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

Mon Nov 10 06:12:40 CET 2014

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
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________________________________________
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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