Re: [Phonopy-users] negative frequencies, cp2k interface

[Atsushi T. <atz...@gm...>]

I got the message from Kadioglu to my e-mail address with the input
structure unattached here in case, but I also send my reply to the
mailing list to ask someone's help (e.g. other cp2k interface users
etc)

Thanks. But...

1) For the latest version, I needed to install cp2k_input_tools
(https://pypi.org/project/cp2k-input-tools/), but for v2.2.0, I need
cp2k_tools (https://pypi.org/project/cp2k-tools/). Can this be the
reason for it? I am not sure about this. Could you contact with the
developer of this plugin, Tiziano Müller? And in case, please make
issues on github (https://github.com/phonopy/phonopy/issues) for
discussion if this is more the phonopy problem. Otherwise, better to
discuss on cp2k*-tools.
2) I could not run the test because I get error message running with
v2.2.0 as follows:

(phonopytest) togo@nmac% phonopy --cp2k -c cp2k.inp -d --dim 1 1 1
        _
  _ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_|                            |_|    |___/
                                       2.2.0

Traceback (most recent call last):
  File "/Users/togo/.miniconda/envs/phonopytest/bin/phonopy", line 7,
in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/Users/togo/phonopytest/phonopy/scripts/phonopy", line 463, in <module>
    symprec=symprec)
  File "/Users/togo/phonopytest/phonopy/phonopy/cui/collect_cell_info.py",
line 68, in collect_cell_info
    command_name=command_name)
  File "/Users/togo/phonopytest/phonopy/phonopy/interface/__init__.py",
line 161, in read_crystal_structure
    unitcell = read_cp2k(cell_filename)
  File "/Users/togo/phonopytest/phonopy/phonopy/interface/cp2k.py",
line 91, in read_cp2k
    raise NotImplementedError("unit cell can only be specified via ABC")
NotImplementedError: unit cell can only be specified via ABC

Togo

On Tue, Mar 10, 2020 at 11:01 AM Atsushi Togo <atz...@gm...> wrote:
>
> Hi,
>
> For the performance problem to create displacements, could you send
> your test case (input structure and supercell size) and tell me which
> version was faster then 2.4.2?
>
> Togo
>
> On Tue, Mar 10, 2020 at 1:04 AM Kadioglu Özge <ozg...@ep...> wrote:
> >
> > Hello,
> >
> > I am working on phonon properties of MOFs. There are some challenging structures that I constantly have negative frequencies for. I managed to decrease the number of negative frequencies by pushing the geometry optimization more and using K-points while optimizing on cp2k. However, I still had negative frequencies, then I did cell-optimization but afterwards the number of negative frequencies increased again.
> >
> > I checked the previous email threads, seems like I should check the eigenvectors corresponding to the negative frequencies. I did that by using --eigvecs tag and got the eigenvectors written in mesh.yaml file. But i do not know how to move on after this point. How do we move the normal modes with negative frequencies before trying a new optimization? If you have any other suggestion for me to check I would be very glad.
> >
> > Also, with the version 2.4.2, it takes much longer for the displacements to be created. It was only couple of seconds with the previous versions of phonopy, for a system consisting of 200-300 atoms, now it is 1-2 minutes to create cp2k input files with the displacements. May i ask why did it change significantly?
> >
> > PS: I am using phonon --cp2k interface.
> >
> > Thanks in advance.
> >
> >
> >
> > ---
> > Özge Kadioglu
> >
> > Doctoral Assistant
> > Laboratory of Molecular Simulation (LSMO)
> > École Polytechnique Fédérale de Lausanne
> >
> >
> > _______________________________________________
> > Phonopy-users mailing list
> > Pho...@li...
> > https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
>
>
> --
> Atsushi Togo



-- 
Atsushi Togo