LAMMPS Stops Printing Files after 5.441x10^7 Timesteps

Nicole_Fortoul · November 3, 2014, 6:48pm

Hello Everyone,

I am somewhat new to LAMMPS. I am simulation a SNARE protein bundle consisting of 4 alpha helices. I am running this system in STAMPEDE currently. I am performing displacement control simulations on two C-terminal beads of the alpha helices. I hold 2 beads fixed. After 10^7 timesteps I move one of the beads and hold it fixed again, wait 10^7 timesteps and repeat. The strange thing is, after a total of 5.441x10^7 timesteps the simulation stops printing to any files (.xyz and a log file). No errors show up. It just stops printing. However, the simulation continues to run on STAMPEDE. I tried restarting the simulation at different points in the trajectory and it always stops at 5.441x10^7 timesteps. Because there are no errors and the simulation continues to run, I have no idea what could be happening.

I have provided the input script below:

Coarse Grained DNA AT

Simulation Setup

units real
dimension 3
boundary f f f
atom_style full

Styles of Potentials and bonds

pair_style hybrid lj/cut 15.0 table linear 1000

bond_style hybrid harmonic table linear 10000

Read in data about structure

read_data data_bundle_MJ_DC_15A_disp.data

Read in Pair Coefficients for LJ (Note eij is -eij)

