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[lammps-users] Issues with Restart Command


From: MASATO KOIZUMI <mkoizumi@...3709...>
Date: Thu, 26 Apr 2018 22:54:44 -0700

Dear LAMMPS Users,

Hello All. 

I am currently experiencing an issue with the restart command.

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