CP2K/ASE vibration analysis question

[Chanwoo Noh]

Dear all,

I have some question about using ASE tools for CP2K.

I want to perform the vibration analysis using ASE interface, because some of the atoms of my system should be constrained.

If some atoms are constrained, then normal CP2K calculation does not create the output file of .mol. (https://groups.google.com/forum/#!searchin/cp2k/vibration$20%7Csort:relevance/cp2k/vS_s3781V4g/_aryuXQrDAAJ)

In this link, S Ling suggested to use the  CP2K/ASE interface in this situation.

When I follow the tutorial (https://wiki.fysik.dtu.dk/ase/ase/vibrations/vibrations.html?highlight=vibration), calculating vibrational normal modes function, Vibrations() works.

However, when I use the Infrared() function, following error message occurs.

  File "test.py", line 75, in <module>

    main()

  File "test.py", line 72, in main

    ir.run()

  File "/home/chanwoo/PROGRAM/ASE/ase/ase/vibrations/vibrations.py", line 129, in run

    self.calculate(filename, fd)

  File "/home/chanwoo/PROGRAM/ASE/ase/ase/vibrations/vibrations.py", line 146, in calculate

    dipole = self.calc.get_dipole_moment(self.atoms)

  File "/home/chanwoo/PROGRAM/ASE/ase/ase/calculators/calculator.py", line 361, in get_dipole_moment

    return self.get_property('dipole', atoms)

  File "/home/chanwoo/PROGRAM/ASE/ase/ase/calculators/calculator.py", line 374, in get_property

    raise NotImplementedError

NotImplementedError

I think that a dipole moment of molecules is needed when IR intensity is calculated, but the CP2K/ASE interface doesn't support the dipole moment calculation.

Is there any method to implement the Infrared function?

I would appreciate for any suggestions and comments.

The python script for calculating normal modes is as follows.

test.py

#!/usr/bin/python

from __future__ import division, print_function

import os

from ase.structure import molecule

from ase.optimize import BFGS

from ase.calculators.cp2k import CP2K

from ase.vibrations import Vibrations

from ase.vibrations import Infrared

inp="""

&FORCE_EVAL

    METHOD Quickstep

    &DFT

        &PRINT

            &MOMENTS

                PERIODIC    FALSE

            &END

        &END

        BASIS_SET_FILE_NAME BASIS_MOLOPT

        POTENTIAL_FILE_NAME GTH_POTENTIALS

        &MGRID

            CUTOFF 400

        &END MGRID

        &XC

            &XC_FUNCTIONAL PBE

            &END XC_FUNCTIONAL

        &END XC

        &POISSON

            PERIODIC NONE

            PSOLVER MT

        &END POISSON

    &END DFT

    &SUBSYS

        &KIND O 

            BASIS_SET DZVP-MOLOPT-SR-GTH

            POTENTIAL GTH-PBE-q6

        &END KIND

        &KIND H

            BASIS_SET DZVP-MOLOPT-SR-GTH

            POTENTIAL GTH-PBE-q1

        &END KIND

    &END SUBSYS

&END FORCE_EVAL

"""

def main():

    calc = CP2K(basis_set=None,

            basis_set_file=None,

            max_scf=None,

            charge=None,

            cutoff=None,

            force_eval_method=None,

            potential_file=None,

            poisson_solver=None,

            pseudo_potential=None,

            stress_tensor=False,

            uks=None,

            xc=None,

            label='test_H2O_GOPT', inp=inp)

    h2o = molecule('H2O', calculator = calc)

    h2o.center(vacuum=2.0)

    BFGS(h2o).run()

    print(h2o.get_potential_energy())

    vib = Vibrations(h2o)

    vib.run()

    vib.summary()

    ir = Infrared(h2o)

    ir.run()

    ir.summary()

main()

[Ole Schütt]

Dear Chanwoo,

adding support for get_dipole_moment() to the ASE Calculator is probably
rather straightforward. While I would be happy to do the python part,
I'm not quite sure how things work on the CP2K side. Therefore, I would
suggest you to first try to figuring out why CP2K does not print the
molden output in the first place:


https://github.com/cp2k/cp2k/blob/master/cp2k/src/motion/vibrational_analysis.F#L454

Cheers,
Ole

On 2016-10-04 04:23, Chanwoo Noh wrote:
> Dear all,
>
> I have some question about using ASE tools for CP2K.
> I want to perform the vibration analysis using ASE interface, because
> some of the atoms of my system should be constrained.
> If some atoms are constrained, then normal CP2K calculation does not
> create the output file of .mol.
> (https://groups.google.com/forum/#!searchin/cp2k/vibration$20%7Csort:relevance/cp2k/vS_s3781V4g/_aryuXQrDAAJ

> [1])

> In this link, S Ling suggested to use the  CP2K/ASE interface in this
> situation.
>
> When I follow the tutorial
> (https://wiki.fysik.dtu.dk/ase/ase/vibrations/vibrations.html?highlight=vibration

> [2]), calculating vibrational normal modes function, Vibrations()

> TEST.PY

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>
> Links:
> ------
> [1]
> https://groups.google.com/forum/#!searchin/cp2k/vibration$20%7Csort:relevance/cp2k/vS_s3781V4g/_aryuXQrDAAJ
> [2]
> https://wiki.fysik.dtu.dk/ase/ase/vibrations/vibrations.html?highlight=vibration
> [3] https://groups.google.com/group/cp2k
> [4] https://groups.google.com/d/optout

[Chanwoo Noh]

Dear Ole,

I really thank you for your suggestion.

As you mentioned, I will try to figure out the reason that cp2k does not print the molden output.

If I find it, I will post the result on this board.

Chanwoo

[Iain Bethune]

Dear Chanwoo, all,

Support for molden output from vibrational analysis with fixed atoms has just been added in r17502 - please try it out and let me know if you run into problems. Thanks to Tobi Kraemer for pointing this out in the first place and for some testing!

- Iain

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Project Manager, EPCC

Email: ibet...@epcc.ed.ac.uk
Twitter: @IainBethune @PrimeGrid @CP2Kproject
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[Chanwoo Noh]

Dear Iain Bethune

I really thanks to you and Tobi Kraemer for the support.

I would try it out, and I will report if there is some problems.

Chanwoo