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Re: [lammps-users] 'master list distance cutoff' changes strangely after restarting the simulation
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Re: [lammps-users] 'master list distance cutoff' changes strangely after restarting the simulation


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 6 Sep 2017 08:53:03 -0400



On Wed, Sep 6, 2017 at 6:22 AM, Zhuangli cai <980046700@...1306...4...> wrote:
Dear lammps user:

I want to compute the gyration of radius of a single PE chain using airebo potential. After a simulation, I continued the simulation by a read_restart command. Then a strange thing occured that the 'master list distance cutoff' changes from 12.2 to 8 in the log file and the gyration of radius also changed a lot. I did not change the pair cutoff and the neighbor artificially.

​thanks for being so diligent and noticing this and also *many* thanks for providing a suitable complete(!) input deck to reproduce this.
we will have to take a closer look at what is causing this. this is something that should not happen.

there is a very simple workaround: you should move the "pair_style" command _after_ the read_restart command. that will initialize the cutoffs correctly.

axel.

 

This is a part of the log information of previous simulation:
LAMMPS (1 Mar 2016-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
Reading data file ...
  orthogonal box = (0 0 0) to (100 100 100)
  2 by 2 by 2 MPI processor grid
  reading atoms ...
  206 atoms
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12.2
  ghost atom cutoff = 12.2
  binsize = 6.1, bins = 17 17 17
Setting up cg style minimization ...
  Unit style    : metal
Memory usage per processor = 5.83205 Mbytes


This is a part of the log information of restart simulation:
LAMMPS (1 Mar 2016-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
Reading restart file ...
  restart file = 1 Mar 2016-ICMS, LAMMPS = 1 Mar 2016-ICMS
  orthogonal box = (0 0 0) to (100 100 100)
  2 by 2 by 2 MPI processor grid
  206 atoms
Resetting global state of Fix nvt Style nvt from restart file info
Neighbor list info ...
  1 neighbor list requests
  update every 5 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8
  ghost atom cutoff = 8
  binsize = 4, bins = 25 25 25
Setting up Verlet run ...
  Unit style    : metal
  Current step  : 40000000
  Time step     : 0.0005
Memory usage per processor = 4.10673 Mbytes


All the settings of restart simulation are the same as those of previous simulation. The input files and data file of previous and  restart simulations are all attached.

Any advice is welcome and I will appreciate it very much.
    

regards
Zhuangli Cai
                                     

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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.