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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -38.560170 0.0000000) to (22.260640 38.560170 6.2546998) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8580631 5.4114469 6.2546998 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.560170 0.0000000) to (22.260640 38.560170 6.2546998) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8580631 5.4114469 6.2546998 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.560170 0.0000000) to (22.260640 38.560170 6.2546998) create_atoms CPU = 0.001 seconds 458 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 29 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 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 20 atoms, new total = 896 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.898 | 4.898 | 4.898 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3749.9836 0 -3749.9836 -930.59223 89 0 -3783.8097 0 -3783.8097 -21952.678 Loop time of 6.8588 on 1 procs for 89 steps with 896 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 = -3749.98358813156 -3783.80591840236 -3783.80967238628 Force two-norm initial, final = 34.093175 0.22436372 Force max component initial, final = 6.1259202 0.048253124 Final line search alpha, max atom move = 1.0000000 0.048253124 Iterations, force evaluations = 89 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8489 | 6.8489 | 6.8489 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041002 | 0.0041002 | 0.0041002 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005844 | | | 0.09 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3094.00 ave 3094 max 3094 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: 47552.0 ave 47552 max 47552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47552 Ave neighs/atom = 53.071429 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.898 | 4.898 | 4.898 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -3783.8097 0 -3783.8097 -21952.678 10737.744 95 0 -3784.2984 0 -3784.2984 -7823.5677 10644.252 Loop time of 0.380259 on 1 procs for 6 steps with 896 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3783.80967238628 -3784.29771355006 -3784.29840373336 Force two-norm initial, final = 156.25498 0.47413704 Force max component initial, final = 116.18116 0.064907531 Final line search alpha, max atom move = 0.00030104030 1.9539782e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37879 | 0.37879 | 0.37879 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021855 | 0.00021855 | 0.00021855 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001246 | | | 0.33 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3141.00 ave 3141 max 3141 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: 48200.0 ave 48200 max 48200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48200 Ave neighs/atom = 53.794643 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.036 | 5.036 | 5.036 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3784.2984 0 -3784.2984 -7823.5677 Loop time of 1.789e-06 on 1 procs for 0 steps with 896 atoms 111.8% 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 | | 1.789e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3141.00 ave 3141 max 3141 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: 48236.0 ave 48236 max 48236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48236 Ave neighs/atom = 53.834821 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.036 | 5.036 | 5.036 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 -3784.2984 -3784.2984 22.146875 77.120341 6.2320903 -7823.5677 -7823.5677 4.1053173 -23468.297 -6.5112184 2.3028307 486.6988 Loop time of 1.34e-06 on 1 procs for 0 steps with 896 atoms 149.3% 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 | | 1.34e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3141.00 ave 3141 max 3141 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24118.0 ave 24118 max 24118 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48236.0 ave 48236 max 48236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48236 Ave neighs/atom = 53.834821 Neighbor list builds = 0 Dangerous builds = 0 896 -3784.29840373336 eV 2.30283071380589 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07