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 = 4.0499994 4.0499994 4.0499994 Created orthogonal box = (0.0000000 -69.678825 0.0000000) to (34.839413 69.678825 4.0499994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6496345 5.6496345 4.0499994 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -69.678825 0.0000000) to (34.839413 69.678825 4.0499994) create_atoms CPU = 0.004 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6496345 5.6496345 4.0499994 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -69.678825 0.0000000) to (34.839413 69.678825 4.0499994) create_atoms CPU = 0.003 seconds 594 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 32 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_117656786760_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.466 | 5.466 | 5.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3935.1811 0 -3935.1811 5312.8848 97 0 -3977.7994 0 -3977.7994 4221.8659 Loop time of 4.48915 on 1 procs for 97 steps with 1186 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 = -3935.18110947076 -3977.7961611654 -3977.79944471783 Force two-norm initial, final = 31.066578 0.13099163 Force max component initial, final = 5.6896877 0.0089707076 Final line search alpha, max atom move = 1.0000000 0.0089707076 Iterations, force evaluations = 97 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3625 | 4.3625 | 4.3625 | 0.0 | 97.18 Neigh | 0.057293 | 0.057293 | 0.057293 | 0.0 | 1.28 Comm | 0.041177 | 0.041177 | 0.041177 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02819 | | | 0.63 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9812.00 ave 9812 max 9812 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: 206804.0 ave 206804 max 206804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206804 Ave neighs/atom = 174.37099 Neighbor list builds = 2 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.465 | 5.465 | 5.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -3977.7994 0 -3977.7994 4221.8659 19663.309 105 0 -3978.1175 0 -3978.1175 37.762534 19766.126 Loop time of 0.287811 on 1 procs for 8 steps with 1186 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 = -3977.79944471784 -3978.11614057739 -3978.11748375171 Force two-norm initial, final = 104.18871 0.85559650 Force max component initial, final = 95.027585 0.62639554 Final line search alpha, max atom move = 0.00029373279 0.00018399291 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24951 | 0.24951 | 0.24951 | 0.0 | 86.69 Neigh | 0.028774 | 0.028774 | 0.028774 | 0.0 | 10.00 Comm | 0.0026931 | 0.0026931 | 0.0026931 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006832 | | | 2.37 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9806.00 ave 9806 max 9806 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: 206684.0 ave 206684 max 206684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206684 Ave neighs/atom = 174.26981 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.604 | 5.604 | 5.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3978.1175 0 -3978.1175 37.762534 Loop time of 6.374e-06 on 1 procs for 0 steps with 1186 atoms 172.6% 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 | | 6.374e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9806.00 ave 9806 max 9806 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: 206684.0 ave 206684 max 206684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206684 Ave neighs/atom = 174.26981 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.604 | 5.604 | 5.604 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 -3978.1175 -3978.1175 34.808779 140.39892 4.0445387 37.762534 37.762534 50.728898 37.003406 25.555298 2.5410584 405.85288 Loop time of 6.866e-06 on 1 procs for 0 steps with 1186 atoms 276.7% 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 | | 6.866e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9806.00 ave 9806 max 9806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103342.0 ave 103342 max 103342 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206684.0 ave 206684 max 206684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206684 Ave neighs/atom = 174.26981 Neighbor list builds = 0 Dangerous builds = 0 1186 -3905.49429407087 eV 2.54105838485321 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05