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

Sun Nov 9 00:11:51 CET 2014

but when I write

from ase.structures import molecule
atoms = molecule( 'CH4' )
multiple = atoms.repeat(4,4,4)
dyn = VelocityVerlet(multiple, 2*units.fs)

is something wrong there with the repeat function, as I thought it wiil
solve multiple unit molecules simultaneously!!

On Sat, Nov 8, 2014 at 11:30 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
wrote:

>  On 11/08/2014 09:04 PM, Zahid Hasan wrote:
>
> and I did not understand, "The way different molecule sets are accessed
> in currently not unified in ASE" that you wrote.
>
> you cannot do for all available modules as you can with tmfp06d:
> from ase.data.tmfp06d import data as tmfp06d
> from ase.structure import molecule
> molecule('ScH', data=tmfp06d)
>
> You need to look into the python files under ase/data, read the code what
> they do,
> if they contain interesting molecules, and how the structures of molecules
> can be accessed.
>
> Best regards,
>
> Marcin
>
>
> On Sat, Nov 8, 2014 at 9:01 PM, Zahid Hasan <missionpagla at gmail.com>
> wrote:
>
>> Dear Marcin,
>> Thanks a lot. It realy helped me.
>>
>>  And although in VMD the texture is good, but I could not find any
>> option to show the bonds and forces between atoms like in ASE GUI. I think
>> you have worked a lot with VMD, so definitely you know better whether any
>> way exists.
>>
>>  And another question, if I write like,
>>
>>  from ase.structures import molecule
>> atoms = molecule( 'CH4' )
>> multiple = atoms.repeat(4,4,4)
>>
>>  will the Methane molecule be repeated with relevant covalent bonds in
>> three directions of coordinate? And is it also possible in ASE to carry out
>> molecular dynamics calculation of available G2 Set molecules?
>>
>>  Thanks,
>> Zahid
>>
>> On Sat, Nov 8, 2014 at 5:36 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
>> wrote:
>>
>>>  On 11/08/2014 12:02 PM, Zahid Hasan wrote:
>>>
>>> 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?
>>>
>>>  what is the error message you get when converting with ase-gui?
>>> VMD does not read traj files.
>>> This works for me on Windows (with the ASE msi installed after GPAW msi):
>>> from ase.structure import molecule
>>> from ase.calculators.emt import EMT
>>> from ase.optimize import QuasiNewton
>>> m=molecule('H2O')  # H2O from the G2 set
>>> m.set_calculator(EMT())
>>> o=QuasiNewton(m, trajectory='m.traj')
>>> o.run()
>>> Then, in the command prompt:
>>> ase-gui m.traj -o m.xyz
>>>
>>>
>>>  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?
>>>
>>>  when molecules are concerned ASE can read xyz, pdb files which you can
>>> generate in other programs.
>>>
>>> You can list the molecule names by accessing the modules located under
>>> the ase/data directory:
>>> from ase.data.g2 import data  # this is the G2 set
>>> print data.keys()
>>> or
>>> from ase.data.tmfp06d import data  # doi:10.1063/1.2162161
>>> print data.keys()
>>>
>>> In order to use a set different that G2 (see help for the molecule
>>> method: python -c "from ase.structure import molecule; help(molecule)"):
>>> from ase.data.tmfp06d import data as tmfp06d
>>> from ase.structure import molecule
>>> molecule('ScH', data=tmfp06d)
>>>
>>> The way different molecule sets are accessed in currently not unified in
>>> ASE - they were
>>> created ad hoc for the purpose of different projects.
>>>
>>> Best regards,
>>>
>>> Marcin
>>>
>>>
>>>  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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>>>>
>>>
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>>
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