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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -44.204638 0.0000000) to (54.134924 44.204638 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1910201 5.4494359 5.9736509 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -44.204638 0.0000000) to (54.134924 44.204638 8.9604763) create_atoms CPU = 0.002 seconds 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1910201 5.4494359 5.9736509 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -44.204638 0.0000000) to (54.134924 44.204638 8.9604763) create_atoms CPU = 0.002 seconds 1757 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 3 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 59 atoms, new total = 3455 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.547 | 6.547 | 6.547 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13300.313 0 -13300.313 1169.2487 409 0 -13532.815 0 -13532.815 -60233.218 Loop time of 17.1527 on 1 procs for 409 steps with 3455 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 = -13300.3131544467 -13532.8029117225 -13532.8154294549 Force two-norm initial, final = 59.463093 0.34108675 Force max component initial, final = 6.5697926 0.027954717 Final line search alpha, max atom move = 1.0000000 0.027954717 Iterations, force evaluations = 409 785 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.679 | 16.679 | 16.679 | 0.0 | 97.24 Neigh | 0.30124 | 0.30124 | 0.30124 | 0.0 | 1.76 Comm | 0.072517 | 0.072517 | 0.072517 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1004 | | | 0.59 Nlocal: 3455.00 ave 3455 max 3455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10033.0 ave 10033 max 10033 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: 471244.0 ave 471244 max 471244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 471244 Ave neighs/atom = 136.39479 Neighbor list builds = 10 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 409 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.549 | 6.549 | 6.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 409 0 -13532.815 0 -13532.815 -60233.218 42885.104 438 0 -13563.846 0 -13563.846 -12770.409 41367.136 Loop time of 0.656308 on 1 procs for 29 steps with 3455 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 = -13532.815429455 -13563.8444101912 -13563.8458881982 Force two-norm initial, final = 2178.1111 9.5560509 Force max component initial, final = 1906.4174 5.1695282 Final line search alpha, max atom move = 0.00011692932 0.00060446942 Iterations, force evaluations = 29 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61 | 0.61 | 0.61 | 0.0 | 92.94 Neigh | 0.028634 | 0.028634 | 0.028634 | 0.0 | 4.36 Comm | 0.0024276 | 0.0024276 | 0.0024276 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01525 | | | 2.32 Nlocal: 3455.00 ave 3455 max 3455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10167.0 ave 10167 max 10167 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: 481766.0 ave 481766 max 481766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 481766 Ave neighs/atom = 139.44023 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.688 | 6.688 | 6.688 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13563.846 0 -13563.846 -12770.409 Loop time of 1.756e-06 on 1 procs for 0 steps with 3455 atoms 170.8% 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 | | 1.756e-06 | | |100.00 Nlocal: 3455.00 ave 3455 max 3455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10172.0 ave 10172 max 10172 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: 485326.0 ave 485326 max 485326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 485326 Ave neighs/atom = 140.47062 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.688 | 6.688 | 6.688 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 -13563.846 -13563.846 52.627826 88.409276 8.8908275 -12770.409 -12770.409 193.97861 -38703.869 198.66296 2.2788027 7693.4327 Loop time of 2.015e-06 on 1 procs for 0 steps with 3455 atoms 198.5% 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 | | 2.015e-06 | | |100.00 Nlocal: 3455.00 ave 3455 max 3455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10172.0 ave 10172 max 10172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 242663.0 ave 242663 max 242663 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 485326.0 ave 485326 max 485326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 485326 Ave neighs/atom = 140.47062 Neighbor list builds = 0 Dangerous builds = 0 3455 -13075.234177578 eV 2.27880267117708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18