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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -36.948065 0.0000000) to (26.126227 36.948065 5.1737640) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6105107 5.7957749 5.1737640 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.948065 0.0000000) to (26.126227 36.948065 5.1737640) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6105107 5.7957749 5.1737640 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.948065 0.0000000) to (26.126227 36.948065 5.1737640) create_atoms CPU = 0.001 seconds 410 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 810 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_143977152728_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.947 | 4.947 | 4.947 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2435.9037 0 -2435.9037 169213.08 494 0 -3188.6722 0 -3188.6722 -64424.712 Loop time of 5.56663 on 1 procs for 494 steps with 810 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 = -2435.90374131284 -3188.66920778056 -3188.6722066345 Force two-norm initial, final = 1767.9990 0.17680883 Force max component initial, final = 584.61483 0.019396333 Final line search alpha, max atom move = 1.0000000 0.019396333 Iterations, force evaluations = 494 931 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4066 | 5.4066 | 5.4066 | 0.0 | 97.13 Neigh | 0.075991 | 0.075991 | 0.075991 | 0.0 | 1.37 Comm | 0.045671 | 0.045671 | 0.045671 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03837 | | | 0.69 Nlocal: 810.000 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4965.00 ave 4965 max 4965 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: 109172.0 ave 109172 max 109172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109172 Ave neighs/atom = 134.78025 Neighbor list builds = 11 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 494 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.945 | 4.945 | 4.945 Mbytes Step Temp E_pair E_mol TotEng Press Volume 494 0 -3188.6722 0 -3188.6722 -64424.712 9988.609 543 0 -3208.7228 0 -3208.7228 -190.44715 9514.8848 Loop time of 0.353314 on 1 procs for 49 steps with 810 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3188.67220663449 -3208.72155604522 -3208.72284349426 Force two-norm initial, final = 794.49014 3.2701635 Force max component initial, final = 655.37164 2.5752225 Final line search alpha, max atom move = 0.00017087820 0.00044004939 Iterations, force evaluations = 49 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33039 | 0.33039 | 0.33039 | 0.0 | 93.51 Neigh | 0.0076541 | 0.0076541 | 0.0076541 | 0.0 | 2.17 Comm | 0.0025565 | 0.0025565 | 0.0025565 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01272 | | | 3.60 Nlocal: 810.000 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5056.00 ave 5056 max 5056 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: 114412.0 ave 114412 max 114412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114412 Ave neighs/atom = 141.24938 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3208.7228 0 -3208.7228 -190.44715 Loop time of 2.08e-06 on 1 procs for 0 steps with 810 atoms 192.3% 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 | | 2.08e-06 | | |100.00 Nlocal: 810.000 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5122.00 ave 5122 max 5122 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: 114560.0 ave 114560 max 114560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114560 Ave neighs/atom = 141.43210 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.084 | 5.084 | 5.084 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 -3208.7228 -3208.7228 26.548467 72.436138 4.947762 -190.44715 -190.44715 -117.60902 -39.042236 -414.69019 2.2745645 2706.8055 Loop time of 2.464e-06 on 1 procs for 0 steps with 810 atoms 284.1% 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 | | 2.464e-06 | | |100.00 Nlocal: 810.000 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5122.00 ave 5122 max 5122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57280.0 ave 57280 max 57280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114560.0 ave 114560 max 114560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114560 Ave neighs/atom = 141.43210 Neighbor list builds = 0 Dangerous builds = 0 810 -3208.72284349426 eV 2.27456452404444 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06