Author Topic: display bonds in builder - tolerance  (Read 4010 times)

0 Members and 1 Guest are viewing this topic.

Offline amitwsu

  • Regular QuantumATK user
  • **
  • Posts: 19
  • Country: us
  • Reputation: 0
    • View Profile
display bonds in builder - tolerance
« on: October 25, 2015, 22:41 »
I am new to VNL so maybe this issue has been addressed before, however, I could not find a satisfactory solution. In a simple FCC lattice I want to display the structure such that all atoms are not bonded to all other atoms. Presently they look like as shown in the attached figure. I would like to control how the bonds are drawn - something like draw bond only if the distance is less than xx angstrom. Is there a way to do that in builder?

The reason is I want to play around with interstitials and its easy to visualize those if the lattice is cleared of the clutter.  I tried "Bond Control" - Fuzz factor but it does not do what I want.
Thanks in advance.
Amit

Offline Anders Blom

  • QuantumATK Staff
  • Supreme QuantumATK Wizard
  • *****
  • Posts: 5410
  • Country: dk
  • Reputation: 89
    • View Profile
    • QuantumATK at Synopsys
Re: display bonds in builder - tolerance
« Reply #1 on: October 26, 2015, 10:07 »
Actually in this structure, what  you are seeing is the correct picture and there isn't really any other way to show it. All bonds that you see go to nearest-neighbor atoms. So no matter how you specify the rule for drawing  bonds, either you will have no bonds, or those you are already seeing. In fcc silver (or whatever element you have), the atoms are 12-fold coordinated, so there isn't any alternative to having 12 bonds on each atom!

Offline amitwsu

  • Regular QuantumATK user
  • **
  • Posts: 19
  • Country: us
  • Reputation: 0
    • View Profile
Re: display bonds in builder - tolerance
« Reply #2 on: October 27, 2015, 13:48 »
Thanks Anders,
 Yes the distance criterion won't work for this situation. Is there a way to turn-off bond display? I used bond control - fuzz factor and that worked fine. I am wondering if there is another way to do that.
Also, Can I click on on two atoms and display bond length?

Offline Jess Wellendorff

  • QuantumATK Staff
  • Supreme QuantumATK Wizard
  • *****
  • Posts: 933
  • Country: dk
  • Reputation: 29
    • View Profile
Re: display bonds in builder - tolerance
« Reply #3 on: October 27, 2015, 15:54 »
- To turn off the display of bonds: Graphics --> Properties --> Atoms --> Bonds --> untick "visible".
- You can hover over any displayed bond with the mouse and the bond length will be displayed.

Offline amitwsu

  • Regular QuantumATK user
  • **
  • Posts: 19
  • Country: us
  • Reputation: 0
    • View Profile
Re: display bonds in builder - tolerance
« Reply #4 on: January 21, 2016, 21:47 »
Jess,
Where do I find Graphics .......... Bonds in the Menu. I use Mac OS X version. I cannot seem to find the way to display bond length.
thanks
amit

Offline Jess Wellendorff

  • QuantumATK Staff
  • Supreme QuantumATK Wizard
  • *****
  • Posts: 933
  • Country: dk
  • Reputation: 29
    • View Profile
Re: display bonds in builder - tolerance
« Reply #5 on: January 22, 2016, 08:48 »
OK, so you use VNL-ATK 2014.3. In the Viewer, you can choose "Properties --> Atoms" and choose "Ball" from the Preset options. This will remove the graphical representation of bonds between atoms.