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


From: portem4 <portem4@...707...>
Date: Wed, 23 May 2018 00:33:32 -0400

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.

Sincerely,

Malcolm Porterfield