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