[ase-users] [gpaw-users] ASE installation for windows
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Fri Nov 14 14:08:54 CET 2014
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 <mailto: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 <mailto:ntben at fysik.dtu.dk>
> www.fysik.dtu.dk <http://www.fysik.dtu.dk>
> ________________________________________
> Fra: ase-users-bounces at listserv.fysik.dtu.dk
> <mailto:ase-users-bounces at listserv.fysik.dtu.dk>
> [ase-users-bounces at listserv.fysik.dtu.dk
> <mailto:ase-users-bounces at listserv.fysik.dtu.dk>] på vegne af
> Marcin Dulak [Marcin.Dulak at fysik.dtu.dk
> <mailto: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><mailto: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><mailto: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><mailto: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><mailto: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><mailto: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><mailto: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><mailto: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><mailto: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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