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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -55.101027 0.0000000) to (33.740207 55.101027 8.5700212) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4419689 5.3320188 5.7133475 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -55.101027 0.0000000) to (33.740207 55.101027 8.5700212) create_atoms CPU = 0.007 seconds 1491 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4419689 5.3320188 5.7133475 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -55.101027 0.0000000) to (33.740207 55.101027 8.5700212) create_atoms CPU = 0.006 seconds 1491 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2952 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.945 | 6.945 | 6.945 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12019.284 0 -12019.284 15734.684 41 0 -12117.215 0 -12117.215 -6756.6681 Loop time of 3.92329 on 1 procs for 41 steps with 2952 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 = -12019.2837414006 -12117.2035827087 -12117.2151924704 Force two-norm initial, final = 150.28839 0.52629636 Force max component initial, final = 26.959581 0.12860348 Final line search alpha, max atom move = 1.0000000 0.12860348 Iterations, force evaluations = 41 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.739 | 3.739 | 3.739 | 0.0 | 95.30 Neigh | 0.14414 | 0.14414 | 0.14414 | 0.0 | 3.67 Comm | 0.017836 | 0.017836 | 0.017836 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02227 | | | 0.57 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10418.0 ave 10418 max 10418 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: 514840.0 ave 514840 max 514840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514840 Ave neighs/atom = 174.40379 Neighbor list builds = 2 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.945 | 6.945 | 6.945 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -12117.215 0 -12117.215 -6756.6681 31865.397 44 0 -12117.455 0 -12117.455 -1954.2704 31732.923 Loop time of 0.269413 on 1 procs for 3 steps with 2952 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12117.2151924704 -12117.4534707957 -12117.4545819246 Force two-norm initial, final = 161.83713 0.77570884 Force max component initial, final = 117.44893 0.26867618 Final line search alpha, max atom move = 0.00011651833 3.1305701e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26382 | 0.26382 | 0.26382 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010661 | 0.0010661 | 0.0010661 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004531 | | | 1.68 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10423.0 ave 10423 max 10423 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: 515218.0 ave 515218 max 515218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 515218 Ave neighs/atom = 174.53184 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.083 | 7.083 | 7.083 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12117.455 0 -12117.455 -1954.2704 Loop time of 6.244e-06 on 1 procs for 0 steps with 2952 atoms 192.2% 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 | | 6.244e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10433.0 ave 10433 max 10433 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: 515476.0 ave 515476 max 515476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 515476 Ave neighs/atom = 174.61924 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.083 | 7.083 | 7.083 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 -12117.455 -12117.455 33.667521 110.20205 8.5528184 -1954.2704 -1954.2704 -12.237236 -5864.112 13.538071 2.2717448 872.77505 Loop time of 6.876e-06 on 1 procs for 0 steps with 2952 atoms 276.3% 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 | | 6.876e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10433.0 ave 10433 max 10433 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257738.0 ave 257738 max 257738 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 515476.0 ave 515476 max 515476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 515476 Ave neighs/atom = 174.61924 Neighbor list builds = 0 Dangerous builds = 0 2952 -12117.4545819246 eV 2.27174480369856 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05