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Re: [lammps-users] out of range atoms - cannot compute PPPM
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Re: [lammps-users] out of range atoms - cannot compute PPPM


From: Jana Pritam <pritam.jana@...3660...>
Date: Mon, 19 Jun 2017 17:00:18 +0000

Hi Arun,
The box dimension is 52*54*70 in real unit and I used 384 water molecules. So the number density of water is 0.002 Angstroms ^-3.
Best
Pritam
On 19 Jun 2017, at 19:09, S Arun Srikant Sridhar <ss3763@...1685...> wrote:

Hi Pritam

Can you please mention what density you are starting from ?

It would be helpful if you post the  output from lammps

Arun

On 06/19/17, Jana Pritam <pritam.jana@...3660...> wrote:

Dear all,

I tried to overcome this problem by changing timestep, check the initial configuration, neighbour skin and previous suggestions from Axel. What I understood from the video of the equilibration, during the NPT simulations when the box squeezed and equivalent to the  length of water molecules, the error appears. When I was running NVT, there is no such problem. Could you please make some comment which other things I should check? I add here input script. 

newton          on
variable         T equal 298.0
variable      T1 equal 360.0
variable         DT  equal 0.25
timestep        ${DT}
thermo          1
units       real
atom_style        full
dimension  3
boundary          p p p
kspace_style    pppm 1.0e-4
include            system_water.in.init
read_data       system_water.data
include           system_water.in.settings
group             spce type 1 2 
neighbor         3.0 bin
neigh_modify    every 1 delay 1 check yes
velocity          all create ${T1} 19289 mom yes rot yes dist gaussian
unfix fShakeSPCE
minimize        1.0e-4 1.0e-4 10000 100000
fix                  fShakeSPCE all shake 0.0001 20 0 b 1 a 1
fix     NVT all nvt temp ${T1} ${T1} 100.0
dump            dump_NVT all atom 10 all_NVT.dump
run   1000
fix   NVT all nvt temp ${T1} $T 100.0
run    1000
unfix     NVT
fix               NPT all npt temp $T $T 100.0 iso 1.0 1.0 100.0
run50000
clear

 Best 
Pritam
-------------

On 19 Jun 2017, at 16:35, Axel Kohlmeyer <akohlmey@...24...> wrote:



On Mon, Jun 19, 2017 at 6:54 AM, Mohammad Rafat Sadat<msadat@...3324...>wrote:
I beg to differ on that. It may not be the only solution but it is a solution which worked for me on several occasions (used neighbor 3.0 bin instead of 1.0, correct me if this is a wrong thing to do) .

increasing the neighborlist skin ​sounds like workaround ​that avoids the symptom, but may not solve the problem. what you need to understand is, *why* atoms move so fast, that they move too large a distance between time steps. for that it is crucial to know, whether this only happens at the beginning of a run or also during a run. absolute values for run parameters are not a good handle to differentiate between "good" and "bad", as what is a good choice is determined by the system itself, its potentials, constituent elements, simulation parameters (time integration fix, time step, temperature, pressure etc.) and more.

in general, it is often a bad idea to start a simulation immediately with fix npT. the nose-hoover thermostat and barostat algorithms are good for maintaining the desired ensemble, but are often ill suited to get you there (efficiently). as arun hinted at, i have discussed this in great detail multiple times in the past, and you should be able to find those e-mails in the mailing list archives.

​axel.​



If you increase the skin distance then the atoms will have less probability to move out of the processor sub domain and getting 'lost'. However, too much increase in skin distance may not be a good idea. Possibility of bad geometry, forcefield parameters, too large timesteps shouldn't be neglected as well. I believe there are other solutions listed in the past. Section error page clearly outlines this problem:

"Out of range atoms - cannot compute PPPM
One or more atoms are attempting to map their charge to a PPPM grid point that is not owned by a processor. This is likely for one of two reasons, both of them bad. First, it may mean that an atom near the boundary of a processor’s sub-domain has moved more than 1/2 the neighbor skin distance without neighbor lists being rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the neigh_modify command. The safest settings are “delay 0 every 1 check yes”. Second, it may mean that an atom has moved far outside a processor’s sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc."




Mohammad Rafat Sadat
Graduate Assistant (PhD candidate)
Department of Civil Engineering and Engineering Mechanics,
University of Arizona,
PO Box 210072 • 1209 E. Second Street, Room 207A, Tucson, AZ 85721

On Mon, Jun 19, 2017 at 3:35 AM, ss3763<ss3763@...1685...>wrote:
 Increasing the neighbour skin distance is  not the solution. 

Please refer to the archives both of you. 


Arun 



Sent from my T-Mobile 4G LTE Device
-------- Original message --------
From: Mohammad Rafat Sadat <msadat@...3324...>
Date: 6/19/2017 06:21 (GMT-05:00)
To: ss3763 <ss3763@...1685...>
Cc: Jana Pritam <pritam.jana@...3660...>, LAMMPS Users Mailing List <lammps-users@...42...e.net>
Subject: Re: [lammps-users] out of range atoms - cannot compute PPPM

There are indeed archived solutions of this common problem. The very typical solution is to increase the neighbor skin distance. 

Mohammad Rafat Sadat
Graduate Assistant (PhD candidate)
Department of Civil Engineering and Engineering Mechanics,
University of Arizona,
PO Box 210072 • 1209 E. Second Street, Room 207A, Tucson, AZ 85721

On Mon, Jun 19, 2017 at 3:10 AM, ss3763<ss3763@...1685...>wrote:
Hi again. 

This is expected during equilibration. 

Now question is how to equilibrate the system.

Again I would ask you please refer to the archives for the solutions. 

There are good suggestions by Dr.Axel.

Good luck
Arun. 




Sent from my T-Mobile 4G LTE Device
-------- Original message --------
From: Jana Pritam <pritam.jana@...3660...>
Date: 6/19/2017 04:58 (GMT-05:00)
To: LAMMPS Users Mailing List <lammps-users@...42...e.net>
Subject: Re: [lammps-users] out of range atoms - cannot compute PPPM

Hi Arun, 
Thank you very much. I checked the initial geometry and the box dimension. They are fine. What I understood from the simulations, when I run with NVT, there is no such kind of error. When I use NPT simulations, volume of the box is changed to obtain the required pressure and the error appears. 
Best
Pritam
-----
On 18 Jun 2017, at 18:03, S Arun Srikant Sridhar <ss3763@...1685...> wrote:

Hi Pritam. 

Please search the archives for the solutions. 

Check the initial geometry and observe thermodynamic outputs and the box dimensions

Arun 


On 06/18/17,Jana Pritam<pritam.jana@...3660...> wrote:
Dear all,
I am using SPCE/fw water model for NPT simulation with periodic boundary condition along x,y,z. I use fix shake command. I obtain an error with "out of range atoms - cannot compute PPPM”
Could you please help me to overcome this problem? If you need more information I will be happy to supply it.
Best
Pritam
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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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