shake

Dear lammps-users

I have written a class to remove or add molecules during simulation. Now I want to use shake for this molecules. Which methods defined in fix_shake.cpp I have to call in my class to adjust the shake lists and clusters for deleted and added molecules? Is it that straight forward or much more complicated?

Thank you very much.
Best regards
Sabine

There are no such methods in fix shake. You'd have to add them.
No one has ever wanted to do that before.

Steve

The same question you posted also applies to other fixes like "fix
rigid". Creating new molecules might also effect group membership and
computes. Solving your problem in a general way might be difficult.

I remember you proposed writing a GCMC fix for lammps a few months
ago. This sounds like a really important contribution to LAMMPS.
Please don't give up just because you can not solve this minor
technical hurdle.

Users can always use stiff harmonic constraints and small time steps.
In addition, users could write a for loop which periodically runs
LAMMPS for a few hundred timesteps, and invokes the "group" and "fix
shake" (or rigid, etc..) commands to update the list of atoms affected
by each fix. This seems like a reasonable concession that would
hopefully not introduce significant artifacts or slow down the
simulation too much.

  For me the big question is: How general is this? Could this fix be
used for multiple species of molecules, or only for water?

  Anyway, thanks for working on this, and don't give up.
Cheers!

Andrew

Thank you Andrew

Andrew Jewett <[email protected]…24…> 10/3/2012 11:53 PM >>>
The same question you posted also applies to other fixes like “fix
rigid”. Creating new molecules might also effect group membership and
computes. Solving your problem in a general way might be difficult.

I remember you proposed writing a GCMC fix for lammps a few months
ago. This sounds like a really important contribution to LAMMPS.
Please don’t give up just because you can not solve this minor
technical hurdle.

Users can always use stiff harmonic constraints and small time steps.
In addition, users could write a for loop which periodically runs
LAMMPS for a few hundred timesteps, and invokes the “group” and “fix
shake” (or rigid, etc…) commands to update the list of atoms affected
by each fix. This seems like a reasonable concession that would
hopefully not introduce significant artifacts or slow down the
simulation too much.

I am currently trying this approach.

For me the big question is: How general is this? Could this fix be
used for multiple species of molecules, or only for water?

At the moment it is only for water. It could be generalized to multiple species of molecules, but at the moment I have no resources to do so.

Regards

Sabine

Anyway, thanks for working on this, and don’t give up.
Cheers!

Andrew

On Mon, Oct 8, 2012 at 10:38 AM, Sabine Leroch <[email protected]>

  For me the big question is: How general is this? Could this fix be
used for multiple species of molecules, or only for water?

At the moment it is only for water. It could be generalized to multiple
species of molecules, but at the moment I have no resources to do so.

Either way, if you don't mind, please post your code when you get it
working, (even if it only works on a particular system). It sounds
cool.
Cheers and good luck.
Andrew