What is a correct .cosmo file style

[GangqiangYu]

I obtained the .cosmo file (e.g., ethanol.cosmo as shown the attachment) by performing the Dmol3 caculation in Materials Studio package, but this file style is different from that provided at https://github.com/usnistgov/COSMOSAC (e.g., LFQSCWFLJHTTHZ-UHFFFAOYSA-N.cosmo as shown the attachment). How do I get the same files as yours, and what post-processing is required? I look forward to hearing from you！ ethanol.zip

[ianhbell]

Yes, it seems that Dmol3 has changed their cosmo file format. Interested in updating the parser?

[GangqiangYu]

It is failed to obtain a sigma profile by running the python script based on the cosmo file with changed style , but it is successful for your cosmo file. Thank you very much for your help! I am very interested in updating the parser to obtain sigma files successfully.

[ianhbell]

We might want to be a bit thoughtful about trying to support all the different cosmo formats that have been generated by Dmol3. Can you do a bit of research to track down the documentation for their different formats?

[GangqiangYu]

I will produce some cosmo files by using the Dmol3 calculation, and then send to you. What do you think ?

[ianhbell]

I'm looking for something more conclusive: documentation from Dmol3 staff about all changes that have happened to this file format over the years so that it is clear that we are covering all the relevant formats.

[GangqiangYu]

It is a good idea! What can I do ?

[ianhbell]

Ask the support team of Dmol3 for a complete changelog of their cosmo file format.

[mabounassif]

Is there a plan to support nwchem COSMO files? or other rather open source alternatives?

[mabounassif]

Would be happy to help out with the parser for that bit.

[ianhbell]

Do you have an example you can share?

[mabounassif]

I'm still learning the ropes on how to effectively use COSMO with nwchem. I ran the following nw file that I've taken from one of their tutorials:

start  
echo  
 title "h2o"  
geometry  
 o                  .0000000000         .0000000000        -.0486020332  
 h                  .7545655371         .0000000000         .5243010666  
 h                 -.7545655371         .0000000000         .5243010666  
end  
basis
 o library 6-31g**  
 h library 6-31g**  
end  
cosmo  
 dielec 78.0  
 radius 1.40  
        1.16  
        1.16  
 lineq  0  
end  
task scf energy

The output is attached. Let me know if it makes sense h2o.txt .

[ianhbell]

Not clear to me, can you extract the segment charge densities on the segments? I don't see that.

[mabounassif]

It seems to me that they don't have segment charge densities, Instead they have charge density on a specified set of grid points which might mean that some processing needs to be done to calculate the segment charge densities. I'm still validating the assumption. In the following paper, they seem to have figured it out. https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c01478

[ianhbell]

Well, if you can figure out how to do it, I would be very interested. It would be nice to have a fully-open implementation from start to finish.

[mabounassif]

I've found that a xyz file is generate that is the charge density of the surface. Attached is an example. I'm not too knowledgeable but couldn't we use this directly to calculate the sigma profile? Instead of using segments? I guess not given that the sigma profile is e/A^2 cosmo.xyz.txt

[ianhbell]

I dunno. Can you ask on their forums? We need something like looks like one of the cosmo files: https://github.com/usnistgov/COSMOSAC/blob/master/profiles/UD/cosmo/ACKALUBLCWJVNB-UHFFFAOYSA-N.cosmo

[mabounassif]

After a lot of head banging, I've decided to use mopac. example.cos.txt

[ianhbell]

So now you need a parser for that file, and to re-parameterize all of COSMO-SAC. Good luck!

[ianhbell]

I was a little bit joking in my previous comment, but that is actually what is required.

[tcxiaoma]

Hi, I also encountered the same problem. What version of Dmol3(MS) should match the program?