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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -60.149793 0.0000000) to (30.074896 60.149793 3.5200004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5318337 4.5318337 3.5200004 Created 584 atoms using lattice units in orthogonal box = (0.0000000 -60.149793 0.0000000) to (30.074896 60.149793 3.5200004) create_atoms CPU = 0.002 seconds 584 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5318337 4.5318337 3.5200004 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -60.149793 0.0000000) to (30.074896 60.149793 3.5200004) create_atoms CPU = 0.002 seconds 586 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 32 1 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1168 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.455 | 5.455 | 5.455 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5134.741 0 -5134.741 9774.3626 23 0 -5180.8158 0 -5180.8158 11054.392 Loop time of 1.00307 on 1 procs for 23 steps with 1168 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 = -5134.74103027753 -5180.81078951828 -5180.8158191507 Force two-norm initial, final = 44.136666 0.23866993 Force max component initial, final = 10.003721 0.035026734 Final line search alpha, max atom move = 1.0000000 0.035026734 Iterations, force evaluations = 23 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9885 | 0.9885 | 0.9885 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0083212 | 0.0083212 | 0.0083212 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00625 | | | 0.62 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8762.00 ave 8762 max 8762 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: 205296.0 ave 205296 max 205296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205296 Ave neighs/atom = 175.76712 Neighbor list builds = 0 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.455 | 5.455 | 5.455 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -5180.8158 0 -5180.8158 11054.392 12735.353 31 0 -5181.3551 0 -5181.3551 -216.90931 12815.142 Loop time of 0.242715 on 1 procs for 8 steps with 1168 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 = -5180.8158191507 -5181.35028660658 -5181.35514228817 Force two-norm initial, final = 172.21033 3.8238452 Force max component initial, final = 153.10588 2.9521632 Final line search alpha, max atom move = 0.00013413936 0.00039600126 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23459 | 0.23459 | 0.23459 | 0.0 | 96.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018161 | 0.0018161 | 0.0018161 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006313 | | | 2.60 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8732.00 ave 8732 max 8732 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: 204104.0 ave 204104 max 204104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204104 Ave neighs/atom = 174.74658 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.593 | 5.593 | 5.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5181.3551 0 -5181.3551 -216.90931 Loop time of 6.546e-06 on 1 procs for 0 steps with 1168 atoms 168.0% 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 | | 6.546e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8732.00 ave 8732 max 8732 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: 203856.0 ave 203856 max 203856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203856 Ave neighs/atom = 174.53425 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.593 | 5.593 | 5.593 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 -5181.3551 -5181.3551 30.059208 121.23741 3.516489 -216.90931 -216.90931 19.212298 -301.22265 -368.71757 2.2046571 434.87492 Loop time of 6.575e-06 on 1 procs for 0 steps with 1168 atoms 289.0% 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 | | 6.575e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8732.00 ave 8732 max 8732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101928.0 ave 101928 max 101928 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203856.0 ave 203856 max 203856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203856 Ave neighs/atom = 174.53425 Neighbor list builds = 0 Dangerous builds = 0 1168 -5181.35514228817 eV 2.20465707621865 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01