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 = 2.8553126 2.8553126 2.8553126 Created orthogonal box = (0.0000000 -33.784514 0.0000000) to (41.377410 33.784514 6.9940589) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7288469 4.3437232 4.6627059 Created 836 atoms using lattice units in orthogonal box = (0.0000000 -33.784514 0.0000000) to (41.377410 33.784514 6.9940589) create_atoms CPU = 0.002 seconds 836 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7288469 4.3437232 4.6627059 Created 842 atoms using lattice units in orthogonal box = (0.0000000 -33.784514 0.0000000) to (41.377410 33.784514 6.9940589) create_atoms CPU = 0.001 seconds 842 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 = 10 16 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 = 1678 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_577453891941_005#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 = 10 16 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) = 5.954 | 5.954 | 5.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5293.8805 0 -5293.8805 204484.4 132 0 -6686.0828 0 -6686.0828 6564.393 Loop time of 5.92837 on 1 procs for 132 steps with 1678 atoms 91.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5293.88054828195 -6686.07656658707 -6686.08282112645 Force two-norm initial, final = 1939.6813 0.22399447 Force max component initial, final = 338.04232 0.036217625 Final line search alpha, max atom move = 0.65940513 0.023882088 Iterations, force evaluations = 132 252 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8264 | 5.8264 | 5.8264 | 0.0 | 98.28 Neigh | 0.046724 | 0.046724 | 0.046724 | 0.0 | 0.79 Comm | 0.029286 | 0.029286 | 0.029286 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02596 | | | 0.44 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8192.00 ave 8192 max 8192 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: 377840.0 ave 377840 max 377840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 377840 Ave neighs/atom = 225.17282 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 16 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 : 132 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.958 | 5.958 | 5.958 Mbytes Step Temp E_pair E_mol TotEng Press Volume 132 0 -6686.0828 0 -6686.0828 6564.393 19554.21 138 0 -6686.4356 0 -6686.4356 -3.039107 19629.225 Loop time of 0.215653 on 1 procs for 6 steps with 1678 atoms 89.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6686.08282112642 -6686.43539935678 -6686.43560023159 Force two-norm initial, final = 166.81517 0.51499016 Force max component initial, final = 154.43035 0.095499511 Final line search alpha, max atom move = 0.00024269419 2.3177176e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2114 | 0.2114 | 0.2114 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068648 | 0.00068648 | 0.00068648 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003564 | | | 1.65 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8709.00 ave 8709 max 8709 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: 378380.0 ave 378380 max 378380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 378380 Ave neighs/atom = 225.49464 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 = 10 16 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) = 6.095 | 6.095 | 6.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6686.4356 0 -6686.4356 -3.039107 Loop time of 2.156e-06 on 1 procs for 0 steps with 1678 atoms 185.5% 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 | | 2.156e-06 | | |100.00 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8680.00 ave 8680 max 8680 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: 376824.0 ave 376824 max 376824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376824 Ave neighs/atom = 224.56734 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 = 10 16 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) = 6.095 | 6.095 | 6.095 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 -6686.4356 -6686.4356 41.381812 67.889975 6.986956 -3.039107 -3.039107 -4.2310041 -3.5653325 -1.3209845 2.2141705 1324.6239 Loop time of 4.132e-06 on 1 procs for 0 steps with 1678 atoms 193.6% 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 | | 4.132e-06 | | |100.00 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8680.00 ave 8680 max 8680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 188412.0 ave 188412 max 188412 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 376824.0 ave 376824 max 376824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376824 Ave neighs/atom = 224.56734 Neighbor list builds = 0 Dangerous builds = 0 1678 -6686.43560023159 eV 2.21417050316696 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06