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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -48.871701 0.0000000) to (59.855365 48.871701 9.9073306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7395556 6.0252782 6.6048870 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -48.871701 0.0000000) to (59.855365 48.871701 9.9073306) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7395556 6.0252782 6.6048870 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.871701 0.0000000) to (59.855365 48.871701 9.9073306) create_atoms CPU = 0.002 seconds 1755 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 19 31 4 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 3495 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_099716416216_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.613 | 5.613 | 5.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10652.168 0 -10652.168 38497.002 102 0 -11706.317 0 -11706.317 1573.0169 Loop time of 17.7385 on 1 procs for 102 steps with 3495 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 = -10652.1676069604 -11706.3059062437 -11706.3172168856 Force two-norm initial, final = 713.66082 0.28532777 Force max component initial, final = 90.985785 0.055123017 Final line search alpha, max atom move = 1.0000000 0.055123017 Iterations, force evaluations = 102 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.619 | 17.619 | 17.619 | 0.0 | 99.33 Neigh | 0.075331 | 0.075331 | 0.075331 | 0.0 | 0.42 Comm | 0.015401 | 0.015401 | 0.015401 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02863 | | | 0.16 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7710.00 ave 7710 max 7710 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: 266156.0 ave 266156 max 266156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266156 Ave neighs/atom = 76.153362 Neighbor list builds = 4 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.616 | 5.616 | 5.616 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -11706.317 0 -11706.317 1573.0169 57962.511 109 0 -11706.813 0 -11706.813 5.2317105 58075.877 Loop time of 1.014 on 1 procs for 7 steps with 3495 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 = -11706.3172168857 -11706.8131100666 -11706.8131173471 Force two-norm initial, final = 167.91857 0.56908657 Force max component initial, final = 167.87209 0.36493295 Final line search alpha, max atom move = 0.0014088073 0.00051412019 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0089 | 1.0089 | 1.0089 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057706 | 0.00057706 | 0.00057706 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0045 | | | 0.44 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7690.00 ave 7690 max 7690 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: 266566.0 ave 266566 max 266566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266566 Ave neighs/atom = 76.270672 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.754 | 5.754 | 5.754 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11706.813 0 -11706.813 5.2317105 Loop time of 1.993e-06 on 1 procs for 0 steps with 3495 atoms 200.7% 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 | | 1.993e-06 | | |100.00 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7695.00 ave 7695 max 7695 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: 266050.0 ave 266050 max 266050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266050 Ave neighs/atom = 76.123033 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.754 | 5.754 | 5.754 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 -11706.813 -11706.813 59.736276 98.328653 9.8872962 5.2317105 5.2317105 0.80372541 4.8441252 10.047281 2.511807 1868.8153 Loop time of 2.148e-06 on 1 procs for 0 steps with 3495 atoms 232.8% 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 | | 2.148e-06 | | |100.00 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7695.00 ave 7695 max 7695 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133025.0 ave 133025 max 133025 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 266050.0 ave 266050 max 266050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266050 Ave neighs/atom = 76.123033 Neighbor list builds = 0 Dangerous builds = 0 3495 -11706.8131173471 eV 2.51180702662487 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19