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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: portem4 <portem4@...707...>
Date: Wed, 23 May 2018 11:55:47 -0400

Thank you for the clarification.


Malcolm Porterfield

On 2018-05-23 11:40, Axel Kohlmeyer wrote:
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@...24... [3]
College of Science & Technology, Temple University, Philadelphia PA,
International Centre for Theoretical Physics, Trieste. Italy.