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

Zahid Hasan missionpagla at gmail.com
Tue Nov 18 02:01:51 CET 2014 

Dear all,
Is it possible to calculate the change of atom electron density (wave
function) with temperature using ASE or GPAW? If yes, is there any relevant
tutorials for that?

Thanks,
Zahid

On Sat, Nov 15, 2014 at 11:28 AM, Martin Hangaard Hansen <mhah at fysik.dtu.dk>
wrote:

>  You should also check the convergence criterion in the calculator if
> using gpaw for md. Try convergence={'density': 1.0e-5}, It causes drift in
> temperature if it is not strict enough.
>
> Best regards
> Martin Hangaard
>
>
> ---- Zahid Hasan skrev ----
>
>
>  Thanks.
>
> On Fri, Nov 14, 2014 at 2:08 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
> wrote:
>
>>  Hi,
>>
>> On 11/10/2014 01:11 PM, Zahid Hasan wrote:
>>
>> Dear all,
>> Your feedback helped me to get the things going. Here I am attaching the
>> python file of molecular dynamics. During the calculation the temperature
>> change is huge although NVE (Velocity Verlet) method is used. After the
>> calculation if you see the expansion of the bonds, it seems to be a bit
>> problematic. So requesting you to look at it to find out whether any reason
>> behind? May be I am doing something wrong.
>>
>> please read https://wiki.fysik.dtu.dk/ase/ase/md.html about choosing the
>> time step.
>>
>> Best regards,
>>
>> Marcin
>>
>>
>>  Thank you,
>> Zahid
>>
>>
>>
>> On Mon, Nov 10, 2014 at 6:12 AM, Niels Bendtsen Halck <ntben at fysik.dtu.dk
>> > wrote:
>>
>>> Not sure but I don't think molecule sets a cell. Maybe something like
>>> ch4.center (vacuum=2)
>>> Ch4-4 = ch4.repeat ((4, 4, 4)).
>>>
>>> However md people use more advanced methods for feeling a slab with
>>> solvent molecules.
>>>
>>> Niels Bendtsen Halck
>>> Ph.d.-studerende
>>> FYS-CAMD
>>> DTU Fysik
>>> Bygning 307
>>> 2800 Kgs. Lyngby
>>> Direkte telefon 45253177
>>> ntben at fysik.dtu.dk
>>> www.fysik.dtu.dk
>>> ________________________________________
>>> Fra: ase-users-bounces at listserv.fysik.dtu.dk [
>>> ase-users-bounces at listserv.fysik.dtu.dk] p&#229; vegne af Marcin Dulak [
>>> Marcin.Dulak at fysik.dtu.dk]
>>> Sendt: 9. november 2014 16:55
>>> Til: Zahid Hasan
>>> Cc: ase-users
>>> Emne: Re: [ase-users] [gpaw-users] ASE installation for windows
>>>
>>> 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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