[ase-users] [gpaw-users] ASE installation for windows
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Sun Nov 9 16:55:41 CET 2014
Hi,
On 11/09/2014 12:11 AM, Zahid Hasan 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)
maybe you need a calculator attached to the atoms.
Please follow ASE tutorials:
https://wiki.fysik.dtu.dk/ase/tutorials/tutorials.html
When reporting problems please provide the full script and verbatim error.
Best regards,
Marcin
>>
>> 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 <mailto: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 <mailto: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
>> <mailto: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
>>> <mailto: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
>>>> <mailto: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
>>>>> <mailto: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
>>>>> <mailto: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
>>>>> <mailto: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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