[ase-users] [gpaw-users] ASE installation for windows
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Sat Nov 8 23:30:38 CET 2014
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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