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

Sun Nov 9 00:47:45 CET 2014

I have searched the ASE/DATA folder. Unfortunately I am not finding all the
molecular structures of G2 set, although in cmd I am getting the name of
the molecules.

Thanks.

On Sun, Nov 9, 2014 at 12:11 AM, Zahid Hasan <missionpagla at gmail.com> wrote:

> 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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>>>>
>>>
>>
>>
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