[ase-users] [gpaw-users] ASE installation for windows
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Sat Nov 8 23:28:00 CET 2014
Hi,
On 11/08/2014 09:01 PM, Zahid Hasan 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.
you can also try a program called "jmol".
>
> And another question, if I write like,
>
> from ase.structures import molecule
> atoms = molecule( 'CH4' )
> multiple = atoms.repeat(4,4,4)
i don't think this is what you want.
In order to view the structure do:
from ase.visualize import view
view(multiple)
>
> 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?
yes, please follow ASE tutorials:
https://wiki.fysik.dtu.dk/ase/tutorials/surface.html#molecular-dynamics
Best regards,
Marcin
>
> 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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