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Re: [lammps-users] Problem with ave/time and ave/chunck
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Re: [lammps-users] Problem with ave/time and ave/chunck


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 27 Jun 2017 14:38:04 -0400



On Tue, Jun 27, 2017 at 12:49 PM, Hasan, Mohammad [mihasan] <M.Hasan4@...6600...> wrote:

Thanks for the immediate response,


I tried micelle example and it worked. It seems the problem occurs when the simulation configuration is retrieved from a restart file.


I attached the restart file and the input code, can someone please confirm if the problem occurs on their machine?

​emailing restart files is not a good idea. they are in general not portable betwe​en different compiled LAMMPS versions and between platforms.
a data file would be better. ...and you will probably find, that when you restart from a data file, you will get the output files you desire. the same will happen, if you do a "reset_timestep 0", like it is done in the micelle example before defining the averaging fixes.

axel.


 


Thank you very much,

M. Hasan


From: Axel Kohlmeyer <akohlmey@...24...>
Sent: 27 June 2017 16:12
To: Hasan, Mohammad [mihasan]
Cc: lammps-users@...396...sourceforge.net
Subject: Re: [lammps-users] Problem with ave/time and ave/chunck
 
On Tue, Jun 27, 2017 at 10:57 AM, Hasan, Mohammad [mihasan]
<M.Hasan4@...5925...00...> wrote:
> Dear all,
>
>
>
> I am having a problem in outputting data per chunk. The problem is that the
> generated output files (generated by either ave/time or ave/chunk commands)
> are empty although they shouldn’t be. I am using LAMMMPS version
> 31-March-2017.
>
>
>
> The input code is given below:
>
>
>
> ###
>
> read_restart Restart.file
>
> change_box all z final -57.5 137.5
>
>
>
> pair_style lj/cut/coul/long 13
>
> pair_modify tail yes
>
> kspace_style pppm 1.0e-5
>
>
>
> neighbor 2.0 bin
>
> neigh_modify delay 10 check yes
>
>
>
> region EDGE block 1.2 38.5 1.2 38.5 77.5 78.5
>
> delete_atoms region EDGE mol yes
>
>
>
> compute HMOL all chunk/atom molecule
>
> compute MSD all msd/chunk HMOL
>
>
>
> fix TEMP all nvt temp 300 300 8
>
>
>
> fix 1 all ave/time 1 1 1 c_MSD[*] file MSD.out mode vector
>
> fix 2 all ave/chunk 1 1 1 HMOL vz file tmp.vz
>
>
>
> timestep 2
>
> run 100
>
> ###
>
> Any idea on why this happens?

no.

when i add your computes and ave fixes to the micelle example of the
LAMMPS distribution, and run the input with the latest LAMMPS version
(i.e. 23 June 2017), i do get output files.

axel.

>
>
>
> Thank you very much,
>
> M. Hasan
>
>
>
>
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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
The Homepage of Axel Kohlmeyer


College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.