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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -39.600343 0.0000000) to (8.0833861 39.600343 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8500317 5.2800457 5.9032705 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.600343 0.0000000) to (8.0833861 39.600343 8.8549058) create_atoms CPU = 0.002 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8500317 5.2800457 5.9032705 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.600343 0.0000000) to (8.0833861 39.600343 8.8549058) create_atoms CPU = 0.001 seconds 242 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 3 21 3 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1653.1757 0 -1653.1757 19488.34 44 0 -1691.5099 0 -1691.5099 7804.8638 Loop time of 0.702712 on 1 procs for 44 steps with 480 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 = -1653.17569170825 -1691.50871991212 -1691.50988978982 Force two-norm initial, final = 45.326971 0.10824955 Force max component initial, final = 9.3929054 0.030622333 Final line search alpha, max atom move = 1.0000000 0.030622333 Iterations, force evaluations = 44 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68937 | 0.68937 | 0.68937 | 0.0 | 98.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0071234 | 0.0071234 | 0.0071234 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006215 | | | 0.88 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4096.00 ave 4096 max 4096 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: 83660.0 ave 83660 max 83660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83660 Ave neighs/atom = 174.29167 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -1691.5099 0 -1691.5099 7804.8638 5668.9968 53 0 -1691.6827 0 -1691.6827 -5.6155656 5700.9313 Loop time of 0.0922981 on 1 procs for 9 steps with 480 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 = -1691.50988978982 -1691.6825191474 -1691.68266507094 Force two-norm initial, final = 54.161072 0.34020942 Force max component initial, final = 48.062435 0.13415738 Final line search alpha, max atom move = 0.0015771456 0.00021158573 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.088095 | 0.088095 | 0.088095 | 0.0 | 95.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090513 | 0.00090513 | 0.00090513 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003298 | | | 3.57 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4096.00 ave 4096 max 4096 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: 81800.0 ave 81800 max 81800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81800 Ave neighs/atom = 170.41667 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.674 | 4.674 | 4.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1691.6827 0 -1691.6827 -5.6155656 Loop time of 6.595e-06 on 1 procs for 0 steps with 480 atoms 197.1% 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 | | 6.595e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4063.00 ave 4063 max 4063 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: 81376.0 ave 81376 max 81376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81376 Ave neighs/atom = 169.53333 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.674 | 4.674 | 4.674 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 -1691.6827 -1691.6827 8.0724632 79.84979 8.8443508 -5.6155656 -5.6155656 25.495537 -4.683896 -37.658338 2.2739196 291.38225 Loop time of 8.098e-06 on 1 procs for 0 steps with 480 atoms 0.0% 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 | | 8.098e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4063.00 ave 4063 max 4063 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40688.0 ave 40688 max 40688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81376.0 ave 81376 max 81376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81376 Ave neighs/atom = 169.53333 Neighbor list builds = 0 Dangerous builds = 0 480 -1691.68266507094 eV 2.2739195864301 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01