LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 Created orthogonal box = (0 -58.712 0) to (29.354 58.712 4.03208) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.98464 4.98464 4.03208 Created 426 atoms create_atoms CPU = 0.000378132 secs 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.98464 4.98464 4.03208 Created 426 atoms create_atoms CPU = 0.000245094 secs 426 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1146) System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 32 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 840 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2808.5617 0 -2808.5617 565.61372 23 0 -2814.9603 0 -2814.9603 -3934.034 Loop time of 0.183408 on 1 procs for 23 steps with 840 atoms 72.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2808.56169317 -2814.95781779 -2814.96026991 Force two-norm initial, final = 12.8959 0.120201 Force max component initial, final = 3.84559 0.023467 Final line search alpha, max atom move = 1 0.023467 Iterations, force evaluations = 23 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18123 | 0.18123 | 0.18123 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013535 | 0.0013535 | 0.0013535 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008221 | | | 0.45 Nlocal: 840 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6300 ave 6300 max 6300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110368 ave 110368 max 110368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110368 Ave neighs/atom = 131.39 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -2814.9603 0 -2814.9603 -3934.034 13898.054 26 0 -2814.9991 0 -2814.9991 -1421.7635 13854.477 Loop time of 0.0216241 on 1 procs for 3 steps with 840 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2814.96026991 -2814.9989627 -2814.99906864 Force two-norm initial, final = 34.763 0.125179 Force max component initial, final = 25.3285 0.0229138 Final line search alpha, max atom move = 0.00139779 3.20286e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02081 | 0.02081 | 0.02081 | 0.0 | 96.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020909 | 0.00020909 | 0.00020909 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006049 | | | 2.80 Nlocal: 840 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6300 ave 6300 max 6300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96352 ave 96352 max 96352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96352 Ave neighs/atom = 114.705 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.093 | 5.093 | 5.093 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2814.9991 0 -2814.9991 -1421.7635 Loop time of 9.53674e-07 on 1 procs for 0 steps with 840 atoms 209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 840 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6300 ave 6300 max 6300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100496 ave 100496 max 100496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100496 Ave neighs/atom = 119.638 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.093 | 5.093 | 5.093 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2814.9991 -2814.9991 29.314735 117.42409 4.0248247 -1421.7635 -1421.7635 -2.5909521 -4262.9215 0.22212713 2.5902656 435.00372 Loop time of 1.90735e-06 on 1 procs for 0 steps with 840 atoms 52.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.907e-06 | | |100.00 Nlocal: 840 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6300 ave 6300 max 6300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50248 ave 50248 max 50248 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100496 ave 100496 max 100496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100496 Ave neighs/atom = 119.638 Neighbor list builds = 0 Dangerous builds = 0 840 -2814.99906864405 eV 2.59026556941343 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:00