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 = 3.6131481 3.6131481 3.6131481 Created orthogonal box = (0.0000000 -63.820921 0.0000000) to (36.847026 63.820921 6.2581561) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6687732 5.7275185 6.2581561 Created 1248 atoms using lattice units in orthogonal box = (0.0000000 -63.820921 0.0000000) to (36.847026 63.820921 6.2581561) create_atoms CPU = 0.008 seconds 1248 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6687732 5.7275185 6.2581561 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -63.820921 0.0000000) to (36.847026 63.820921 6.2581561) create_atoms CPU = 0.008 seconds 1252 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 25 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 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2492 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_173787283511_004#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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 12.46 | 12.46 | 12.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8065.1603 0 -8065.1603 37065.665 140 0 -8667.5307 0 -8667.5307 1577.0986 Loop time of 29.0757 on 1 procs for 140 steps with 2492 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 = -8065.16027834835 -8667.52276492844 -8667.53068123581 Force two-norm initial, final = 600.87946 0.35016364 Force max component initial, final = 106.46111 0.033856956 Final line search alpha, max atom move = 1.0000000 0.033856956 Iterations, force evaluations = 140 250 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.307 | 28.307 | 28.307 | 0.0 | 97.36 Neigh | 0.5871 | 0.5871 | 0.5871 | 0.0 | 2.02 Comm | 0.10588 | 0.10588 | 0.10588 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07603 | | | 0.26 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17223.0 ave 17223 max 17223 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: 954832.0 ave 954832 max 954832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 954832 Ave neighs/atom = 383.15891 Neighbor list builds = 5 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 140 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.46 | 12.46 | 12.46 Mbytes Step Temp E_pair E_mol TotEng Press Volume 140 0 -8667.5307 0 -8667.5307 1577.0986 29433.499 142 0 -8667.5639 0 -8667.5639 19.219423 29469.151 Loop time of 0.63246 on 1 procs for 2 steps with 2492 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 = -8667.53068123599 -8667.56116143586 -8667.56390940516 Force two-norm initial, final = 60.725534 2.4551663 Force max component initial, final = 49.449021 1.5949938 Final line search alpha, max atom move = 7.4162241e-05 0.00011828832 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62405 | 0.62405 | 0.62405 | 0.0 | 98.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023022 | 0.0023022 | 0.0023022 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006105 | | | 0.97 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17209.0 ave 17209 max 17209 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: 954184.0 ave 954184 max 954184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 954184 Ave neighs/atom = 382.89888 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 11.97 | 11.97 | 11.97 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8667.5639 0 -8667.5639 19.219423 Loop time of 8.229e-06 on 1 procs for 0 steps with 2492 atoms 194.4% 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 | | 8.229e-06 | | |100.00 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17209.0 ave 17209 max 17209 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: 953688.0 ave 953688 max 953688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 953688 Ave neighs/atom = 382.69984 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 11.97 | 11.97 | 11.97 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 -8667.5639 -8667.5639 36.864963 127.76878 6.2564658 19.219423 19.219423 -83.47098 54.43617 86.693079 2.3315511 1017.1485 Loop time of 8.761e-06 on 1 procs for 0 steps with 2492 atoms 239.7% 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 | | 8.761e-06 | | |100.00 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17209.0 ave 17209 max 17209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 476844.0 ave 476844 max 476844 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 953688.0 ave 953688 max 953688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 953688 Ave neighs/atom = 382.69984 Neighbor list builds = 0 Dangerous builds = 0 2492 -8667.56390940516 eV 2.33155109701789 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31