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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -71.573599 0.0000000) to (43.829699 71.573599 8.8549365) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0687407 5.1123999 5.9032910 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.573599 0.0000000) to (43.829699 71.573599 8.8549365) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0687407 5.1123999 5.9032910 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.573599 0.0000000) to (43.829699 71.573599 8.8549365) create_atoms CPU = 0.003 seconds 2358 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 41 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 4710 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_028979335952_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 11.34 | 11.34 | 11.34 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15522.825 0 -15522.825 45319.411 92 0 -16606.176 0 -16606.176 7158.5039 Loop time of 43.7433 on 1 procs for 92 steps with 4710 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15522.8249530519 -16606.1614682764 -16606.1758608779 Force two-norm initial, final = 902.33588 0.55396528 Force max component initial, final = 109.06615 0.10796223 Final line search alpha, max atom move = 1.0000000 0.10796223 Iterations, force evaluations = 92 171 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.632 | 43.632 | 43.632 | 0.0 | 99.74 Neigh | 0.038621 | 0.038621 | 0.038621 | 0.0 | 0.09 Comm | 0.029426 | 0.029426 | 0.029426 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04371 | | | 0.10 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12577.0 ave 12577 max 12577 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: 625200.0 ave 625200 max 625200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 625200 Ave neighs/atom = 132.73885 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.37 | 11.37 | 11.37 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -16606.176 0 -16606.176 7158.5039 55556.745 95 0 -16606.802 0 -16606.802 -2.7463918 55836.603 Loop time of 1.42783 on 1 procs for 3 steps with 4710 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 = -16606.1758608779 -16606.8000700036 -16606.8016227072 Force two-norm initial, final = 430.29370 1.5569899 Force max component initial, final = 262.20969 1.1606778 Final line search alpha, max atom move = 0.00011553248 0.00013409598 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4233 | 1.4233 | 1.4233 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061476 | 0.00061476 | 0.00061476 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003877 | | | 0.27 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12898.0 ave 12898 max 12898 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: 625872.0 ave 625872 max 625872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 625872 Ave neighs/atom = 132.88153 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16606.802 0 -16606.802 -2.7463918 Loop time of 2.21e-06 on 1 procs for 0 steps with 4710 atoms 181.0% 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 | | 2.21e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12876.0 ave 12876 max 12876 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: 625536.0 ave 625536 max 625536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 625536 Ave neighs/atom = 132.81019 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 10.88 | 10.88 | 10.88 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 -16606.802 -16606.802 43.896953 143.43977 8.8677825 -2.7463918 -2.7463918 -33.355612 -0.088775331 25.205212 2.2078762 1768.2647 Loop time of 2.444e-06 on 1 procs for 0 steps with 4710 atoms 286.4% 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 | | 2.444e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12876.0 ave 12876 max 12876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 312768.0 ave 312768 max 312768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 625536.0 ave 625536 max 625536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 625536 Ave neighs/atom = 132.81019 Neighbor list builds = 0 Dangerous builds = 0 4710 -16606.8016227072 eV 2.20787622396954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:46