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

Fri Nov 14 23:43:17 CET 2014

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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