pair_coeff 1 1 lj/cut 0.2142 4.4
pair_coeff 1 2 lj/cut 0.1098 4.7
pair_coeff 1 3 lj/cut 0.1206 4.8
pair_coeff 1 4 lj/cut 0.1152 4.7
pair_coeff 1 5 lj/cut 0.1170 4.7
pair_coeff 1 6 lj/cut 0.1062 4.6
pair_coeff 1 7 lj/cut 0.1188 4.9
pair_coeff 1 8 lj/cut 0.0702 4.8
pair_coeff 1 9 lj/cut 0.0594 4.2
pair_coeff 1 10 lj/cut 0.0558 4.0
pair_coeff 1 11 lj/cut 0.0270 4.4
pair_coeff 1 12 lj/cut 0.0234 4.3
pair_coeff 1 13 lj/cut 0.0126 4.5
pair_coeff 1 14 lj/cut 0.0018 4.6
pair_coeff 1 15 table pair_1_15.table modLJ
pair_coeff 1 16 table pair_1_16.table modLJ
pair_coeff 1 17 lj/cut 0.0648 4.6
pair_coeff 1 18 table pair_1_18.table modLJ
pair_coeff 1 19 table pair_1_19.table modLJ
pair_coeff 1 20 lj/cut 0.0324 4.4
pair_coeff 2 2 lj/cut 0.1260 5.0
pair_coeff 2 3 lj/cut 0.1494 5.0
pair_coeff 2 4 lj/cut 0.1188 5.0
pair_coeff 2 5 lj/cut 0.1260 5.0
pair_coeff 2 6 lj/cut 0.0918 4.8
pair_coeff 2 7 lj/cut 0.1314 5.2
pair_coeff 2 8 lj/cut 0.1008 5.1
pair_coeff 2 9 lj/cut 0.0486 4.5
pair_coeff 2 10 lj/cut 0.0306 4.3
pair_coeff 2 11 lj/cut 0.0198 4.7
pair_coeff 2 12 table pair_2_12.table modLJ
pair_coeff 2 13 lj/cut 0.0108 4.8
pair_coeff 2 14 table pair_2_14.table modLJ
pair_coeff 2 15 table pair_2_15.table modLJ
pair_coeff 2 16 table pair_2_16.table modLJ
pair_coeff 2 17 lj/cut 0.0522 4.9
pair_coeff 2 18 table pair_2_18.table modLJ
pair_coeff 2 19 table pair_2_19.table modLJ
pair_coeff 2 20 lj/cut 0.0234 4.7
pair_coeff 3 3 lj/cut 0.1584 5.1
pair_coeff 3 4 lj/cut 0.1314 5.0
pair_coeff 3 5 lj/cut 0.1440 5.0
pair_coeff 3 6 lj/cut 0.1206 4.9
pair_coeff 3 7 lj/cut 0.1224 5.3
pair_coeff 3 8 lj/cut 0.1044 5.2
pair_coeff 3 9 lj/cut 0.0648 4.6
pair_coeff 3 10 lj/cut 0.0342 4.4
pair_coeff 3 11 lj/cut 0.0270 4.8
pair_coeff 3 12 lj/cut 0.0216 4.6
pair_coeff 3 13 lj/cut 0.0198 4.8
pair_coeff 3 14 lj/cut 0.0018 5.0
pair_coeff 3 15 table pair_3_15.table modLJ
pair_coeff 3 16 table pair_3_16.table modLJ
pair_coeff 3 17 lj/cut 0.0612 5.0
pair_coeff 3 18 lj/cut 0.0090 5.2
pair_coeff 3 19 table pair_3_19.table modLJ
pair_coeff 3 20 lj/cut 0.0342 4.8
pair_coeff 4 4 lj/cut 0.1332 5.0
pair_coeff 4 5 lj/cut 0.1458 5.0
pair_coeff 4 6 lj/cut 0.1206 4.8
pair_coeff 4 7 lj/cut 0.1080 5.2
pair_coeff 4 8 lj/cut 0.0882 5.1
pair_coeff 4 9 lj/cut 0.0666 4.5
pair_coeff 4 10 lj/cut 0.0234 4.3
pair_coeff 4 11 lj/cut 0.0270 4.7
pair_coeff 4 12 table pair_4_12.table modLJ
pair_coeff 4 13 lj/cut 0.0018 4.8
pair_coeff 4 14 table pair_4_14.table modLJ
pair_coeff 4 15 table pair_4_15.table modLJ
pair_coeff 4 16 table pair_4_16.table modLJ
pair_coeff 4 17 lj/cut 0.0234 4.9
pair_coeff 4 18 lj/cut -0.0000 5.1
pair_coeff 4 19 table pair_4_19.table modLJ
pair_coeff 4 20 lj/cut 0.0090 4.7
pair_coeff 5 5 lj/cut 0.1512 5.0
pair_coeff 5 6 lj/cut 0.1332 4.8
pair_coeff 5 7 lj/cut 0.1116 5.2
pair_coeff 5 8 lj/cut 0.0990 5.1
pair_coeff 5 9 lj/cut 0.0684 4.5
pair_coeff 5 10 lj/cut 0.0288 4.3
pair_coeff 5 11 lj/cut 0.0270 4.7
pair_coeff 5 12 lj/cut 0.0036 4.6
pair_coeff 5 13 lj/cut 0.0072 4.8
pair_coeff 5 14 table pair_5_14.table modLJ
pair_coeff 5 15 table pair_5_15.table modLJ
pair_coeff 5 16 table pair_5_16.table modLJ
pair_coeff 5 17 lj/cut 0.0324 4.9
pair_coeff 5 18 lj/cut 0.0072 5.1
pair_coeff 5 19 table pair_5_19.table modLJ
pair_coeff 5 20 lj/cut 0.0216 4.7
pair_coeff 6 6 lj/cut 0.1170 4.7
pair_coeff 6 7 lj/cut 0.0918 5.1
pair_coeff 6 8 lj/cut 0.0684 5.0
pair_coeff 6 9 lj/cut 0.0576 4.4
pair_coeff 6 10 lj/cut 0.0270 4.2
pair_coeff 6 11 lj/cut 0.0126 4.6
pair_coeff 6 12 table pair_6_12.table modLJ
pair_coeff 6 13 table pair_6_13.table modLJ
pair_coeff 6 14 table pair_6_14.table modLJ
pair_coeff 6 15 table pair_6_15.table modLJ
pair_coeff 6 16 table pair_6_16.table modLJ
pair_coeff 6 17 lj/cut 0.0108 4.8
pair_coeff 6 18 table pair_6_18.table modLJ
pair_coeff 6 19 table pair_6_19.table modLJ
pair_coeff 6 20 lj/cut 0.0090 4.6
pair_coeff 7 7 lj/cut 0.1152 5.4
pair_coeff 7 8 lj/cut 0.0882 5.3
pair_coeff 7 9 lj/cut 0.0486 4.7
pair_coeff 7 10 lj/cut 0.0450 4.5
pair_coeff 7 11 lj/cut 0.0036 5.0
pair_coeff 7 12 lj/cut 0.0018 4.8
pair_coeff 7 13 lj/cut 0.0036 5.0
pair_coeff 7 14 lj/cut 0.0180 5.1
pair_coeff 7 15 lj/cut -0.0000 5.0
pair_coeff 7 16 table pair_7_16.table modLJ
pair_coeff 7 17 lj/cut 0.0666 5.2
pair_coeff 7 18 lj/cut 0.0378 5.4
pair_coeff 7 19 table pair_7_19.table modLJ
pair_coeff 7 20 lj/cut 0.0666 5.0
pair_coeff 8 8 lj/cut 0.0810 5.2
pair_coeff 8 9 lj/cut 0.0360 4.6
pair_coeff 8 10 lj/cut 0.0396 4.4
pair_coeff 8 11 lj/cut 0.0162 4.8
pair_coeff 8 12 lj/cut 0.0144 4.7
pair_coeff 8 13 lj/cut 0.0252 4.9
