|Posted on Wednesday, September 17, 2008 - 10:54 am: |
Is there a way for an administrator to make certain keywords for Gaussian default so that they are included in each job?
There appears to be a problem with WebMO sending the correct structure to Gaussian before Gaussian runs a calculation. If a build formaldehyde using the WebMO editor and then clean-up the geometry, Gaussian returns CS symmetry. If I just build formaldehyde and then add the hydrogens (without cleaning up the geometry), Gaussian returns C2V symmetry. It seems that adding the keywords symm=loose takes care of the problem.
Post Number: 49
|Posted on Wednesday, September 17, 2008 - 1:30 pm: |
To address the first issues: you can easily add keywords to Gaussian by default by modifying the default job template. Using WebMO 9, this can be done using the built-in Job Template editor. Using WebMO 8 and earlier this required editing the gaussian.tmpl job template file from the command line.
Second: I cannot reproduce the issue with formaldehyde and Gaussian. I always get C2V symmetry. Please send me a copy of the input file generated by WebMO in the problematic case, along with EXACTLY what sequence of events you are using to generate the geometry, and your WebMO version.
Post Number: 50
|Posted on Wednesday, September 17, 2008 - 3:27 pm: |
After investigation, WebMO is working correctly, as designed. Basically, when you cleanup "geometry" it is using the current hybridization of the carbon atom, which is sp3. To set this to the correct sp2, do a cleanup "hybridization" after adding hydrogens. You can easily add hydrogens, cleanup hybridization, and then cleanup the geometry using the "comprehensive" cleanup on either the menu or toolbar. Essentially, this I ALWAYS use the comprehensive cleanup.
While confusing, it is important to have access to each independent step for cases where WebMO "guess" the hybridization incorrectly. For example, inorganic or organometallic compounds. In this case, you can explicitly set the hybridization and let WebMO set the geometry accordingly, without having WebMO override your selection.
To summarize, unless you have a good reason, always use COMPREHENSIVE cleanup.