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

Panu Sam-Ang panu.sam-ang at stonybrook.edu
Fri Jun 30 23:10:26 CEST 2017 

Hi Simon,

Thank you so much for your answer. I added PYTHONPATH to where you
suggested and it is working now!    (I did not use setup.py script).

Best,
Panu

On Fri, Jun 30, 2017 at 5:34 AM, Simon Rittmeyer <simon.rittmeyer at tum.de>
wrote:

> Hi Panu,
>
> as Ivan already pointed out, this mostly seems to be an issue with your
> python path.
>
> Does your current pythonpath contain "/Users/Panu/Dropbox/Nanosciences/Codes/ASE/ase/"?
> Or did you install this branch via the setup.py script?
>
> If not, then of course your python interpreter will not be able to find
> the respective modules but always resort to the ase version you probably
> installed beforehand. You then have two possibilities:
>
> 1) To find out, which files your python interpreter actually reads, type
>
>         python -c "import ase; print(ase.__file__)
>
> on the command line. This should point to the __init__.pyc in the above
> mentioned folder. If it does, but you still you cannot your calculator, you
> should check whether the files are actually there.
>
> If, however, the correct __init__.pyc is not used, please check your
> PYTHONPATH environment variable. You can do this via
>
>         echo $PYTHONPATH
>
> on the command line. If the directory mentioned above is not part of it,
> then add it. Again, this can be done via one line in your ~/.bashrc file
> (or on a Mac, probably rather ~/.bash_profile):
>
>         export PYTHONPATH=/Users/Panu/Dropbox/Nanosciences/Codes/
> ASE/ase/:$PYTHONPATH
>
> Note that you'll have to source the ~/.bashrc file first to apply the
> changes (or open a new terminal):
>
>         source ~/.bashrc
>
> Then check again, whether your PYTHONPATH contains the correct path.
>
> 2) An alternative to adjusting the PYTHONPATH would be to change to your
> kitnwchem branch and then run the setup.py file. This will install the
> current branch user-wide (which is presumably want you want anyway).
>
>         cd /Users/Panu/Dropbox/Nanosciences/Codes/ASE/ase
>         git checkout kitnwchem
>         python setup.py install --user
>
>
> Hope this helps.
>
>
> Best,
> Simon.
>
> Simon P. Rittmeyer, M.Sc.
>
> Technical University of Munich (TUM)
> Department of Chemistry
> Chair for Theoretical Chemistry
>
> Lichtenbergstr. 4
> 85747 Garching, Germany
>
> Tel: +49 89 289 13810
> Room CH62110
>
> simon.rittmeyer at tum.de
> https://www.th4.ch.tum.de
>
> > Am 29.06.2017 um 22:11 schrieb Panu Sam-Ang via ase-users <
> ase-users at listserv.fysik.dtu.dk>:
> >
> > Hi Ivan,
> >
> > Thank you for your answer.  I followed your instruction and I still got
> the same error message.  Below is the screenshot of the result:
> >
> > <Screen Shot 2017-06-29 at 3.08.09 PM.png>
> >
> > I also tried to switched branches again and got the same thing:
> >
> > <Screen Shot 2017-06-29 at 4.09.47 PM.png>
> >
> > <Screen Shot 2017-06-29 at 4.10.25 PM.png>
> >
> > Do you know why this is so?
> >
> > Best,
> > Panu
> >
> > On Thu, Jun 29, 2017 at 12:29 PM, Kondov, Ivan (SCC) <
> ivan.kondov at kit.edu> wrote:
> > 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> 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]
> > Sent: Tuesday, June 20, 2017 5:22 PM
> > To: Kondov, Ivan (SCC)
> >
> >
> > Cc: 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>
> 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@
> 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
> > 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>
> wrote:
> >
> > Hi Panu,
> >
> > 2017-06-06 21:38 GMT+02:00 Panu Sam-Ang <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>
> > > 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>:
> > >> > 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
> > >> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> > >
> > >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > ase-users mailing list
> > ase-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20170630/8715f043/attachment.html>

More information about the ase-users mailing list