I am trying to create an xyz file with orca to open it in IboView. However, if I save it without changing the orca input, the xyz file is not created properly. What should I change ! Opt revPBE def2-TZVP to in order to create xyz normally with orca? And is there a place where these input commands are collected?
It’s Windows and the latest version.
I’m not quite sure what you’re trying to do, and what you mean by creating an XYZ file “with” ORCA?
Avogadro’s ORCA input generator puts the Cartesian coordinates in the input file itself within the geometry block. If you want to save your geometry from Avogadro to an XYZ file, you should use **Export Molecule…*, but that doesn’t involve ORCA at all.
If you look at this pdf p20-22, you can see that Avogadro created an Orca output file and created xyz with Orca. The Avogadro used there is an old version, so it doesn’t seem to be applicable now. I may have misunderstood the text.
An ORCA input file is just a text file, right? As are the output files and as are XYZ files. That means you can edit them in a normal text editor like Notepad – you don’t need to use Avogadro to create every input file, for example, it’s just that it can be really convenient for it to do it for you.
In general ORCA can be given an input geometry in two ways. The first is by putting it in the input file itself as part of the coordinates block, which comes at the end of the file and looks like:
...
* xyz -1 1
C 0.94700 0.48119 1.00837
C 2.28751 0.54183 0.66342
...
O 9.86811 4.71557 -0.46776
*
Alternatively you can just instruct ORCA to read a geometry from another file. For info on how exactly to do that see the excellent ORCA manual.
That page of the guide you posted is telling you to set up a transition state search with ORCA and to use the XYZ files of the optimized reactant and product geometries that ORCA generated at the end of the optimization runs that you should have already done. So Avogadro doesn’t need to create any XYZ files, you should use XYZ files that you already have.
That means writing an input file that tells ORCA where to find those XYZ files. The easiest way to do that is to create the input file in a text editor and to copy the example in your guide, with help from the manual.
You could use the input file generator in Avogadro but you would then need to manually make the changes in the text box at the bottom of the dialog and Avogadro isn’t really benefitting you much.
Avogadro was useful on e.g. page 10 because it
- Automatically adds the geometry that you have drawn into the file
- Writes all the keywords and stuff that you need into the file to do the kind of calculation you want to do without you having to look up the correct syntax/name/spelling for everything in the ORCA manual
For this later step you can’t really make use of those any more.
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There is an ORCA forum at https://orcaforum.kofo.mpg.de/index.php that might be better suited to your question.
“!Opt revPBE dev2-TZVP” refers to the instructions used to generate an optimized geometry in ORCA. The revPBE is the level of theory, in this case a density functional, and dev2-TZVP is the basis set. Just replace these with the level of theory and basis set that you want, consulting the ORCA manual for assistance if needed.
However, if the geometry need not be optimized (other than the force-field optimization available in Avogadro), it should be theoretically possible to make an xyz file given only the atomic coordinates. (This is assuming that IboView treats the 2nd line solely as a title and doesn’t try to parse the energy given in that line). You shouldn’t even need to run ORCA at all in this case. However, I don’t know if Avogadro can put the coordinates in the right format including the # of decimal places.
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Sorry The xyz file could be created with ‘Export Molecules’ without using Orca.
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