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Re: [lammps-users] Molecules and Fixed Boundary Conditions
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Re: [lammps-users] Molecules and Fixed Boundary Conditions

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 23 May 2018 11:40:59 -0400

On Wed, May 23, 2018 at 12:33 AM, portem4 <portem4@...707...> wrote:
Hello All,

   I would like to know if it is possible in LAMMPS to delete entire molecules as they move across a fixed boundary. Currently I am simulating the explosive boiling of water on a gold substrate. I constrain the water using fix RATTLE with bond and angle constraints which results in the creation of 528 frozen angles (which makes sense because I have 528 water molecules). I have periodic boundary conditions in the x and y direction while I have a fixed boundary condition in the z-direction. As the water molecules increase in temperature they move in the positive z-direction for a time until they cross the positive z-boundary of my simulation box. At that point I get the error: Shake atoms 235 567 987 missing on proc 0 at step 35699. I believe I get this error because parts of molecules are being deleted resulting in molecule fragments. Fix evaporate provides a work around to this because of its molecule flag but I am curious if there is a simpler way to get rid entire water molecules as they cross a fixed boundary (in my case the positive z-boundary). I am using the 5-Sep-17, 64-bit Windows version of LAMMPS. Any insight will be greatly appreciated.

​fix evaporate is the tool to use.​
​ when you tell LAMMPS to just ignore lost atoms, it cannot remove entire molecules and their corresponding topology data, because that information is already lost by the time the check is done.



Malcolm Porterfield

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Dr. Axel Kohlmeyer  akohlmey@...92......
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.