Non Covalent Interactions (NCI) Plots from ORCA output file

Step by step procedure

• Consider Benzene dimer system
• Do a MP2/cc-PVDZ energy calculation
• 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/
• If you dont have NCIplot program download it from Prof. Yang’s website “http://www.chem.duke.edu/~yang/Software/softwareNCI.html “
• 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

s(ρ) plot for the SCF 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 🙂

Assigning Basis Functions to an Element in ORCA

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.

Optimization and Vibrational Frequency calculations in ORCA

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.

Trans 1,3-Butadiene

• 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 

IR SPECTRUM

-----------

Mode freq (cm**-1) T**2
------------------------------
 6: 178.61 0.394977
 7: 278.14 2.099386
 8: 497.45 0.501350
 9: 518.83 8.127666
 10: 755.92 0.030467
 11: 863.54 85.705496
 12: 868.18 0.309096
 13: 894.30 0.003668
 14: 944.43 0.014689
 15: 954.13 4.179210
 16: 1009.77 28.746482
 17: 1204.76 0.001709
 18: 1252.71 3.383897
 19: 1265.99 0.002593
 20: 1360.38 12.277415
 21: 1417.21 0.004015
 22: 1644.95 13.275400
 23: 1703.41 0.008188
 24: 3063.54 0.014400
 25: 3070.96 23.532020
 26: 3077.98 0.715895
 27: 3080.23 0.000818
 28: 3173.59 16.220014
 29: 3174.09 0.023730

orca_mapspc filename.log ir –w50

p ‘otfreq.log.ir.dat’ u 1:($2*-1+1000) w l lw 2,’otfreq.log.ir.stk’ u 1:2 w impulses lw 2 lt 1 lc 3 (gnuplot command)

creates the data required to plot IR spectrum and plotting this in the gnuplot will give you nice plot like the one below

Infrared spectrum of Trans 1,3-Butadadiene molecule

to learn more about these calculations refer to ORCA manual