LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -35.897098 0.0000000) to (31.087798 35.897098 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5798613 5.5226304 6.0968189 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -35.897098 0.0000000) to (31.087798 35.897098 6.0968189) create_atoms CPU = 0.001 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5798613 5.5226304 6.0968189 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -35.897098 0.0000000) to (31.087798 35.897098 6.0968189) create_atoms CPU = 0.001 seconds 628 atoms in group lower Displacing atoms ... 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 17 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1249 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_103383163946_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.483 | 5.483 | 5.483 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5177.5634 0 -5177.5634 88301.817 121 0 -5524.3282 0 -5524.3282 12207.103 Loop time of 3.11164 on 1 procs for 121 steps with 1249 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5177.56342519139 -5524.32389843801 -5524.32820687671 Force two-norm initial, final = 634.00730 0.22042737 Force max component initial, final = 172.84266 0.049390503 Final line search alpha, max atom move = 1.0000000 0.049390503 Iterations, force evaluations = 121 214 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0106 | 3.0106 | 3.0106 | 0.0 | 96.75 Neigh | 0.067805 | 0.067805 | 0.067805 | 0.0 | 2.18 Comm | 0.018605 | 0.018605 | 0.018605 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01458 | | | 0.47 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7546.00 ave 7546 max 7546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 282074.0 ave 282074 max 282074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 282074 Ave neighs/atom = 225.83987 Neighbor list builds = 4 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 121 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.483 | 5.483 | 5.483 Mbytes Step Temp E_pair E_mol TotEng Press Volume 121 0 -5524.3282 0 -5524.3282 12207.103 13607.633 128 0 -5524.8438 0 -5524.8438 -25.903547 13701.591 Loop time of 0.137335 on 1 procs for 7 steps with 1249 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 = -5524.3282068767 -5524.84338552004 -5524.84381326109 Force two-norm initial, final = 195.10465 1.1806898 Force max component initial, final = 164.05187 0.90125457 Final line search alpha, max atom move = 0.00018780643 0.00016926140 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13408 | 0.13408 | 0.13408 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060471 | 0.00060471 | 0.00060471 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002646 | | | 1.93 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7519.00 ave 7519 max 7519 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 281760.0 ave 281760 max 281760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281760 Ave neighs/atom = 225.58847 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.621 | 5.621 | 5.621 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5524.8438 0 -5524.8438 -25.903547 Loop time of 1.708e-06 on 1 procs for 0 steps with 1249 atoms 117.1% 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 | | 1.708e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7519.00 ave 7519 max 7519 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 281034.0 ave 281034 max 281034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281034 Ave neighs/atom = 225.00721 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.621 | 5.621 | 5.621 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 -5524.8438 -5524.8438 31.118577 72.208535 6.0976534 -25.903547 -25.903547 -105.49129 -32.601309 60.381958 2.203896 923.52921 Loop time of 2.675e-06 on 1 procs for 0 steps with 1249 atoms 224.3% 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 | | 2.675e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7519.00 ave 7519 max 7519 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140517.0 ave 140517 max 140517 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 281034.0 ave 281034 max 281034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281034 Ave neighs/atom = 225.00721 Neighbor list builds = 0 Dangerous builds = 0 1249 -5490.83189907749 eV 2.20389596229285 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03