pair_coeff 8 14 lj/cut 0.0198 5.0
pair_coeff 8 15 lj/cut 0.0144 4.8
pair_coeff 8 16 lj/cut 0.0126 5.0
pair_coeff 8 17 lj/cut 0.0540 5.0
pair_coeff 8 18 lj/cut 0.0450 5.2
pair_coeff 8 19 lj/cut 0.0090 5.2
pair_coeff 8 20 lj/cut 0.0450 4.8
pair_coeff 9 9 lj/cut 0.0216 4.0
pair_coeff 9 10 lj/cut 0.0144 3.8
pair_coeff 9 11 table pair_9_11.table modLJ
pair_coeff 9 12 table pair_9_12.table modLJ
pair_coeff 9 13 table pair_9_13.table modLJ
pair_coeff 9 14 table pair_9_14.table modLJ
pair_coeff 9 15 table pair_9_15.table modLJ
pair_coeff 9 16 table pair_9_16.table modLJ
pair_coeff 9 17 table pair_9_17.table modLJ
pair_coeff 9 18 table pair_9_18.table modLJ
pair_coeff 9 19 table pair_9_19.table modLJ
pair_coeff 9 20 table pair_9_20.table modLJ
pair_coeff 10 10 lj/cut 0.0522 3.6
pair_coeff 10 11 lj/cut 0.0072 4.0
pair_coeff 10 12 lj/cut 0.0018 3.9
pair_coeff 10 13 table pair_10_13.table modLJ
pair_coeff 10 14 lj/cut 0.0018 4.2
pair_coeff 10 15 table pair_10_15.table modLJ
pair_coeff 10 16 table pair_10_16.table modLJ
pair_coeff 10 17 lj/cut -0.0000 4.2
pair_coeff 10 18 table pair_10_18.table modLJ
pair_coeff 10 19 table pair_10_19.table modLJ
pair_coeff 10 20 table pair_10_20.table modLJ
pair_coeff 11 11 table pair_11_11.table modLJ
pair_coeff 11 12 table pair_11_12.table modLJ
pair_coeff 11 13 table pair_11_13.table modLJ
pair_coeff 11 14 table pair_11_14.table modLJ
pair_coeff 11 15 table pair_11_15.table modLJ
pair_coeff 11 16 table pair_11_16.table modLJ
pair_coeff 11 17 lj/cut 0.0054 4.7
pair_coeff 11 18 table pair_11_18.table modLJ
pair_coeff 11 19 table pair_11_19.table modLJ
pair_coeff 11 20 table pair_11_20.table modLJ
pair_coeff 12 12 table pair_12_12.table modLJ
pair_coeff 12 13 table pair_12_13.table modLJ
pair_coeff 12 14 table pair_12_14.table modLJ
pair_coeff 12 15 table pair_12_15.table modLJ
pair_coeff 12 16 table pair_12_16.table modLJ
pair_coeff 12 17 table pair_12_17.table modLJ
pair_coeff 12 18 table pair_12_18.table modLJ
pair_coeff 12 19 table pair_12_19.table modLJ
pair_coeff 12 20 table pair_12_20.table modLJ
pair_coeff 13 13 table pair_13_13.table modLJ
pair_coeff 13 14 table pair_13_14.table modLJ
pair_coeff 13 15 table pair_13_15.table modLJ
pair_coeff 13 16 table pair_13_16.table modLJ
pair_coeff 13 17 table pair_13_17.table modLJ
pair_coeff 13 18 table pair_13_18.table modLJ
pair_coeff 13 19 table pair_13_19.table modLJ
pair_coeff 13 20 table pair_13_20.table modLJ
pair_coeff 14 14 lj/cut 0.0108 4.8
pair_coeff 14 15 table pair_14_15.table modLJ
pair_coeff 14 16 table pair_14_16.table modLJ
pair_coeff 14 17 lj/cut -0.0000 4.8
pair_coeff 14 18 table pair_14_18.table modLJ
pair_coeff 14 19 table pair_14_19.table modLJ
pair_coeff 14 20 table pair_14_20.table modLJ
pair_coeff 15 15 table pair_15_15.table modLJ
pair_coeff 15 16 table pair_15_16.table modLJ
pair_coeff 15 17 lj/cut -0.0000 4.7
pair_coeff 15 18 lj/cut 0.0396 4.9
pair_coeff 15 19 lj/cut -0.0000 4.8
pair_coeff 15 20 table pair_15_20.table modLJ
pair_coeff 16 16 table pair_16_16.table modLJ
pair_coeff 16 17 lj/cut 0.0180 4.8
pair_coeff 16 18 lj/cut 0.0432 5.0
pair_coeff 16 19 lj/cut 0.0018 4.9
pair_coeff 16 20 table pair_16_20.table modLJ
pair_coeff 17 17 lj/cut 0.0720 4.9
pair_coeff 17 18 table pair_17_18.table modLJ
pair_coeff 17 19 table pair_17_19.table modLJ
pair_coeff 17 20 table pair_17_20.table modLJ
pair_coeff 18 18 table pair_18_18.table modLJ
pair_coeff 18 19 table pair_18_19.table modLJ
pair_coeff 18 20 table pair_18_20.table modLJ
pair_coeff 19 19 table pair_19_19.table modLJ
pair_coeff 19 20 table pair_19_20.table modLJ
pair_coeff 20 20 table pair_20_20.table modLJ
pair_coeff 1 21 none
pair_coeff 1 22 none
pair_coeff 2 21 none
pair_coeff 2 22 none
pair_coeff 3 21 none
pair_coeff 3 22 none
pair_coeff 4 21 none
pair_coeff 4 22 none
pair_coeff 5 21 none
pair_coeff 5 22 none
pair_coeff 6 21 none
pair_coeff 6 22 none
pair_coeff 7 21 none
pair_coeff 7 22 none
pair_coeff 8 21 none
pair_coeff 8 22 none
pair_coeff 9 21 none
pair_coeff 9 22 none
pair_coeff 10 21 none
pair_coeff 10 22 none
pair_coeff 11 21 none
pair_coeff 11 22 none
pair_coeff 12 21 none
pair_coeff 12 22 none
pair_coeff 13 21 none
pair_coeff 13 22 none
pair_coeff 14 21 none
pair_coeff 14 22 none
pair_coeff 15 21 none
pair_coeff 15 22 none
pair_coeff 16 21 none
pair_coeff 16 22 none
pair_coeff 17 21 none
pair_coeff 17 22 none
pair_coeff 18 21 none
pair_coeff 18 22 none
pair_coeff 19 21 none
pair_coeff 19 22 none
pair_coeff 20 21 none
pair_coeff 20 22 none
pair_coeff 21 21 none
pair_coeff 21 22 none
pair_coeff 22 22 none

