Append file(s) to job upon submission

[mjuhasz]

Hello,

Is there a way to append a file to a job at submission time, for example to perform calculations that refer to files that are separate from the job input file? The example I have encountered is NEB transition state calculations in ORCA, which require one of the two required molecule geometries be provided in a separate .xyx file [e.g. "product.xyz in the example below]. It seems that the separate file is unavoidable, i.e. there does not appear to be a way to enter the geometry within the input file itself.

Note: An xyz file from a previous job can be accessed using its absolute path, (e.g. "/home/webmo/webmo/USER/JOB#/output.xyz". However, in this case, ORCA expects different formatting (two additional lines at the start of the xyz file) than what is generated by WebMO, so this does not solve the issue completely.

Code: Select all

! B3LYP 6-31G(d) 
! NEB-TS
! FREQ

%neb 
  neb_end_xyzfile "product.xyz"
end
* xyz 0 1
...input geometry goes here
*

[mjuhasz]

Upon looking further at this, I noticed that the format for the xyz file generated by WebMO from the Build Molecule interface (i.e. File>Export Molecule... and the selecting XYZ format) differs from format of the input.xyz and output.xyz files that appear in the directory for a completed job. The xyz file exported from the Build Molecule interface does match the format expected by ORCA.

[schmidt]

WebMO does support such jobs using previous geometries, including NEB-like jobs.

However, this is not (yet) supported for Orca. In other cases, you simply reference the job via the job number, and WebMO fetches / formats the geometry appropriate. It would be straightforward to to this for the case you note, as well, in a future update.