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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -52.896258 0.0000000) to (37.403303 52.896258 5.7039502) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9587540 6.7658004 5.7039502 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -52.896258 0.0000000) to (37.403303 52.896258 5.7039502) create_atoms CPU = 0.007 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9587540 6.7658004 5.7039502 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -52.896258 0.0000000) to (37.403303 52.896258 5.7039502) create_atoms CPU = 0.007 seconds 694 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 = 9 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1376 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 = 9 25 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) = 5.103 | 5.103 | 5.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4463.5021 0 -4463.5021 22070.964 54 0 -4624.5094 0 -4624.5094 4679.1417 Loop time of 2.67107 on 1 procs for 54 steps with 1376 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 = -4463.5021189059 -4624.50660393153 -4624.50940176081 Force two-norm initial, final = 155.34651 0.12470992 Force max component initial, final = 24.665682 0.018053020 Final line search alpha, max atom move = 1.0000000 0.018053020 Iterations, force evaluations = 54 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6046 | 2.6046 | 2.6046 | 0.0 | 97.51 Neigh | 0.030132 | 0.030132 | 0.030132 | 0.0 | 1.13 Comm | 0.019441 | 0.019441 | 0.019441 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01689 | | | 0.63 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7874.00 ave 7874 max 7874 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: 197644.0 ave 197644 max 197644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197644 Ave neighs/atom = 143.63663 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.098 | 5.098 | 5.098 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -4624.5094 0 -4624.5094 4679.1417 22570.471 61 0 -4624.8397 0 -4624.8397 -113.09731 22702.97 Loop time of 0.236296 on 1 procs for 7 steps with 1376 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 = -4624.50940176081 -4624.83898656353 -4624.83969594866 Force two-norm initial, final = 125.81712 3.2488047 Force max component initial, final = 109.01355 2.3670540 Final line search alpha, max atom move = 0.00021141456 0.00050042969 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22953 | 0.22953 | 0.22953 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014282 | 0.0014282 | 0.0014282 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005333 | | | 2.26 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7301.00 ave 7301 max 7301 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: 195464.0 ave 195464 max 195464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195464 Ave neighs/atom = 142.05233 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 = 9 26 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) = 5.237 | 5.237 | 5.237 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4624.8397 0 -4624.8397 -113.09731 Loop time of 6.335e-06 on 1 procs for 0 steps with 1376 atoms 173.6% 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 | | 6.335e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7301.00 ave 7301 max 7301 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: 194344.0 ave 194344 max 194344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194344 Ave neighs/atom = 141.23837 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 = 9 26 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) = 5.237 | 5.237 | 5.237 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 -4624.8397 -4624.8397 37.390059 106.4589 5.7035409 -113.09731 -113.09731 -155.45467 -16.803324 -167.03393 2.6784909 909.33189 Loop time of 6.545e-06 on 1 procs for 0 steps with 1376 atoms 305.6% 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 | | 6.545e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7301.00 ave 7301 max 7301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97172.0 ave 97172 max 97172 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 194344.0 ave 194344 max 194344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194344 Ave neighs/atom = 141.23837 Neighbor list builds = 0 Dangerous builds = 0 1376 -4624.83969594866 eV 2.67849088630103 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03