#pair_write 1 15 1000 r 3 10 lj11.table lj11

group Syb molecule 1
group Syx molecule 2
group SN1 molecule 3
group SN2 molecule 4
group PB_Syb molecule 5
group PB_Syx molecule 6
group C_term_Syb id 63
group C_term_Syx id 131
group all molecule 1 2 3 4
group 1 type 1
group 2 type 2
group 3 type 3
group 4 type 4
group 5 type 5
group 6 type 6
group 7 type 7
group 8 type 8
group 9 type 9
group 10 type 10
group 11 type 11
group 12 type 12
group 13 type 13
group 14 type 14
group 15 type 15
group 16 type 16
group 17 type 17
group 18 type 18
group 19 type 19
group 20 type 20
group 21 type 21
group 22 type 22

neighbor 7.5 multi #Neighborlist cutoff is 7.5 A longer than Rc
neigh_modify delay 10 #delay building of neighborlist until after 10 steps from last
neigh_modify exclude group Syb Syb #no neighbors from x to x
neigh_modify exclude group Syx Syx
neigh_modify exclude group SN1 SN1
neigh_modify exclude group SN2 SN2
neigh_modify exclude group PB_Syb all
neigh_modify exclude group PB_Syb PB_Syb
neigh_modify exclude group PB_Syx all
neigh_modify exclude group PB_Syx PB_Syx

