510
H 5.952095 -0.000000 6.111666
H -0.804451 0.000000 6.256622
H 3.843779 -0.000000 7.389981
H 1.356747 0.000000 7.443338
O 2.470565 2.000488 1.370963
C 2.470565 3.214390 1.370963
H 3.271322 3.793035 0.885453
H 1.669808 3.793035 1.856473
*
——————————————————————————————
Imp. Note: In the 3rd line of input file 3-21G is defined as basis function, but once ORCA reads the new basis assigned in the NewGto section it leaves out 3-21G and does the calculation with provided MG3S basis set. I have tested removing the 3-21G token without much success. If you have a better way of doing this please let me know.
Doing an optimization and frequency calculations in ORCA is very simple. In this post I will be discussing an example that is optmization and frequency calculation of 1,3-butadiene. The input file for this calculation is given below.
Key word RKS is for RHF calculation
TightSCF for very strict convergence criteria
Numfreq option is for vibrational analysis
6-31g* basis set is built using built in basis sets using basis module
! RKS TightSCF Opt NumFreq PModel
%basis
BASIS _6_31G
Pol _d
end
* xyz 0 1
C 0.634421 -0.368567 0.023632
C -0.634568 0.368787 0.022514
C 1.825862 0.205027 -0.004043
C -1.825740 -0.205205 -0.004482
H 2.731233 -0.374193 -0.007837
H 1.939130 1.275281 -0.024904
H 0.561937 -1.444085 0.041525
H -0.562125 1.444354 0.038156
H -2.731211 0.373804 -0.009896
H -1.938665 -1.275646 -0.022954
*
The calculation will be done in few minutes unless you start with a very bad guess. The output will show the hartree fock energy and frequencies
------------------------- --------------------
FINAL SINGLE POINT ENERGY -154.493204060410
------------------------- --------------------
*** OPTIMIZATION RUN DONE ***
List of frequencies along with Thermo chemical analysis is given in the end