[lammps-users] Question on gayberne example


Hi everyone,
I am a new lammps user and I am studing the example in lammps.
About the gayberne example, I want to know how to visulize the result. It mentioned that the animation was performed with Pymol after converting dump.ellipse to ellipse.py with the pymol asphere tool. I have gotten the ellipse.py file, but cannot vis it with pymol which is the educational version. How to do that?
Another question is the script in.ellipse.gayberne in the examples direction is not consistent with the script on the website http://lammps.sandia.gov/movies.html#ellipse. I think the file in the example direction is right, doesnot it? And in the script, there is a line compute_modify 1_temp extra {dof}, but I donnot find the definition of compute-ID of 1_temp. What's the effect of the this line?<br>Also in the script, there are several line<br>compute rot all temp/asphere<br>group spheroid type 1<br>variable dof equal count(spheroid)+2<br>compute_modify rot extra {dof}
It define the variable dof= the number of spheroid plus 2, why do that? However it is a physical question, maybe I should find the answer from book or literature.
Thanks in advance.

Bests,
Bin
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Answers below.

Steve


Hi everyone,
I am a new lammps user and I am studing the example in lammps.
About the gayberne example, I want to know how to visulize the result. It mentioned that the animation was performed with Pymol after converting dump.ellipse to ellipse.py with the pymol asphere tool. I have gotten the ellipse.py file, but cannot vis it with pymol which is the educational version. How to do that?

I don’t know about the educational version. I just have the free version and it works fine.


Another question is the script in.ellipse.gayberne in the examples direction is not consistent with the script on the website http://lammps.sandia.gov/movies.html#ellipse. I think the file in the example direction is right, doesnot it?

The script in the examples dir is newer, so use that one as your starting point.


And in the script, there is a line compute_modify 1_temp extra ${dof}, but I donnot find the definition of compute-ID of 1_temp. What’s the effect of the this line?

The fix 1 (which is npt/asphere) defines a temperature compute which has the ID 1_temp,
which this command is adding extra DOF to. See the fix npt/asphere doc page
for info on this compute which it defines.



Also in the script, there are several line
compute rot all temp/asphere
group spheroid type 1
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
It define the variable dof= the number of spheroid plus 2, why do that? However it is a physical question, maybe I should find the answer from book or literature.

yes, this is just tweaking the degrees of freedom for ellipsoinds - I would read the command doc pages
to see what they do to adjust the DOF.

Hi Steve,
Thank you very much for your answer. But also I have questions about that. And I should depict it clearly.

  1. Visulization issue. What’s the command opening the ellispe.py file in pymol?
    I have produced the ellispe.py file using the pymol_asphere tool. And install a Windows version of pymol. As wrote in the file pymol_asphere\examples\readme, Launch PyMol on this input and you should see a viz of ellipsoids in a box of LJ particles: pymol ellipse.py
    When I type pymol ellispe.py, it shows syntax error. As following

pymol ellipse.py
Traceback (most recent call last):
File “C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py”, line 464, in parse
exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
File “”, line 1
pymol ellipse.py
^
SyntaxError: invalid syntax

When I type load ellipse.py, it shows

load ellipse.py
CmdLoad: “ellipse.py” loaded as “ellipse.py”.
But there are nothing in the graphic interface
So how to visulize the ellipse.py file in pymol?

  1. Yes, I use the script in example dir as my starting point. While I should mention that the script on the website maybe wrong. When I run that one, it shows syntax error with fix command.
  2. I am really confused with why subtract the degrees of freedom with the number of spheriod plus 2, please let me know if you have any idea.

Thanks for your great effort.
Sincerely,
Bin
10年6月14日,周一, Steve Plimpton [email protected] 写道:

The directions in the examples/README are:

Launch PyMol on this input and you should see a viz of
ellipsoids in a box of LJ particles:
pymol ellipse.py

and are for a Linux box with a command line interface.
I don’t use Windows or PyMol on Windows, so I don’t
know how to do the equivalent on that box. Probably launch
PyMol and load a *.py file in some manner.

Steve