how to use ASE's nebcode and nwchem interface?


  • Guest -
2:36:10 PM PST - Wed, Feb 1st 2012
I am trying to use ASE and the nwchem interface they have provided to run an NEB calculation. However, regardless of the complexity of the system, I am unable to find a transition state even in systems where I know what that transition state is (it says that convergence is not reached). Is there a way for me to provide an initial guess for the transition state in the job script when using the neb code? Or is there something I else I should be doing that I have neglected?

Thanks

Forum Vet
3:19:38 PM PST - Wed, Feb 1st 2012
My understanding is there is no NWChem interface for ASE. To investigate your question, I just downloaded the latest ASE version, and there is no setup for NWChem. So, I am unable to provide any input or guidance.

Bert

Quote: Feb 1st 9:36 pm
I am trying to use ASE and the nwchem interface they have provided to run an NEB calculation. However, regardless of the complexity of the system, I am unable to find a transition state even in systems where I know what that transition state is (it says that convergence is not reached). Is there a way for me to provide an initial guess for the transition state in the job script when using the neb code? Or is there something I else I should be doing that I have neglected?

Thanks

Gets Around
11:53:20 AM PST - Fri, Feb 3rd 2012
Hi,

there exist a simple interface to nwchem in ase: https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/calculators/nwchem.py
Please post your complete python script on ase-users mailing list https://wiki.fysik.dtu.dk/ase/mailinglists.html

Marcin

Forum Vet
12:13:28 PM PST - Tue, Feb 7th 2012
Looking at the nwchem.py script, which does not come from the NWChem developer's team it looks like ASE only gets gradients from NWChem. So, ASE itself does the NEB calculation using the gradients I assume. You might want to try doing a very coarse convergence of the NEB to see if that does converge. If it does, then the convergence criteria in the nwchem.py might not be tight enough.

Bert


Quote:Marcindulak Feb 3rd 6:53 pm
Hi,

there exist a simple interface to nwchem in ase: https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/calculators/nwchem.py
Please post your complete python script on ase-users mailing list https://wiki.fysik.dtu.dk/ase/mailinglists.html

Marcin

Gets Around
8:16:07 AM PST - Wed, Feb 8th 2012
The problem may be with https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/calculators/nwchem.py which
(due to the fact that is very experimental) does not extract forces by default.
In order for ASE optimizers to work you would have to uncomment (as for ASE revision 2476) the lines 137:
# f.write('\ntask ' + task + ' gradient\n')
and 148:
# self.read_forces()

Marcin

Forum Vet
10:09:55 AM PST - Wed, Feb 8th 2012
Hi Marcin,

Good find, overlooked that one. Line 138: f.write('\ntask ' + task + ' energy\n') can be commented out though as NWChem will do an energy calculation before a gradient anyway.

Bert


Quote:Marcindulak Feb 8th 3:16 pm
The problem may be with https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/calculators/nwchem.py which
(due to the fact that is very experimental) does not extract forces by default.
In order for ASE optimizers to work you would have to uncomment (as for ASE revision 2476) the lines 137:
# f.write('\ntask ' + task + ' gradient\n')
and 148:
# self.read_forces()

Marcin

Gets Around
12:41:01 PM PST - Wed, Feb 8th 2012
Well, not really a find. I'm just ASE contributor, so i know that.
I have performed few optimizations with Nwchem in ASE, so I guess NEB should work too.
In the (maybe near) future the Nwchem interface in ASE will be improved and covered by tests,
and as you already noted i'm working on making RPMS of Nwchem (http://nwchemgit.github.io/Special_AWCforum/st/id262/RPMS_of_NWchem.html). I'm very close to have 6.1 RPMS built.
Tthe decision to make Nwchem open made that possible!

Forum Vet
12:47:36 PM PST - Wed, Feb 8th 2012
Once you have RPMS for 6.1, could you let me know (bert.dejong@pnnl.gov). We'll add a link to those RPMS to our download pages.

Bert


Quote:Marcindulak Feb 8th 7:41 pm
Well, not really a find. I'm just ASE contributor, so i know that.
I have performed few optimizations with Nwchem in ASE, so I guess NEB should work too.
In the (maybe near) future the Nwchem interface in ASE will be improved and covered by tests,
and as you already noted i'm working on making RPMS of Nwchem (http://nwchemgit.github.io/Special_AWCforum/st/id262/RPMS_of_NWchem.html). I'm very close to have 6.1 RPMS built.
Tthe decision to make Nwchem open made that possible!


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