timestep 43.41000000 #fs
reset_timestep 0

atom_modify sort 0 2
run_style verlet
#fix 1 1 langevin 000.0 000.0 33.05 48279 zero yes #ID group-ID Lang Tstart Tstop damp seed (set total Fr to zero)
fix 2 2 langevin 000.0 000.0 37.30 48279 zero yes
fix 3 3 langevin 000.0 000.0 40.53 48279 zero yes
fix 4 4 langevin 000.0 000.0 32.17 48279 zero yes
fix 5 5 langevin 000.0 000.0 32.17 48279 zero yes
fix 6 6 langevin 000.0 000.0 29.61 48279 zero yes
fix 7 7 langevin 000.0 000.0 48.27 48279 zero yes
fix 8 8 langevin 000.0 000.0 44.25 48279 zero yes
fix 9 9 langevin 000.0 000.0 25.06 48279 zero yes
fix 10 10 langevin 000.0 000.0 22.35 48279 zero yes
fix 11 11 langevin 000.0 000.0 31.82 48279 zero yes
fix 12 12 langevin 000.0 000.0 29.51 48279 zero yes
fix 13 13 langevin 000.0 000.0 35.28 48279 zero yes
fix 14 14 langevin 000.0 000.0 37.64 48279 zero yes
fix 15 15 langevin 000.0 000.0 36.22 48279 zero yes
fix 16 16 langevin 000.0 000.0 38.57 48279 zero yes
fix 17 17 langevin 000.0 000.0 39.63 48279 zero yes
fix 18 18 langevin 000.0 000.0 41.71 48279 zero yes
fix 19 19 langevin 000.0 000.0 35.30 48279 zero yes
#fix 20 20 langevin 000.0 000.0 30.57 48279 zero yes
fix 21 all nve
fix freeze PB_Syb setforce 0.0 0.0 0.0
fix freeze2 PB_Syx setforce 0.0 0.0 0.0

thermo 10000 #output thermodynamics every this many steps
thermo_style multi
dump VMD0 all xyz 10000 1041_bundle.xyz

fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000
displace_atoms PB_Syb move -0.1349 0.1954 0.9714 units box
fix freeze PB_Syb setforce 0.0 0.0 0.0
run 10000000

sjplimp · November 4, 2014, 2:52pm

I have no idea what could be happening.

Neither do I. It’s not likely a LAMMPS problem,
rather a system issue. But you can take your

last restart file, start running from it and see

if the system goes further.

Steve

Nicole_Fortoul · November 4, 2014, 2:54pm

Hi Steve,

Thanks for the suggestion. I’ve actually done that several times and the system stops at 5.441 x10^7 timesteps no matter what restart file I use. It is so strange that I get no errors or anything. It just stops.

Thank you,
Nicole

sjplimp · November 4, 2014, 3:14pm

If you are using the most current version of LAMMPS,

the please post an inputs script and restart file
that starts right before the offending timestep, and
if we can reproduce the problem, we can probably
figure out if its a bug.

Steve

Nicole_Fortoul · November 5, 2014, 6:13pm

Hello all,

The strange thing is that every time a simulation starts it (from no matter what restart file), it will run for 5.441 x 10^7 timesteps. So this phenomenon cannot be repeated in that way. One would have to simulate a total of 5.441 x 10^7 timesteps. I actually re ran the simulation on a local machine and I do not run into this problem. Currently I am trying to run the simulation on STAMPEDE from TACC. So I am not sure if there is some default setting by STAMPEDE that I am unaware of that is stopping me simulation early (~1 hour and 40 min clock time). I have provided the script I use to run my simulation below

#!/bin/bash
#SBATCH -J random8k# Job Name
#SBATCH -o random8k.o%j # Output and error file name
#SBATCH -p normal # Queue name
#SBATCH -n 8 # Total num of mpi tasks requested
#SBATCH -t 15:00:00 # Run time (hh:mm:ss)

module load intel/14.0.1.106 mvapich2/2.0b
module load lammps/09Oct14
ibrun lmp_stampede < in_bundle_MJ_DC.in

Thank you
Nicole

sjplimp · November 6, 2014, 2:28pm

I assume you are not running out of your queue time, e,g. 15 hours?
It seems odd that the stopping point is so precise (54.41 M steps).

I suggest you ask the Stampede sysadmins, or post an email
to the Stampede user group and see if anyone has an idea.

Steve