[ase-users] getting Hamiltonian and overlap matrices from NWChem

Thu Jun 29 18:29:04 CEST 2017

Hi Panu,

you do not have to configure new PYTHONPATH if you have any git branch of ASE on your computer, then you should do:

git checkout master

git checkout -b kitnwchem

git remote add ikondov_ase https://gitlab.com/ikondov/ase.git

git pull ikondov_ase kitnwchem

You can switch any time to your master branch with "git checkout master"

If you have cloned kitnwchem branch directly into a new folder named 'kitnwchem', for example with

git clone https://gitlab.com/ikondov/ase kitnwchem

then you should set PYTHONPATH correspondingly.

Best regards,

Ivan

________________________________
Von: Panu Sam-Ang <panu.sam-ang at stonybrook.edu>
Gesendet: Mittwoch, 28. Juni 2017 22:27
An: Kondov, Ivan (SCC)
Cc: ase-users at listserv.fysik.dtu.dk
Betreff: Re: [ase-users] getting Hamiltonian and overlap matrices from NWChem

Hi Ivan,

I forked your ASE project and cloned it to my computer. I then did "$git checkout kitnwchem" to switch/get the kitnwchem branch (is this correct)?    I saved your script in the previous email and saved it as "NH3.py" and ran it using "$python NH3.py$ and got this import error:

Panus-MacBook-Air:ASE Panu$ python NH3.py

Traceback (most recent call last):

  File "NH3.py", line 2, in <module>

    from ase.calculators.nwchem import KITnwchem

ImportError: cannot import name KITnwchem

Could you tell me how to fix this?   I am very new to git and ASE and not sure what I did wrong here.   I am guessing I have to set the new path to ASE in kitnwchem, is this correct?

Thank you.

Best,

Panu

On Wed, Jun 21, 2017 at 12:46 PM, Kondov, Ivan (SCC) <ivan.kondov at kit.edu<mailto:ivan.kondov at kit.edu>> wrote:
Dear Panu,

you can check out this branch

https://gitlab.com/ikondov/ase/tree/kitnwchem

For historical reasons the mentioned methods are in a derived class which has a slightly different parameter keys. Here a simple use:

from ase.calculators.nwchem import KITnwchem
from ase.build import molecule
mol = molecule('NH3')
params = {
    'title': 'ammonia',
    'task': 'energy',
    'basis set name': 'sto-3g',
    'total charge': 0,
    'multiplicity': 1,
    'use dft': True,
    'density functional': 'b3lyp'
}
calc = KITnwchem(**params)
mol.set_calculator(calc)
print(calc.get_mos(mol))
print(calc.get_fock_overlap())

I think this can be used for the time being. I can migrate the relevant two or three methods to the base class but for that I will need time. Please let me know.

Best regards,
Ivan

From: Panu Sam-Ang [mailto:panu.sam-ang at stonybrook.edu<mailto:panu.sam-ang at stonybrook.edu>]
Sent: Tuesday, June 20, 2017 5:22 PM
To: Kondov, Ivan (SCC)

Cc: ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] getting Hamiltonian and overlap matrices from NWChem

Thank you, Ivan.  Could you share the code?

Best,
Panu

On Tue, Jun 20, 2017 at 6:11 AM, Kondov, Ivan (SCC) <ivan.kondov at kit.edu<mailto:ivan.kondov at kit.edu>> wrote:
Dear Panu,

you only need the eigenvectors (the molecular orbitals) and the eigenvalues (molecular orbital energies) to restore the fock matrix and the overlap matrix. To make nwchem write them out you have to put the line

print "final vectors analysis" "final vectors"

in the dft section of the input. See

http://www.nwchem-sw.org/index.php/Release66:Hartree-Fock_Theory_for_Molecules#Printing_Information_from_the_SCF_Module

I have an own code for all this including reading the orbitals with the ASE nwchem calculator. I can share it if you like.

Best regards,
Ivan

From: ase-users-bounces at listserv.fysik.dtu.dk<mailto:ase-users-bounces at listserv.fysik.dtu.dk> [mailto:ase-users-bounces at listserv.fysik.dtu.dk<mailto:ase-users-bounces at listserv.fysik.dtu.dk>] On Behalf Of Panu Sam-Ang via ase-users
Sent: Tuesday, June 06, 2017 10:19 PM
To: Ask Hjorth Larsen
Cc: ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] getting Hamiltonian and overlap matrices from NWChem

Thank you, Ask.  That's helpful!

On Tue, Jun 6, 2017 at 4:15 PM, Ask Hjorth Larsen <asklarsen at gmail.com<mailto:asklarsen at gmail.com>> wrote:
Hi Panu,

2017-06-06 21:38 GMT+02:00 Panu Sam-Ang <panu.sam-ang at stonybrook.edu<mailto:panu.sam-ang at stonybrook.edu>>:
> Hi Ask,
>
> Thank you for your suggestion.  I just got NWChem installed on my laptop and
> haven't really used it before.  I thought ase.calculators.nwchem or
> ase.calculators.interface would have a function that can do that.  But I
> guess I have to write my own script?

ASE mostly does energies/forces and the more universal electronic
structure quantities like KS eigenvalues and occupation numbers.  Many
codes do not establish the Hamiltonian explicitly, so this is not part
of the standard interface.  You can probably pass any keywords to
NWChem through the standard interface, and then manually extract what
you need from the files saved.  (One could add special functions for
getting the Hamiltonian to the calculator to ease this in the future.)

Best regards
Ask

>
> Best,
> Panu
>
> On Tue, Jun 6, 2017 at 12:31 PM, Ask Hjorth Larsen <asklarsen at gmail.com<mailto:asklarsen at gmail.com>>
> wrote:
>>
>> Hi Panu,
>>
>> How would you get these from NWChem normally?  I guess the way is to
>> enable a keyword so it is saved to a file, and then read the file
>> manually from the script.
>>
>> Best regards
>> Ask
>>
>> 2017-06-05 21:48 GMT+02:00 Panu Sam-Ang via ase-users
>> <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>:
>> > Hello,
>> >
>> > Does anyone know how to get the Hamiltonian and overlap matrices from
>> > using
>> > NWChem as the calculator?   What is the command?
>> >
>> > Thank you,
>> > Panu
>> >
>> > _______________________________________________
>> > ase-users mailing list
>> > ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
>> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>

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