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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -62.301835 0.0000000) to (38.150000 62.301835 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4119047 4.4499063 5.1383093 Created 1181 atoms using lattice units in orthogonal box = (0.0000000 -62.301835 0.0000000) to (38.150000 62.301835 7.7074639) create_atoms CPU = 0.006 seconds 1181 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4119047 4.4499063 5.1383093 Created 1181 atoms using lattice units in orthogonal box = (0.0000000 -62.301835 0.0000000) to (38.150000 62.301835 7.7074639) create_atoms CPU = 0.005 seconds 1181 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 43 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 2339 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.131 | 5.131 | 5.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15823.742 0 -15823.742 -311.40838 14 0 -15859.77 0 -15859.77 -5433.1872 Loop time of 2.85566 on 1 procs for 14 steps with 2339 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 = -15823.7424655762 -15859.7551809828 -15859.7698494917 Force two-norm initial, final = 26.856408 0.34842363 Force max component initial, final = 4.1524185 0.069438453 Final line search alpha, max atom move = 1.0000000 0.069438453 Iterations, force evaluations = 14 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8471 | 2.8471 | 2.8471 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032149 | 0.0032149 | 0.0032149 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005386 | | | 0.19 Nlocal: 2339.00 ave 2339 max 2339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6011.00 ave 6011 max 6011 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: 134464.0 ave 134464 max 134464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134464 Ave neighs/atom = 57.487815 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 14 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.131 | 5.131 | 5.131 Mbytes Step Temp E_pair E_mol TotEng Press Volume 14 0 -15859.77 0 -15859.77 -5433.1872 36638.432 16 0 -15859.935 0 -15859.935 275.93171 36558.55 Loop time of 0.496229 on 1 procs for 2 steps with 2339 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 = -15859.7698494917 -15859.9272613537 -15859.934826912 Force two-norm initial, final = 211.72101 11.422924 Force max component initial, final = 170.20092 10.795111 Final line search alpha, max atom move = 2.4380317e-05 0.00026318823 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49339 | 0.49339 | 0.49339 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054349 | 0.00054349 | 0.00054349 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002297 | | | 0.46 Nlocal: 2339.00 ave 2339 max 2339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6011.00 ave 6011 max 6011 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: 134678.0 ave 134678 max 134678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134678 Ave neighs/atom = 57.579307 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.269 | 5.269 | 5.269 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15859.935 0 -15859.935 275.93171 Loop time of 5.714e-06 on 1 procs for 0 steps with 2339 atoms 192.5% 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 | | 5.714e-06 | | |100.00 Nlocal: 2339.00 ave 2339 max 2339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6011.00 ave 6011 max 6011 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: 134682.0 ave 134682 max 134682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134682 Ave neighs/atom = 57.581018 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.269 | 5.269 | 5.269 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 -15859.935 -15859.935 38.099229 124.60367 7.7009081 275.93171 275.93171 -162.69157 517.79396 472.69275 2.1199001 1105.2176 Loop time of 6.355e-06 on 1 procs for 0 steps with 2339 atoms 299.0% 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 | | 6.355e-06 | | |100.00 Nlocal: 2339.00 ave 2339 max 2339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6011.00 ave 6011 max 6011 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67341.0 ave 67341 max 67341 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134682.0 ave 134682 max 134682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134682 Ave neighs/atom = 57.581018 Neighbor list builds = 0 Dangerous builds = 0 2339 -15859.934826912 eV 2.11990008121659 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04