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Re: [lammps-users] Fwd: atoms lost even i used fix wall/reflact command
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Re: [lammps-users] Fwd: atoms lost even i used fix wall/reflact command


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 17 Jul 2017 10:00:21 -0400

On Mon, Jul 17, 2017 at 9:49 AM, Mathur Nil <nilmathur786@...24...> wrote:
>
> ---------- Forwarded message ----------
> From: Mathur Nil <nilmathur786@...24...>
> Date: Mon, Jul 17, 2017 at 7:05 PM
> Subject: Re: [lammps-users] atoms lost even i used fix wall/reflact command
> To: Axel Kohlmeyer <akohlmey@...24...>
>
>
> Thanks for quick reply,
>
> I equilibrated crystal at 300K with periodic boundary condition. now I used
> last dump configuration of equilibrated crystal and want to heat up to
> around 1500K. but during this, I used fix wall/refelct command.
>
> boundary f f p
>
> fix 11 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE units lattice
>
> I can use that command if and only if I have fix boundary condition in a
> certain direction on which I want to apply that command. The problem is when
> I start my simulation, it shows that my atoms are lost.

if you want to have fixed boundaries, why don't you start with them right away?
you are making your life needlessly complicated. when changing
boundary conditions, you will need to re-equilibrate, so your previous
periodic equilibration is mostly a wasted effort.

also, in your original e-mail you said that you wanted to keep x- and
y- dimensions constant and let the system expand in z-direction.
this is _not at all_ what you are inducing by making the changes you
did. your changes set up a completely different system, i.e. rod that
is replicated in z-directions (but still with fixed box dimensions).

 why don't you just keep all periodic boundaries and apply fix npt and
couple it only to the z direction?

regardless of whether you have fixed boundary conditions or periodic
boundary conditions, the box dimensions are unchanged unless you issue
a command or fix that can change them. perhaps you need to read up
some more about what boundary conditions mean in LAMMPS.

axel.

>
> sorry i reply personally.
>
>
>
> On Mon, Jul 17, 2017 at 6:46 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>> On Mon, Jul 17, 2017 at 8:50 AM, Mathur Nil <nilmathur786@...24...>
>> wrote:
>> > hello all,
>> >
>> > I have a problem regarding atoms lost. I equilibrated crystal at a
>> > certain
>> > temperature with periodic boundary condition. then I want to heat that
>> > crystal by applying fixed boundary condition in x and y and periodic in
>> > the
>> > z direction and I also used fix wall/reflect command so it only expands
>> > in
>> > the z direction. but while I start simulation atoms lost is showing. I
>> > am
>> > not able to figure it out why it is happening. please, can anyone tell
>> > me my
>> > mistakes in above procedure? I tried a lot to figure out.
>>
>> difficult to say. there is not much useful information here. the usual
>> approach for issues with lost atoms, is to dump configurations
>> frequently and visualize the results to see what it happening.
>>
>> but it almost sounds like you are confusing fixed dimensions with
>> fixed boundaries.
>>
>> axel.
>>
>> >
>> >
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>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.