LAMMPS (31 Aug 2021) Reading data file ... orthogonal box = (-0.75841574 -0.81445865 -0.73597454) to (31.771384 31.715341 31.793825) 2 by 4 by 7 MPI processor grid reading atoms ... 3216 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom reading bonds ... 2144 bonds reading angles ... 1216 angles Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 3 = max # of 1-3 neighbors 3 = max # of 1-4 neighbors 4 = max # of special neighbors special bonds CPU = 0.005 seconds read_data CPU = 0.037 seconds Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 9.462 | 9.477 | 9.486 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -34950.397 2675.3249 -29400.081 57764.51 14 300 -36683.902 798.79439 -33010.117 52038.48 Loop time of 0.093767 on 56 procs for 14 steps with 3216 atoms 101.0% CPU use with 56 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -32275.072369532 -35885.0996572603 -35885.1078776279 Force two-norm initial, final = 4836.1281 2739.2444 Force max component initial, final = 2085.9622 696.40210 Final line search alpha, max atom move = 1.0955425e-09 7.6293810e-07 Iterations, force evaluations = 14 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022517 | 0.047149 | 0.077379 | 5.8 | 50.28 Bond | 0.00018096 | 0.00035108 | 0.00053072 | 0.0 | 0.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011846 | 0.041774 | 0.065762 | 6.1 | 44.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004492 | | | 4.79 Nlocal: 57.4286 ave 77 max 33 min Histogram: 1 1 4 4 6 15 11 11 2 1 Nghost: 3437.46 ave 3625 max 3337 min Histogram: 2 12 18 12 4 0 0 0 1 7 Neighs: 19515.6 ave 26411 max 10075 min Histogram: 1 4 1 3 11 11 6 9 7 3 Total # of neighbors = 1092876 Ave neighs/atom = 339.82463 Ave special neighs/atom = 2.0895522 Neighbor list builds = 0 Dangerous builds = 0 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard (2) pair lj/cut/coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Ignoring 'compress yes' for molecular system (../delete_atoms.cpp:126) Deleted 0 atoms, new total = 3216 Deleted 0 bonds, new total = 2144 Deleted 0 angles, new total = 1216 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 9.593 | 9.608 | 9.616 Mbytes Step Temp PotEng KinEng TotEng 0 300 -35885.108 2874.9913 -33010.117 1 341.46911 -36665.188 3272.4024 -33392.786 2 468.30578 -37560.821 4487.9168 -33072.905 3 684.90823 -41021.996 6563.684 -34458.313 4 1001.7831 -45677.267 9600.3925 -36076.874 5 1442.057 -51059.076 13819.671 -37239.406 6 2056.5463 -57761.037 19708.509 -38052.528 7 3010.5154 -66779.819 28850.685 -37929.134 8 12592.912 -85236.645 120681.71 35445.064 ERROR on proc 21: Bond atoms 2497 2499 missing on proc 21 at step 9 (../ntopo_bond_all.cpp:61) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 21 slurmstepd: error: *** STEP 13894868.0 ON cn1087 CANCELLED AT 2024-11-26T16:58:14 *** srun: Job step aborted: Waiting up to 32 seconds for job step to finish. srun: error: cn1088: tasks 28-55: Killed srun: error: cn1087: tasks 0-27: Killed