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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -70.576269 0.0000000) to (40.747228 70.576269 6.0968610) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4735082 5.6180114 6.0968610 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.576269 0.0000000) to (40.747228 70.576269 6.0968610) create_atoms CPU = 0.010 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4735082 5.6180114 6.0968610 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.576269 0.0000000) to (40.747228 70.576269 6.0968610) create_atoms CPU = 0.009 seconds 1610 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 34 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.76 | 11.76 | 11.76 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13381.923 0 -13381.923 75358.504 102 0 -14265.39 0 -14265.39 6192.7711 Loop time of 13.8059 on 1 procs for 102 steps with 3216 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13381.9228212757 -14265.3774590131 -14265.3900062749 Force two-norm initial, final = 1451.0315 0.36559805 Force max component initial, final = 319.24482 0.043119183 Final line search alpha, max atom move = 1.0000000 0.043119183 Iterations, force evaluations = 102 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.367 | 13.367 | 13.367 | 0.0 | 96.82 Neigh | 0.29905 | 0.29905 | 0.29905 | 0.0 | 2.17 Comm | 0.078343 | 0.078343 | 0.078343 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06108 | | | 0.44 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17072.0 ave 17072 max 17072 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: 718048.0 ave 718048 max 718048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 718048 Ave neighs/atom = 223.27363 Neighbor list builds = 3 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.76 | 11.76 | 11.76 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -14265.39 0 -14265.39 6192.7711 35066.551 107 0 -14265.971 0 -14265.971 75.241764 35186.692 Loop time of 0.515255 on 1 procs for 5 steps with 3216 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14265.3900062749 -14265.9685865363 -14265.970690201 Force two-norm initial, final = 298.21465 2.9471087 Force max component initial, final = 279.13476 1.9345378 Final line search alpha, max atom move = 0.00010284318 0.00019895402 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50361 | 0.50361 | 0.50361 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026944 | 0.0026944 | 0.0026944 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008951 | | | 1.74 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17095.0 ave 17095 max 17095 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: 718100.0 ave 718100 max 718100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 718100 Ave neighs/atom = 223.28980 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.28 | 11.28 | 11.28 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14265.971 0 -14265.971 75.241764 Loop time of 6.645e-06 on 1 procs for 0 steps with 3216 atoms 195.6% 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 | | 6.645e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17095.0 ave 17095 max 17095 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: 717672.0 ave 717672 max 717672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 717672 Ave neighs/atom = 223.15672 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.28 | 11.28 | 11.28 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 -14265.971 -14265.971 40.750737 141.74672 6.0915801 75.241764 75.241764 56.50807 81.207065 88.010157 2.1979431 996.05935 Loop time of 7.026e-06 on 1 procs for 0 steps with 3216 atoms 256.2% 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 | | 7.026e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17095.0 ave 17095 max 17095 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 358836.0 ave 358836 max 358836 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 717672.0 ave 717672 max 717672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 717672 Ave neighs/atom = 223.15672 Neighbor list builds = 0 Dangerous builds = 0 3216 -14178.2980220122 eV 2.19794308775416 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15