How can I determine the orientation of the finite size particle in output? I need to know if they are upright or standing?
How can I determine the orientation of the finite size particle in output? I need to know if they are upright or standing?
what atom style are you using? or better yet, can you provide a minimal input example that is demonstrating a small version of the kind of system you are looking at?
axel.
I am using ellipsoid and line, to simulate rigid bodies. I wonder if I understand what you mean. If you mean the commands I use, these commands make the configuration.
atom_style ellipsoid
dimension 2
boundary p p p
lattice sq 0.01
sincerely
sedigheh
How can I determine the orientation of the finite size particle in output? I need to know if they are upright or standing?
what atom style are you using? or better yet, can you provide a minimal input example that is demonstrating a small version of the kind of system you are looking at?
axel.
for this setup you could try using compute property/atom, which will give you access to the quaternions representing the orientation of the ellipsoids. those could be converted to orientation vectors in post-processing.
axel.
Can I visualize the finite size particles by any visualizer software such as VMD or Ovito?
now i try with VMD but it figure the ellipsoids as spherics.
for this setup you could try using compute property/atom, which will give you access to the quaternions representing the orientation of the ellipsoids. those could be converted to orientation vectors in post-processing.
axel.
Can I visualize the finite size particles by any visualizer software such as VMD or Ovito?
now i try with VMD but it figure the ellipsoids as spherics.
There are two README_visualizat_OVITO files which sketch how you can use OVITO to display ellipsoids
https://github.com/jewettaij/moltemplate/tree/master/examples/coarse_grained/ellipsoids_CG_benzene
You will have to use a customized “dump” command in your LAMMPS input script in order to include the ellipsoid orientation information in the trajectory file which OVITO will read. Here is an excerpt from that example:
dump 1 all custom 100 traj.lammpstrj &
id type x y z c_q[1] c_q[2] c_q[3] c_q[4] &
c_shape[1] c_shape[2] c_shape[3] &
angmomx angmomy angmomz
The documentation for the “dump” command is here:
https://lammps.sandia.gov/doc/dump.html
Cheers
Andrew
If you’re curious, these files are included with the “ellipsoids_CG_benzene” example which is included with moltemplate.
(There’s a picture of this system at the bottom of this web page. Moltemplate can build data files with dipoles and ellipses. But you don’t have to use moltemplate to use these OVITO settings and this dump command mentioned above. Credit goes to Otello M. Roscion (U.Southampton) and Matteo Ricci (U.Bologna) who contributed this example, and added features to moltemplate to make this possible.)
Can I visualize the finite size particles by any visualizer software such as VMD or Ovito?
now i try with VMD but it figure the ellipsoids as spherics.There are two README_visualizat_OVITO files which sketch how you can use OVITO to display ellipsoids
https://github.com/jewettaij/moltemplate/tree/master/examples/coarse_grained/ellipsoids_CG_benzeneYou will have to use a customized “dump” command in your LAMMPS input script in order to include the ellipsoid orientation information in the trajectory file which OVITO will read. Here is an excerpt from that example:
dump 1 all custom 100 traj.lammpstrj &
id type x y z c_q[1] c_q[2] c_q[3] c_q[4] &
c_shape[1] c_shape[2] c_shape[3] &
angmomx angmomy angmomz
My apologies. (I posted without reading my own example carefully.)
I just realized that to use this dump command, you will first need to define the “c_q”, and “c_shape” computes, which this dump command refers to. So somewhere in your input script (before the “dump” command), you will need to insert these two “compute” commands into your LAMMPS input script:
compute q all property/atom quatw quati quatj quatk
compute shape all property/atom shapex shapey shapez
The documentation for the “dump” command is here:
The documentation for the “compute” command is here:
https://lammps.sandia.gov/doc/compute.html
This example also includes the following commands to include the rotational degrees of freedom in the temperature (without messing up the pressure, …I think):
compute temp_trasl all temp
compute temp_rototrasl all temp/asphere dof all
compute press_trasl all pressure temp_trasl
Modify temperature to include ellipsoidal degrees of freedom.
thermo_modify temp temp_rototrasl
thermo_modify press press_trasl
Hopefully I didn’t leave anything out this time.
Andrew
P.S. My apologies. This example was more confusing than I realized because some of the LAMMPS input script commands were buried within this file, which is not even a LAMMPS file. (If you’re curious, the “moltemplate” program would then use that file to build an input script which LAMMPS can read.) Now after this correction I think it is (finally) safe to claim that you can use these commands above without worrying about any of the details from this example.