Hi,
I have following few questions.
- Is there any command which automatically can calculate volume of few group of atoms.
- How can i tilt a cylinder
Regards,
Saurav Goel
Hi,
I have following few questions.
1. Is there any command which automatically can calculate volume of few
group of atoms.
atoms don't have a well defined volume. how can you compute
a volume of a group of them?
2. How can i tilt a cylinder
by taking it in your hand, and then turning your hand around. 
please formulate your questions accurate. i assume you are
referring to defining a cylindrical region with the region command.
then the answer is: by adding code for a tilted cylindrical region.
the current code doesn't have that ability.
axel.
Actually you can specify a tilted cylinder, using
the rotate keyword with the region command. I believe
if you specifify a variable with a constant rotation
angle, then you effectively statically rotate the region,
though the rotate option was added to do dynamic rotations.
Steve
Hi Steve,
Many thanks for your advise. I tried using it but was unsuccessful. However, i am still trying, Let see if it works.
In the meantime, I have following queries:
-
I want to simulate interaction between Si- C - O in three independent bodies. While in latest Lammps version, I could figure out tersoff pot. file for Si-C & Si-O interaction. However, didn’t know whether there is any available tersoff pot. function to have C-O interaction. Can u advise any suitable alternative.
-
I have termed the newtonian atoms & thermal atoms combinedly as mobile group so if i equilibrate mobile group as one group there occurs a huge temp. gradient between the thermal atoms & newtonian atoms however, if i equilibrate them separately there is no such problem. The problem got solved. However, I am still keen to know the cause of this.
-
How can i simulate Area Restricted Molecular dynamics simulation in Lammps?
-
I am currently using VMD to view the output in lammps which has got limited features for beginner. However, i am keen to learn that how can i see the colour variation on atoms for viewing temperature & stresses just like the way commercial FEA packages do. I think you might be asking me to try Pizza.py. But as i said is there any easy tool to customise this thing as being a beginner.
Your advise on above points will be highly appreciated.
Regards,
Saurav
2. I have termed the newtonian atoms & thermal atoms combinedly as mobile
group so if i equilibrate mobile group as one group there occurs a huge
temp. gradient between the thermal atoms & newtonian atoms however, if i
equilibrate them separately there is no such problem. The problem got
solved. However, I am still keen to know the cause of this.
this is not "solving" but avoiding. the cause is obviously that what you
considered equilibrated was in fact not equilibrated. GI-GO.
most likely you were using some initial geometry that was close to
equilibrium in one part and not so close for the other part of you system.
if you use a langevin thermostat, you will get better energy dissipation,
particularly with a shorter time constant.
but the consequence is that you force "equipartitioning" of energy
(same as for the two thermostat approach), but that only is a
prerequisite for equilibrium, but not a sufficient criterion. for details
you should stick your nose into some statistical mechanics text
books for a while. you have to know what you are doing and the
answer to those questions lies therein.
3. How can i simulate Area Restricted Molecular dynamics simulation in
Lammps?
what would that be? constant surface area variable cell?
4. I am currently using VMD to view the output in lammps which has got
limited features for beginner. However, i am keen to learn that how can i
see the colour variation on atoms for viewing temperature & stresses just
like the way commercial FEA packages do. I think you might be asking me to
try Pizza.py. But as i said is there any easy tool to customise this thing
as being a beginner.
out of the follwoing pick any two: no cost, easy to use, powerful.
you cannot have it all. VMD is not that difficult to use and with the
upcoming VMD 1.9 release there are now also ways to pass
properties from the trajectory file directly to VMD.
however, i don't really see much of a problem in writing a small
tcl script that reads a file with a documented column oriented format
into VMD after the fact. i find that quite impressive that VMD allows
you to do this, considering that it was not at all every conceived
to do any of these FE-like things, but rather visualize biological
systems.
it all revolves around money. if you round up the cash to pay people
to implement what you want, then you will get it. otherwise you have
to get along with what other people are willing to do for you without
getting paid for it.
in the case of VMD (and the same goes for Pizza.py) i firmly believe
that it is worth the effort of learning how to use them well. it will help
you so much more in the long run, that avoiding to invest the effort
now is just wasting (not only) your time.
axel.