QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: ramkrishna on May 20, 2015, 16:02

Title: coordinate extraction
Post by: ramkrishna on May 20, 2015, 16:02

Dear Sir,
Is it possible to extract the coordinates and lattice parameters of each steps from the optimization trajectory file? Or is it possible to save each coordinate files separately in the time of structure optimization? Actually,  the trajectory file always open the final structure in the builder.

Thanks
Ramkrishna

Title: Re: coordinate extraction
Post by: Anders Blom on May 20, 2015, 17:37

Bring the trajectory object into the Movie Tool instead, then you can step along the different configurations and extract any particular one by sending it to the Builder (using the usual blue "Send To" button).

This can also be done by a script, if you nlread the trajectory object, see the Reference Manual.

Title: Re: coordinate extraction
Post by: ramkrishna on May 20, 2015, 18:42

Hi Anders,
I am using 2014.2 however the movie tool plugin is still inactive. Is it active only for MD simulations, not the geometry optimization?
I have also tried by nlread (as follows), and able to get the coordinates, but not the lattice parameters. The bravais_lattice command is not working.

Code

trajectory = nlread('geo_op_trajectory.nc', object_id='gID001')[0]

for ix,image in enumerate(trajectory.images()):
    elements = image.elements()
    print len(elements)
    print 'Image %i' % ix
    for elem,coords in zip(elements,image.cartesianCoordinates()):
        print elem.symbol(),
        for i in coords:
            print i.inUnitsOf(Angstrom),
        print

Thanks
Ramkrishna

Title: Re: coordinate extraction
Post by: Umberto Martinez on May 20, 2015, 20:47

Code: python

vectors=image.bravaisLattice()

Please check that you have the latest version of the Reference Manual
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.bulkconfiguration.html

Title: Re: coordinate extraction
Post by: ramkrishna on May 21, 2015, 16:12

Thanks Umberto, the command line works perfectly.  :)

However, my another concern is, why the movie tool is inactive for optimization trajectory?  I have also checked the addOns, and it shows that the movie tool is already installed.

Title: Re: coordinate extraction
Post by: Anders Blom on May 21, 2015, 17:54

I'm a bit puzzled myself, I thought it would take optimization trajectories too...

Anyway, I have made a hotfix for you - if you uninstall the MovieTool addon, and install the attached version instead, it should work.

Title: Re: coordinate extraction
Post by: ramkrishna on May 21, 2015, 20:04

Hi Anders,
Thanks for the AddOn but I am getting an error in local installation. The error is as following,

There was an error in importing the add-on module:

In Details
The exception message:
No module named KineticMonteCarlo

Thanks
Ramkrishna

Title: Re: coordinate extraction
Post by: Anders Blom on May 22, 2015, 01:35

Sorry, I based my update on the 2015 version of  this plugin, which has some new features.

Please find attached a new zip file, based on 2014.

Title: Re: coordinate extraction
Post by: ramkrishna on May 22, 2015, 15:49

Hi Anders.
Its working perfectly now. Thanks a lot for your kind support.

Regards
Ramkrishna