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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -46.010916 0.0000000) to (10.844877 46.010916 5.1123240) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0249316 5.1123240 5.1123240 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -46.010916 0.0000000) to (10.844877 46.010916 5.1123240) create_atoms CPU = 0.003 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0249316 5.1123240 5.1123240 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -46.010916 0.0000000) to (10.844877 46.010916 5.1123240) create_atoms CPU = 0.002 seconds 218 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 3 24 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 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 432 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_759493141826_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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1468.2899 0 -1468.2899 33466.209 114 0 -1525.6354 0 -1525.6354 9628.9363 Loop time of 1.99713 on 1 procs for 114 steps with 432 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 = -1468.28990108066 -1525.63403359116 -1525.63544126865 Force two-norm initial, final = 136.50015 0.11514979 Force max component initial, final = 45.128472 0.015203345 Final line search alpha, max atom move = 1.0000000 0.015203345 Iterations, force evaluations = 114 223 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9436 | 1.9436 | 1.9436 | 0.0 | 97.32 Neigh | 0.011516 | 0.011516 | 0.011516 | 0.0 | 0.58 Comm | 0.024832 | 0.024832 | 0.024832 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01722 | | | 0.86 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4627.00 ave 4627 max 4627 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: 74000.0 ave 74000 max 74000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74000 Ave neighs/atom = 171.29630 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.518 | 4.518 | 4.518 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -1525.6354 0 -1525.6354 9628.9363 5101.9227 121 0 -1525.7802 0 -1525.7802 189.98501 5136.3197 Loop time of 0.078027 on 1 procs for 7 steps with 432 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1525.63544126865 -1525.77944055849 -1525.78021208667 Force two-norm initial, final = 55.465217 1.4070167 Force max component initial, final = 41.396788 1.3563476 Final line search alpha, max atom move = 0.00040643733 0.00055127031 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.074289 | 0.074289 | 0.074289 | 0.0 | 95.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093943 | 0.00093943 | 0.00093943 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002798 | | | 3.59 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4679.00 ave 4679 max 4679 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: 73948.0 ave 73948 max 73948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73948 Ave neighs/atom = 171.17593 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 4.656 | 4.656 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1525.7802 0 -1525.7802 189.98501 Loop time of 6.435e-06 on 1 procs for 0 steps with 432 atoms 170.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4695.00 ave 4695 max 4695 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: 73768.0 ave 73768 max 73768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73768 Ave neighs/atom = 170.75926 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 4.656 | 4.656 | 4.656 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 -1525.7802 -1525.7802 10.865173 92.57441 5.106513 189.98501 189.98501 51.396603 425.62723 92.931203 2.450579 292.33744 Loop time of 6.535e-06 on 1 procs for 0 steps with 432 atoms 260.1% 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 | | 6.535e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4695.00 ave 4695 max 4695 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36884.0 ave 36884 max 36884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73768.0 ave 73768 max 73768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73768 Ave neighs/atom = 170.75926 Neighbor list builds = 0 Dangerous builds = 0 432 -1525.78021208667 eV 2.45057902516815 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02