LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
[lammps-users] Restart Command leading to Bad Dynamics
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[lammps-users] Restart Command leading to Bad Dynamics


From: MASATO KOIZUMI <mkoizumi@...3709...>
Date: Sun, 6 May 2018 17:18:22 -0700

Dear Dr. Axel Kohlmeyer and LAMMPS Users,

Hello Dr. Kohlmeyer. Thank you for your advice. I am sure that the restart issue is not due to the first run where I have fix langevin and fix press/berendsen since this initial run is meant to relax the simulation box. Nevertheless, this is a short run (and LAMMPS does not print any WARNING messages) and not part of the actual dynamics of the simulation and the first restart file is printed during the second run where the actual deformation is applied.

My original simulation works fine, but in my restart simulation which reads the restart file from a selected restart file, the LAMMPS terminates due to bad dynamics (FENE Bond too long). (I even eliminated the first run where I have two fixes, but it did not change anything regarding bad dynamics.)

I am not sure why the restart simulation can not replicate the original simulation, when in fact the original simulation works fine. I am confident that I am using the restart command correctly and all of the required commands are reiterated after the read_restart command.

Therefore, I would greatly appreciate if I could request for any suggestions for the bad dynamics due to the restart command. Thank you so much for your time and effort.

In case, I have displayed a portion of my original and restart scripts. 

Sincerely,

Masato Koizumi


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 0.043898_FJC_Single_HET_Strand_Length_4_Harmonic_Force_Probe
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
thermo     1000
thermo_style custom step temp pe etotal epair pxx pyy pzz lx ly lz
run 100000
unfix 2
# Store final simulation box length for strain calculation
variable tmp equal "lx"
variable L0 equal ${tmp}
print "Initial Length, L0: ${L0}"
# Perform Deformation
reset_timestep 0
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_Periodic_200K.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



Restart Script:

units              lj
atom_style         full
read_restart 2000000_Strain_Rate_Periodic_200K.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
# Respecify the previous simulation box length for strain calculation
variable L0 equal 14.136564
print "Initial Length, L0: ${L0}"
# Resume Deformation
fix 4 all deform 1 x variable v_displace v_rate y volume z volume remap v
dump    1 all custom 100000 *_Monomer_Coordinates id type x y z ix iy iz
restart 1000000 *_Strain_Rate_Periodic_200K.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


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
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> lammps-users mailing list
> lammps-users@...12...396...sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>



--
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.