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Re: [lammps-users] fix rigid/npt with triclinic
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Re: [lammps-users] fix rigid/npt with triclinic

From: Trung Nguyen <ndactrung@...24...>
Date: Sun, 27 Aug 2017 23:14:29 -0500

Hi Wes,

it's possible to support triclinic boxes for fix rigid/npt and rigid/nph either by following the reference cited the fix rigid doc (Kamberaj et al), or by borrowing what is implemented in fix nh for updating the full box dimension tensor.

However, please note that fix rigid/npt and rigid/nph with triclinic boxes would be mostly useful for the cases where you only have rigid bodies in the system. For systems of polymer-grafted rigid bodies like yours, I think the workaround along the line Axel suggested would work to the similar effect:

# assuming you're having a triclinic box setup

group nanoparticles type 1
group tethers type 2
fix 1 nanoparticles rigid/nvt temp ...
fix 2 tethers npt temp 1.0 1.0 1.0 xy 1.0 1.0 10.0 ...  dilate all
fix_modify 2 press thermo_press

The reason that it would work is that the simulation triclinic box is to be barostatted by the fix npt, which uses the system pressure tensor as feedback.

Hope it helps,

On Sun, Aug 27, 2017 at 3:34 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:

On Thu, Aug 24, 2017 at 3:15 PM, Wes Barnett <w.barnett@...668...> wrote:
fix rigid/npt has not yet been implemented to work with triclinic boxes in LAMMPS. I'm interested if any users or devs have any kind of implementation of this feature in their own code.

​since nobody has responded publicly, i'd like to add, that i am not aware that this is on the TODO list of any LAMMPS developer. i am copying Trung, who was involved in the nose-hoover based rigid body integrators.

you may look into the regular fix rigid integrators for inspiration.​ the code structure is very similar, watch out for differences in variable names.

I've got a system of 32 nanoparticles functionalized with polymer grafts. The NP's are each a collection of points where the center interacts with the system using lj/expand and the grafts are tethered to non-interacting points on the surface. The surface points and center of each nanoparticle compose a rigid body.

I'm interested in allowing the nanoparticles to pack efficiently in the periodic box. If isotropic pressure coupling is used, their movement is restricted. When I use anisotropic pressure coupling I can already see some changes in packing. We're thinking it would be worthwhile to explore using a triclinic box if there is an implementation available using fit rigid/npt.

​as a workaround, you may try the following (off the top of my head, check docs for details):

group none type 999
fix 1 all rigid/nvt ....
fix 2 none nph ... dilate none
fix_modify 2 press thermo_press




James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering

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