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Re: [lammps-users] fix atoms in simulation box
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Re: [lammps-users] fix atoms in simulation box

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 29 Jul 2017 08:31:19 -0400

On Sat, Jul 29, 2017 at 1:13 AM, Mathur Nil <nilmathur786@...12...24...> wrote:
Dear all,
this is the sample script,

region box block 0 20 0 20 0 40
region box1 block 0 20 0 20 0 20 
region box2 block 0 20 0 20 20 40

group 1 region box1
group 2 region box2

1)    fix 4 2 npt temp.......
2)    fix 4 all npt temp.......(what is the difference between 1&2)

please assume that i have written whole script. i am writting only some points

then i created atoms in these box1 and box2 region. 1
1)If i apply barostaste or thermostate to only one region by excluding other atoms from time integration so what is the meaning of that? if i have periodic boundary condition. this will fix the another region atoms  

2)  or if i apply barostate or thermostate to whole simulation box and want fix other half atoms . i tried fix setforce command but still not able to fix the other half

the problem is where it apply barostate/ thermostate it apply on whole simlation box or only on that region which is time integrated? 

​please note the following:

- fix npt applies a barostat, a thermostat, and ​does time integration of atoms
- a barostat always applies to the entire box, and there can only be one fix active that modifies the box dimension. whether the box expansion also scales atom positions or not or partially can usually be selected with a flag
- time integration and thermostat fixes are only applied to atoms in the fix group (also for other fixes that do thermostatting and/or time integration)
- if you want to immobilize atoms (please do not use the term "fix" in this context as it can be easily confused with atoms that a fix is applied to), you can either exclude them from time integration or you have to make sure that both, velocities and forces, are zero.
- all of the above is described in the LAMMPS manual and has been discussed many times on the mailing list and thus can be found and explained in the mailing list archives, so please make an effort to learn from the material at hand.



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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.