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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -42.386327 0.0000000) to (11.535258 42.386327 7.5515990) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9436820 4.7092494 5.0343993 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -42.386327 0.0000000) to (11.535258 42.386327 7.5515990) create_atoms CPU = 0.001 seconds 254 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9436820 4.7092494 5.0343993 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -42.386327 0.0000000) to (11.535258 42.386327 7.5515990) create_atoms CPU = 0.000 seconds 254 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 26 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 6 atoms, new total = 502 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.860 | 4.860 | 4.860 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3146.8495 0 -3146.8495 53136.729 138 0 -3254.8628 0 -3254.8628 1227.8869 Loop time of 33.2684 on 1 procs for 138 steps with 502 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 = -3146.84949292685 -3254.85982563644 -3254.86278903551 Force two-norm initial, final = 172.95768 0.26583924 Force max component initial, final = 53.512444 0.063591640 Final line search alpha, max atom move = 1.0000000 0.063591640 Iterations, force evaluations = 138 266 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.242 | 33.242 | 33.242 | 0.0 | 99.92 Neigh | 0.014738 | 0.014738 | 0.014738 | 0.0 | 0.04 Comm | 0.0060748 | 0.0060748 | 0.0060748 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005766 | | | 0.02 Nlocal: 502.000 ave 502 max 502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2932.00 ave 2932 max 2932 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: 35348.0 ave 35348 max 35348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35348 Ave neighs/atom = 70.414343 Neighbor list builds = 1 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 138 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.242 | 5.242 | 5.242 Mbytes Step Temp E_pair E_mol TotEng Press Volume 138 0 -3254.8628 0 -3254.8628 1227.8869 7384.5156 139 0 -3254.8639 0 -3254.8639 911.50465 7385.5596 Loop time of 0.376618 on 1 procs for 1 steps with 502 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 = -3254.86278903551 -3254.86278903551 -3254.86394514302 Force two-norm initial, final = 5.6401248 1.0426594 Force max component initial, final = 4.8341103 0.84953822 Final line search alpha, max atom move = 0.00020686330 0.00017573828 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37631 | 0.37631 | 0.37631 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.4571e-05 | 6.4571e-05 | 6.4571e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002393 | | | 0.06 Nlocal: 502.000 ave 502 max 502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2929.00 ave 2929 max 2929 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: 37158.0 ave 37158 max 37158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37158 Ave neighs/atom = 74.019920 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.380 | 5.380 | 5.380 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3254.8639 0 -3254.8639 911.50465 Loop time of 1.595e-06 on 1 procs for 0 steps with 502 atoms 125.4% 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 | | 1.595e-06 | | |100.00 Nlocal: 502.000 ave 502 max 502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2929.00 ave 2929 max 2929 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: 37154.0 ave 37154 max 37154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37154 Ave neighs/atom = 74.011952 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.380 | 5.380 | 5.380 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 -3254.8639 -3254.8639 11.539322 84.772654 7.5500064 911.50465 911.50465 -116.8685 3035.637 -184.25457 2.5071757 1186.2998 Loop time of 1.511e-06 on 1 procs for 0 steps with 502 atoms 132.4% 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 | | 1.511e-06 | | |100.00 Nlocal: 502.000 ave 502 max 502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2929.00 ave 2929 max 2929 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18577.0 ave 18577 max 18577 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37154.0 ave 37154 max 37154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37154 Ave neighs/atom = 74.011952 Neighbor list builds = 0 Dangerous builds = 0 502 -3254.86394514302 eV 2.50717574930549 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34