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 = 4.0500047 4.0500047 4.0500047 Created orthogonal box = (0.0000000 -41.302106 0.0000000) to (20.651053 41.302106 4.0500047) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7656276 4.7656276 4.0500047 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -41.302106 0.0000000) to (20.651053 41.302106 4.0500047) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7656276 4.7656276 4.0500047 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -41.302106 0.0000000) to (20.651053 41.302106 4.0500047) create_atoms CPU = 0.001 seconds 210 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 5 20 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_651801486679_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1369.5081 0 -1369.5081 -1289.2938 62 0 -1379.1668 0 -1379.1668 -3599.6203 Loop time of 0.812327 on 1 procs for 62 steps with 412 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 = -1369.50813616395 -1379.16554123622 -1379.16676155764 Force two-norm initial, final = 8.8204298 0.079877465 Force max component initial, final = 2.7968130 0.014640026 Final line search alpha, max atom move = 1.0000000 0.014640026 Iterations, force evaluations = 62 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78177 | 0.78177 | 0.78177 | 0.0 | 96.24 Neigh | 0.0094816 | 0.0094816 | 0.0094816 | 0.0 | 1.17 Comm | 0.012316 | 0.012316 | 0.012316 | 0.0 | 1.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008755 | | | 1.08 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4498.00 ave 4498 max 4498 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: 57424.0 ave 57424 max 57424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57424 Ave neighs/atom = 139.37864 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -1379.1668 0 -1379.1668 -3599.6203 6908.7571 67 0 -1379.2152 0 -1379.2152 -17.555984 6877.5563 Loop time of 0.0581247 on 1 procs for 5 steps with 412 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1379.16676155763 -1379.21447936072 -1379.21518441914 Force two-norm initial, final = 27.967368 0.19058781 Force max component initial, final = 20.959521 0.12906337 Final line search alpha, max atom move = 0.00029576265 3.8172124e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054898 | 0.054898 | 0.054898 | 0.0 | 94.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007687 | 0.0007687 | 0.0007687 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002458 | | | 4.23 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4484.00 ave 4484 max 4484 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: 57456.0 ave 57456 max 57456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57456 Ave neighs/atom = 139.45631 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1379.2152 0 -1379.2152 -17.555984 Loop time of 6.645e-06 on 1 procs for 0 steps with 412 atoms 195.6% 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 | | 6.645e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4484.00 ave 4484 max 4484 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: 57484.0 ave 57484 max 57484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57484 Ave neighs/atom = 139.52427 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 4.615 | 4.615 | 4.615 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 -1379.2152 -1379.2152 20.66911 82.278428 4.0441421 -17.555984 -17.555984 -30.092534 -11.557762 -11.017656 2.6043103 237.82984 Loop time of 7.367e-06 on 1 procs for 0 steps with 412 atoms 230.8% 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 | | 7.367e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4484.00 ave 4484 max 4484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28742.0 ave 28742 max 28742 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57484.0 ave 57484 max 57484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57484 Ave neighs/atom = 139.52427 Neighbor list builds = 0 Dangerous builds = 0 412 -1379.21518446208 eV 2.60431031744063 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01