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Re: [lammps-users] Issues with Restart Command
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Re: [lammps-users] Issues with Restart Command


From: MASATO KOIZUMI <mkoizumi@...3709...>
Date: Fri, 27 Apr 2018 14:17:38 -0700

Dear Dr. Axel Kohlmeyer,

Hello Dr. Kohlmeyer. Thank you for your e-mail.

Actually, the portion of my original input file that specifies the fix commands is:

fix   1 all langevin 1.0 1.0 2.0 542305
fix   2 all press/berendsen iso 0.0 0.0 10.0
fix   3 all nve
thermo     1000
thermo_style custom step temp pe etotal epair pxx pyy pzz lx ly lz
run 100000
unfix 2

fix 4 all deform 1 x variable v_displace v_rate y volume z volume remap v

Therefore, press/berendsen is unfixed prior to the start of uniaxial deformation such that I am performing the stress strain simulation under NVT ensemble.

Once again, thank you so much for your time and effort.

Sincerely,

Masato Koizumi





On Fri, Apr 27, 2018 at 9:21 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Fri, Apr 27, 2018 at 1:54 AM, MASATO KOIZUMI <mkoizumi@...3709...> wrote:
> Dear LAMMPS Users,
>
> Hello All.
>
> I am currently experiencing an issue with the restart command.

no, i don't think so. it looks to me, that you are using restart
correctly, but that the two inputs for the original and the restarted
runs are inconsistent. in fact, the first run is bogus, as you seem to
have two fixes active that modify the same simulation cell parameters
and that is a *major* mistake. doesn't LAMMPS print a warning about
it?

axel.

>
> I am performing a uniaxial elongation of a simulation box that contains
> polymer chains.
>
> The simulation box are being deformed via fix deform command where I
> specified an equation that describes the rate and displacement of the box
> length.
>
> After carefully reading the run command in the documentation, I am still
> obtaining an error using the restart command. I used the start/stop keywords
> since my fix deform command changes over time. Therefore, I always output
> restart files after every segmented runs.
>
> When I restart my simulation using one of the outputted restart files, I am
> obtaining the exact thermodynamic quantities at the start of the restart
> simulation.
>
> However, after one time interval, I obtain incorrect instantaneous
> simulation box length and other thermodynamic parameters compared to the
> parameters that were to be obtained had the entire simulation was completed.
>
> If I further increased the number of chains and atoms inside the simulation
> box, I would obtain FENE bond too long.
>
> Moreover, I am using the same number of processors in both of my restart and
> in my original input file.
>
> I was curious if anyone had experienced this issue.
>
>
>
> I have displayed a portion of my original script:
>
> units              lj
> atom_style         full
> neighbor           0.36 bin
> neigh_modify       delay 2
> pair_style         lj/cut 2.5
> bond_style hybrid harmonic fene
> special_bonds    lj  0.0 1.0 1.0
> read_data FJC_Single_HET
>
> pair_coeff         * * 1.0 1.0 2.5
> bond_coeff 1*2 fene 30.0 1.5 1.0 1.0
> bond_coeff 3 harmonic 1000.0 1.20
> pair_modify        shift yes
> timestep        0.010
> reset_timestep 0
>
> fix   1 all langevin 1.0 1.0 2.0 542305
> fix   2 all press/berendsen iso 0.0 0.0 10.0
> fix   3 all nve
>
> fix 4 all deform 1 x variable v_displace v_rate y volume z volume remap v
>
> fix 5 all ave/time 4 25 100 c_p[1] c_p[2] c_p[3] c_p[4] c_p[5] c_p[6] file
> press.1
>
> dump    1 all custom 100000 *_Monomer_Coordinates id type x y z ix iy iz
>
> restart 1000000 *_Strain_Rate.restart
>
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
>
>
> And a portion of my restart script if I were to use
> 3000000_Strain_Rate.restart
>
> processors 2 2 1
> units              lj
> atom_style         full
> read_restart 3000000_Strain_Rate.restart
>
> neighbor           0.36 bin
> neigh_modify       delay 2
> pair_style         lj/cut 2.5
> bond_style hybrid harmonic fene
> special_bonds    lj  0.0 1.0 1.0
> pair_coeff         * * 1.0 1.0 2.5
> bond_coeff 1*2 fene 30.0 1.5 1.0 1.0
> bond_coeff 3 harmonic 1000.0 1.20
> pair_modify        shift yes
>
> timestep        0.010
>
> fix   1 all langevin 1.0 1.0 2.0 542305
> fix   3 all nve
> thermo     1000
> thermo_style custom step temp pe etotal epair pxx pyy pzz lx ly lz
>
> fix 4 all deform 1 x variable v_displace v_rate y volume z volume remap v
> compute p all pressure thermo_temp
> fix 5 all ave/time 4 25 100 c_p[1] c_p[2] c_p[3] c_p[4] c_p[5] c_p[6] file
> press.1
> dump    1 all custom 100000 *_Monomer_Coordinates id type x y z ix iy iz
>
> restart 1000000 *_Strain_Rate.restart
>
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
> run 1000000 start 0 stop 10000000
>
>
> I would greatly appreciate if I could request for any suggestions. Thank
> you.
>
> Sincerely,
>
> Masato Koizumi
>
>
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--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.