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 = 4.0515263 4.0515263 4.0515263 Created orthogonal box = (0.0000000 -40.918410 0.0000000) to (28.933685 40.918410 5.7297234) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1059444 6.4185741 5.7297234 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.918410 0.0000000) to (28.933685 40.918410 5.7297234) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1059444 6.4185741 5.7297234 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.918410 0.0000000) to (28.933685 40.918410 5.7297234) 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1768.9076 0 -1768.9076 194068.35 118 0 -2714.5848 0 -2714.5848 6690.1467 Loop time of 1.59042 on 1 procs for 118 steps with 812 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1768.90764390019 -2714.58228985531 -2714.5847515887 Force two-norm initial, final = 2047.1590 0.18081714 Force max component initial, final = 585.90255 0.046520263 Final line search alpha, max atom move = 1.0000000 0.046520263 Iterations, force evaluations = 118 226 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5506 | 1.5506 | 1.5506 | 0.0 | 97.50 Neigh | 0.018228 | 0.018228 | 0.018228 | 0.0 | 1.15 Comm | 0.011532 | 0.011532 | 0.011532 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01002 | | | 0.63 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4811.00 ave 4811 max 4811 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: 107436.0 ave 107436 max 107436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107436 Ave neighs/atom = 132.31034 Neighbor list builds = 3 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.946 | 4.946 | 4.946 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -2714.5848 0 -2714.5848 6690.1467 13567.073 127 0 -2715.0636 0 -2715.0636 -87.432347 13660.727 Loop time of 0.120457 on 1 procs for 9 steps with 812 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2714.5847515887 -2715.06178537635 -2715.06357971273 Force two-norm initial, final = 129.00006 2.3849727 Force max component initial, final = 124.73487 1.5751868 Final line search alpha, max atom move = 0.00025401517 0.00040012133 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11561 | 0.11561 | 0.11561 | 0.0 | 95.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086986 | 0.00086986 | 0.00086986 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003976 | | | 3.30 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5156.00 ave 5156 max 5156 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: 107532.0 ave 107532 max 107532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107532 Ave neighs/atom = 132.42857 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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 -2715.0636 0 -2715.0636 -87.432347 Loop time of 2.981e-06 on 1 procs for 0 steps with 812 atoms 134.2% 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 | | 2.981e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5156.00 ave 5156 max 5156 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: 107340.0 ave 107340 max 107340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107340 Ave neighs/atom = 132.19212 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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 -2715.0636 -2715.0636 28.883024 82.495052 5.7332815 -87.432347 -87.432347 -176.24367 98.804606 -184.85798 2.6267377 637.24237 Loop time of 3.25e-06 on 1 procs for 0 steps with 812 atoms 153.8% 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 | | 3.25e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5156.00 ave 5156 max 5156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53670.0 ave 53670 max 53670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107340.0 ave 107340 max 107340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107340 Ave neighs/atom = 132.19212 Neighbor list builds = 0 Dangerous builds = 0 812 -2715.06357970523 eV 2.62673772826567 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02