How to use Avogadro and ORCA for molecular orbital diagrams, spectroscopy and more!

[@flaym.]

Starting my master's research project in physical chem with no computational experience in a few days and this popped up in my recommended out of nowhere. Great intro for getting started :)

[@DrBenChem]

@@flaym. Thanks! Glad I'm reaching my target audience!

[@billymonday8388]

how is it going so far

[@flaym.]

@@billymonday8388 turns out the computational stuff isn't until later - I've been having fun shooting lasers at molecules in the meantime :)

[@billymonday8388]

@@flaym. im in a similar ship. good luck!

[@flaym.]

@@billymonday8388 you too!

[@rabiafarooq4815]

thanks for the lesson but i have some issues in avogadro like in mine it does not save file as xyz it just saves as .cml

[@DrBenChem]

@@rabiafarooq4815 hi! You need to "export" the structure and select .xyz as the file type - don't use the "save" option.

[@kendorazio2923]

Hi Dr. Ben, thank you your amazing videos. I particularly enjoyed the UV-vis tutorial. Unfortunately, I am struggling to visualize MOs in Avogadro and Jmol. Strangely, neither the .out or generated .cube files are working. The orbital side bar in Avogadro is empty. I have been looking around, but haven't found an explanation. Any pointers would be greatly appreciated. Thanks

[@DrBenChem]

@@kendorazio2923 Hi! Did you remember to use the !LARGEPRINT command? Without it, you can't easily visualise the .out file in Avogadro.

[@kendorazio2923]

@@DrBenChem Thank you! That worked.

[@shrikantyadav9142]

Can we calculate hyperpolarizability by using orca. if not suggest any free software. make a video for that.

[@shrikantyadav9142]

Avogadro software is not working properly to draw a molecule. sometimes it directly shut off.

[@jacktonsabayi8051]

Could you please help me on how to extract energies from gbw file so that I can use them to calculate density of states. Basically, I want to plot density of states vs energy (eV) but I don't know which file in the orca output is suitable. Also could you please tell me how to extract Dos and energy data. Thank you

[@DrBenChem]

@@jacktonsabayi8051 Hi! The "ORBITAL ENERGIES" section in the .out file has what you need, just make sure to use the final set (there are two in the output, one first guess and one optimised)

[@jacktonsabayi8051]

@DrBenChem Thank you for your prompt response. Could you please tell the format of the command line to extract the orbital energies from the (.out) file. I am also interested on how to get Dos from the energies. Can orca calculate Dos and output them?

[@DrBenChem]

@jacktonsabayi8051 unsure how to do this - I've always just extracted them the old fashioned way, the .out file a readable text file so I take it from there manually. You could ask the ORCA forum?

[@mehmetalivat]

Thank you for the lesson. There is something I'm curious about. Is there a way in Orca to include L.S (spin orbit calculations) for optimization energies in an iron-centered molecule? Can you help?

[@DrBenChem]

@@mehmetalivat Hi! The best way to go about that is to set off two calculations - one high spin, and one low spin. You can vary the overall spin of the system by changing the multiplicity in the .ino file, and compare the enthalpy of each result.

[@parker-c7w]

I have issues trying to load the .out file into both avogadro1.2 and avogadro2 , it says "Reading molecular file failed". Also, after performing geometry optimization for a molecule using "! B3LYP def2-SVP Opt" , where can i find the bond angles, or do I need to calculate it manually or specify it in the input. Can you help me?

[@DrBenChem]

@@parker-c7w Hi! For your first point - was LARGEPRINT included in your .inp file? If not, Avogadro won't be able to read your molecule file. If you want to measure bond angles (or lengths, or torsions) then import the molecule (either the .out or the .xyz) and use Avogadro's measure tool - I believe you just select three the three atoms and it should output the angle somewhere on screen. Let me know how it goes!

[@parker-c7w]

@@DrBenChem It turns out that when uploading my .out file, my file path contained a different language which caused the issue. And now I can upload the .out file to avogadro I can see the bond angle now. Thank you! However, do you know how to change the units, or be able to get more decimal places for the bond length and angle? I am writing a report and the more accurate the values the better. Thank you!!

[@DrBenChem]

@@parker-c7w Hi! Sadly, I'm not sure if there are any ways to do that - possibly somewhere lurking in a settings menu there's the option. Speaking as a structural scientist, though, I don't think you need that degree of precision - if the differences are that small, there's a good chance they're not significant anyway.