Re: [Phonopy-users] python-numpy, python-yaml,....

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

Hello,

I have no idea about the installation of those packages. Even if you
solve the installation problem of lxml, you may meet the other
installation problem to install the other package; phonopy relies on
many python packages.

To use virtual environment like vmware or virtual box is much easier.

Togo

On Tue, Mar 20, 2012 at 7:23 AM, Elie M <eli...@ho...> wrote:
> Hello again,
>
> I was trying to use the first option (which you didnt recommend anyhow)
> before I rexort to installing vmware as  I was just giving it a try to
> install the missing libraries in my home computer. I managed to install the
> PyYAML and it worked perfectly fine but then the code complained about the
> python.lxml missing so I downloaded the package (zipped as an rpm file) and
> also unzipped it in the home directory but the code cannot find it. Is the
> lxml package different from the yaml one in some aspects or needs to be
> installed somewhere else.
>
> Thanks once again
>
>
> Elie
>
>> Date: Sun, 18 Mar 2012 15:25:11 +0900
>
>> Subject: Re: [Phonopy-users] python-numpy, python-yaml,....
>> From: atz...@gm...
>> To: eli...@ho...; pho...@li...
>
>>
>> Hi,
>>
>> No. Each supercell with a displacement is not allowed to relax.
>> This may be some help to understand,
>> http://phonopy.sourceforge.net/theory.html#second-order-force-constants
>> .
>>
>> Togo
>>
>> On Sun, Mar 18, 2012 at 1:21 PM, Elie M <eli...@ho...>
>> wrote:
>> > Hi again,
>> >
>> > I have indeed relaxed my structure and then did  a self consistent
>> > calculation and asked (I have done this on Quantum Espresso) the code to
>> > print the forces , which are the Hellmann- Feynmann forces. Are the
>> > forces
>> > phonopy needs the Hellmann Feynmann forces of the optimized relaxed
>> > structure, on each of the atoms? Sorry I am asking a lot of questions
>> > but It
>> > is just because  I really need to produce some results on my project. I
>> > appreciate your help a lot. Thank you
>> >
>> > Elie
>> >
>> >> Date: Sun, 18 Mar 2012 13:14:26 +0900
>> >
>> >> Subject: Re: [Phonopy-users] python-numpy, python-yaml,....
>> >> From: atz...@gm...
>> >> To: eli...@ho...
>> >> CC: pho...@li...
>> >>
>> >> Hello,
>> >>
>> >> Phonopy is the pre- and post-processor of the ab-initio calculation.
>> >> You need to calculate forces on atoms in the supercells with
>> >> displacements using some ab-initio code on modestly powerful
>> >> computers. Then you collect the outputs of the ab-initio code and pass
>> >> them to phonopy. The phonopy calculation itself is not computationally
>> >> demanding.
>> >>
>> >> Togo
>> >>
>> >> On Sun, Mar 18, 2012 at 12:50 PM, Elie M <eli...@ho...>
>> >> wrote:
>> >> > Hello,
>> >> >
>> >> > Thanks very much for the information. In fact I want to use phonopy
>> >> > to
>> >> > compute phonon modes for a 60 carbon atom supercell (i.e 180
>> >> > vibrational
>> >> > modes say the Gamma point). DFPT methods are computationally
>> >> > demanding;
>> >> > Phonopy depends on The finite difference method (right?); can I
>> >> > compute
>> >> > those 180 vibrational modes on a normal computer using Phonopy or
>> >> > will
>> >> > it
>> >> > turn to be computationally expensive in this case?
>> >> >
>> >> > Regards
>> >> >
>> >> > Elie
>> >> >
>> >> >> Date: Sun, 18 Mar 2012 10:59:28 +0900
>> >> >> Subject: Re: [Phonopy-users] python-numpy, python-yaml,....
>> >> >> From: atz...@gm...
>> >> >> To: eli...@ho...
>> >> >> CC: pho...@li...
>> >> >
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> In principle, it is possilbe to install those libraries on your home
>> >> >> directory. But I don't think it's a good idea.
>> >> >> What I recommend is to prepare a machine or a virtual machine to
>> >> >> install a recent linux distribution like Ubuntu. Usually phonoy is
>> >> >> not
>> >> >> compuationally demanding, so you can use an old machine. In fact, I
>> >> >> like to use a virtual machine. For example, you can install Vmware
>> >> >> player on your computer (Windows?) then install Ubuntu on it. The
>> >> >> installation of Ubuntu on vmware is almost automatically done.
>> >> >>
>> >> >> Togo
>> >> >>
>> >> >> On Sun, Mar 18, 2012 at 6:04 AM, Elie M <eli...@ho...>
>> >> >> wrote:
>> >> >> > Dear all,
>> >> >> >
>> >> >> > Sorry to keep bombarding you with my questions. When I was about
>> >> >> > to
>> >> >> > learn
>> >> >> > about phonopy, I went to the Si examples and wanted to open an xml
>> >> >> > file
>> >> >> > then
>> >> >> > I got the following error:
>> >> >> >
>> >> >> > "You need to install python-yaml.
>> >> >> > Traceback (most recent call last):
>> >> >> >   File
>> >> >> > "/home_cluster/fis718/eliemouj/phonopy-1.3-beta/bin/phonopy",
>> >> >> > line
>> >> >> > 275, in ?
>> >> >> >     displacements, natom = file_IO.parse_disp_yaml('disp.yaml')
>> >> >> >   File "./lib64/python/phonopy/hphonopy/file_IO.py", line 379, in
>> >> >> > parse_disp_yaml
>> >> >> > TypeError: 'str' object is not callable
>> >> >> > "
>> >> >> >
>> >> >> > which means python-yaml , numpy and probably all others are not
>> >> >> > installed.
>> >> >> > The Linux server I am using has python 2.4 and I am a normal user
>> >> >> > not
>> >> >> > a
>> >> >> > superuser. Is it still possible to install all of the needed
>> >> >> > libraries
>> >> >> > and
>> >> >> > where should they be installed? in the PYTHONPATH?
>> >> >> >
>> >> >> >
>> >> >> > Thanks
>> >> >> >
>> >> >> > Elie
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > ------------------------------------------------------------------------------
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>> >> >> > _______________________________________________
>> >> >> > Phonopy-users mailing list
>> >> >> > Pho...@li...
>> >> >> > https://lists.sourceforge.net/lists/listinfo/phonopy-users
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Atsushi Togo
>> >> >> http://atztogo.users.sourceforge.net/
>> >> >> atz...@gm...
>> >>
>> >>
>> >>
>> >> --
>> >> Atsushi Togo
>> >> http://atztogo.users.sourceforge.net/
>> >> atz...@gm...
>>
>>
>>
>> --
>> Atsushi Togo
>> http://atztogo.users.sourceforge.net/
>> atz...@gm...



-- 
Atsushi Togo
http://atztogo.users.sourceforge.net/
atz...@gm...