[ase-users] [gpaw-users] ASE installation for windows

[Zahid Hasan]

Yes, I have experienced the problem, when tried to convert the trajectory
file to pdb. The datas are missing there. Unfortunately I could not open
even the ASE trajectory format in VMD, although VMD accepts trajectory
input. Is the ASE-trajectory compatible with VMD?

And one more question, I wanted to simulate Epoxy molecule with ASE. How I
can find out which molecules are available in the ASE databank? And is
there any way to generate the molecule in other software and import in ASE
for further simulation?

Thanks and regards,
Zahid

On Fri, Nov 7, 2014 at 9:35 AM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
wrote:

>  On 11/06/2014 03:35 PM, Zahid Hasan wrote:
>
> If I save the result file in .pdb format with the commands
>
>  dyn = QuasiNewton(slab, trajectory='N2Cu.pdb')
>
> QuasiNewton trajectory keyword saves a file in trajectory format, no
> matter how you name it.
> You can convert the trajectory file into an xyz (or pdb) with:
> ase-gui -o N2Cu.pdb N2Cu.traj
> Note that you miss some information contained in the traj files when doing
> the conversion to xyz/pdb (cell, local magnetic moments, constraints, ...)
> Therefore it's better to work with trajectory files and visualize them
> with ase-gui.
>
>
>  is it possible to open the file and see the results in VMD?
>
> yes.
>
> Best regards,
>
> Marcin
>
>
>
> On Thu, Nov 6, 2014 at 1:54 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
> wrote:
>
>>  On 11/06/2014 01:17 PM, Zahid Hasan wrote:
>>
>> Dear all,
>> Do I need to install Povray seperately to generate image? Is this the
>> software provided in the website http://www.povray.org/download/
>>
>>  yes, but povray won't work directly with ASE on windows due to Linux
>> oriented os.system calls in
>> https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/io/pov.py
>> (povray ... > /dev/null, etc.).
>> Instead you can create the pov/ini povray files with an ASE python script
>> and then open the pov file with povray.
>>
>> Another problem you may encounter is when using ase.lattice module.
>> For some reasons the
>> https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/lattice/spacegroup/spacegroup.dat
>> is not copied
>> during the msi installation of ASE to
>> C:\Python27\LIb\site-packages\ase\lattice\spacegroup.
>> You need to download this file manually.
>>
>> Best regards,
>>
>> Marcin
>>
>>
>>  Thanks,
>> Zahid
>>
>> On Tue, Nov 4, 2014 at 11:52 AM, Zahid Hasan <missionpagla at gmail.com>
>> wrote:
>>
>>> I will request to just upload seperate windows msi installers, which are
>>> compatible with each other and updated.
>>>
>>> On Tue, Nov 4, 2014 at 11:48 AM, Zahid Hasan <missionpagla at gmail.com>
>>> wrote:
>>>
>>>> I have deinstalled the ASE and installed the GPAW installer with ASE
>>>> inside. But unfortunately the test scripts do not work. It works only when
>>>> the seperate ASE installation is existing. Even after the GPAW test run it
>>>> shows runtime error, although it delivers some results!!
>>>>
>>>> On Tue, Nov 4, 2014 at 11:35 AM, Marcin Dulak <
>>>> Marcin.Dulak at fysik.dtu.dk> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> yes, GPAW installer includes ASE.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Marcin
>>>>>
>>>>>
>>>>> On 11/04/2014 10:59 AM, Zahid Hasan wrote:
>>>>>
>>>>>> The installer includes also the latest ASE
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>>  _______________________________________________
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>>
>>
>>
>
>
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