QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: Timbaktoo on August 28, 2009, 09:40

Title: Urgent: Reg. molecular builder
Post by: Timbaktoo on August 28, 2009, 09:40

Hi everyone,

Is there some way/trick that we can put the distorted-CNT prepared using nanotube builder onto molecular builder?

Thanks.

Title: Re: Urgent: Reg. molecular builder
Post by: Anders Blom on August 28, 2009, 09:56

Not sure how you can get a distorted nanotube in the Nanotube Builder, since it's supposed to build perfect tubes only ;) But I guess you can manipulate it slightly.

Anyway, you can quite easily strip the unit cell from the configuration by dropping it from the Nanotube Builder onto the Script Editor. There, remove all the lines defining the PeriodicAtomConfiguration at the bottom, and replace them with

Code

molecule = MoleculeConfiguration(
    elements,
    cartesian_coordinates=coordinates
    )

Then you should be able to drop the system to the Molecular Builder for further manipulations.

Thus, in effect, remove the 4th line from the bottom (containing just "unit_cell,") and replace the line

Code

periodic_atom_configuration = PeriodicAtomConfiguration(

with

Code

molecule = MoleculeConfiguration(

Title: Re: Urgent: Reg. molecular builder
Post by: zh on August 28, 2009, 10:53

i) generate the atomic coordinates of the distorted carbon nanotube; here you may obtain the formated coordinates of atoms by running the script file with "nlPrint(your_configuration)".  
ii) collect these atomic coordinates into a xyz file;
iii) load this xyz file using the "Result Browser" of VNL and drag it onto "Molecule builder";

Title: Re: Urgent: Reg. molecular builder
Post by: Timbaktoo on September 1, 2009, 06:22

Thanks Dr. Bloom. It works!!  :)

@zh: Could you please explain to me the first point you wrote.

Thankyou.

Title: Re: Urgent: Reg. molecular builder
Post by: zh on September 1, 2009, 06:49

For example:

....
bulk_configuration = BulkConfiguration(
    bravais_lattice,
    elements,
    cartesian_coordinates=coordinates
    )
nlPrint(bulk_configuration)

The last line "nlPrint(....)" will print out the coordinates of atoms.

Title: Re: Urgent: Reg. molecular builder
Post by: Timbaktoo on September 1, 2009, 23:31

Thanks zh. I think it should solve my problem now.