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

Sat Nov 8 21:04:07 CET 2014

and I did not understand, "The way different molecule sets are accessed in
currently not unified in ASE" that you wrote.

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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