GAMESS input

[k95g]

Hello,
I'm working on generating a GAMESS output file using the Avogadro input generator. I am looking to find area, charge, and charge density (similar to that found here https://github.com/usnistgov/COSMOSAC/blob/master/profiles/GAMESS_TEST/ETHANOL.gout), but after running GAMESS using those input cards I get the .log file attached here. I've also included the "basic setup" used in Avogadro.

ethanol.log

[ianhbell]

@y-kusaka any idea?

[kwoo]

Hi Have you include the COSMO routine when compiling GAMESS? .cosmo files will not be generated without this. http://211.81.50.59/gamess/gamess_website/COSMO-RS.html

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2022/07/29 6:35、Ian Bell ***@***.***>のメール:  @y-kusaka any idea? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

[k95g]

I did not include it. I put in a request for access to the source file and will update if I experience any issues. Thanks for the help!

[k95g]

Hello,
After submitting a request for the GAMESS source files, I was informed that the connection to COSPRT in GAMESS is broken. Do you know of any other way to generate .cosmo files without the COSMO routine using GAMESS?

[k95g]

Hi @ianhbell @kwoo,
I managed to get area, charge, and charge density out of GAMESS, but I am not getting a .sigma file after running output through to_sigma.py. I saw that this file was recently updated so I thought I would check with you
ethanol.log

.

[ianhbell]

Not sure, I don't use GAMESS. @y-kusaka ?

[y-kusaka]

I think ethanol.log contains COSab data correctly. The regex matching of r"EQUILIBRIUM GEOMETRY[\sa-zA-Z0-9\(\)\./\*\n]+\-+\n(\s[\s\S]+)\n\n\n in the to_sigma.py should extract the coordinates of the atoms (lines 4152-5160 of ethanol.log) as group(1) but something wrong is happening here. Need to figure out a correct regex expression working also for your log file.

[k95g]

@y-kusaka so I suspect there is something in the ethanol.log file that is the source of the issue. After simply copying all the same info (equilibrium geometry, internal coordinates, etc) from the ETHANOL.gout file found here COSMOSAC/profiles/GAMESS_TEST/ETHANOL.gout I was able to get the .sigma file. Any idea how to get a .log file that excludes all of the excess data/info?

[k95g]

Hi @ianhbell,
I've been trying to work through the plot_profiles.py script, but cant seem to figure out where to add the path to my .sigma file. I've been looking through some tutorials on matplotlib, but still run into issues working through the code correctly (iterate over the databases, iterate over the names, etc). Any help would be appreciated.

[ianhbell]

Did you succeed at generating the sigma profile?

[k95g]

If you're referring to generating a methanol/ethanol profile then yes. I'm still trying to figure out how to integrate my .sigma file into the code. I'm sure its straightforward, but my experience with coding/python is limited.

[ianhbell]

@y-kusaka Can you assist?

[k95g]

@y-kusaka @ianhbell I've continued my attempts at generating a sigma profile plot using plot_profiles.py, but am still unsuccessful. I have generated my own "database" and tried iterating over the information in the file, but I cant pass line 38 due to errors like "'str' object has no attribute 'get_profile'" or "'tuple' object has no attribute 'get_profile'". The attached files show where I've made the edits and the .sigma file I am trying to use. If I am going about this completely wrong please let me know.
plot_profiles_edited.txt
ACETIC_ACID.txt

[ianhbell]

You need to create an empty UD-format database (mirror the structure of the existing one), pass that path to cCOSMO.DelawareProfileDatabase, and update the metadata file in complist.txt within the db.

You could drop your file in the UD database folder and update the compslist.txt file, but I would recommend instead to not touch that and instead add your changes to your own db. What are you going to mix acetic acid with?

You are very close!

[k95g]

@ianhbell Thank you very much for your previous response. I was finally able to start generating some sigma profiles. I really appreciate all the help! I'm now looking into activity coefficients using my sigma data. I began working through the COSMO-PurePython.ipynb file using a similar method as the one presented in your previous response (but this time mirroring the VT db), but have run into a problem. The attached files include the python file and error. I've attempted working through the issue by changing some of the syntax, but had no success.
activity_co_edited.txt