Re: [lammps-users] out of range atoms

I am attaching my input script for spce/water model if it will help

# SPC/E water box benchmark

units real

atom_stylefull

boundary p p p

pair_style lj/charmm/coul/charmm 6 9

#kspace_style ewald 1e-4

bond_styleharmonic

angle_style harmonic

read_data data.spce

replicate 6 6 10

neighbor 2.0 bin

neigh_modifyevery 1 delay 10 check yes

minimize 1.0e-4 1.0e-6 100 1000

compute 1 all pe

variable e equal c_1/360

thermo_style custom step density temp press pe ebond eangle v_e lx ly lz

thermo 100

reset_timestep 0

timestep 2

fix 1 all shake 0.0001 20 0 b 1 a 1

fix mom all momentum 1 linear 1 1 1

velocity all create 300 432567

fix 2 all npt temp 300 300 100 iso 1 1 1000

run 100000

unfix 2

reset_timestep 0

fix 2 all nvt temp 300 300 100

#iso 1 1 1000

dump 1 all custom 2000 dump_spce.lammpstrj id type x y z q

dump_modify 1 sort id

run 20000000

quit

Good luck

Arun

On 06/20/17, Jana Pritam <pritam.jana@...6934....> wrote:

Hi Arun,

Thanks for your help. I have attached log file where you will see the minimization and NVT part. lammps_output.png is the NPT part where the error appears.

Best

Pritam

-------------------

From: S Arun Srikant Sridhar <ss3763@...1685...>
Sent: 19 June 2017 20:06:57
To: Jana Pritam
Cc: lammps-users@lists.sourceforge.net
Subject: Re: [lammps-users] out of range atoms - cannot compute PPPM

Also the output from lammps.

after minimization, thermodynamic outputs

thermo_style custom step density temp press pe ke

Thanks

Arun

On 06/19/17, Jana Pritam <pritam.jana@...6933...0...> wrote:

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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From:	"S Arun Srikant Sridhar" <ss3763@...1685...>
Date:	Tue, 20 Jun 2017 11:14:40 -0400