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 = 2.8552583 2.8552583 2.8552583 Created orthogonal box = (0.0000000 -40.781245 0.0000000) to (28.836695 40.781245 4.0379450) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5234032 3.5983452 4.0379450 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.781245 0.0000000) to (28.836695 40.781245 4.0379450) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5234032 3.5983452 4.0379450 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.781245 0.0000000) to (28.836695 40.781245 4.0379450) 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 = 8 ghost atom cutoff = 8 binsize = 4, 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 8 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_942420706858_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2764.6793 0 -2764.6793 127461.88 63 0 -3339.1417 0 -3339.1417 -1967.7316 Loop time of 0.843473 on 1 procs for 63 steps with 812 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 = -2764.67930626888 -3339.13845932265 -3339.14169209992 Force two-norm initial, final = 1086.3642 0.15834020 Force max component initial, final = 362.54626 0.015926123 Final line search alpha, max atom move = 1.0000000 0.015926123 Iterations, force evaluations = 63 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81265 | 0.81265 | 0.81265 | 0.0 | 96.35 Neigh | 0.017235 | 0.017235 | 0.017235 | 0.0 | 2.04 Comm | 0.0072874 | 0.0072874 | 0.0072874 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006297 | | | 0.75 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5940.00 ave 5940 max 5940 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: 136976.0 ave 136976 max 136976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136976 Ave neighs/atom = 168.68966 Neighbor list builds = 2 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.957 | 4.957 | 4.957 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -3339.1417 0 -3339.1417 -1967.7316 9497.2172 66 0 -3339.1579 0 -3339.1579 -68.028458 9486.9215 Loop time of 0.0455717 on 1 procs for 3 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 = -3339.14169209986 -3339.15784271676 -3339.15789085341 Force two-norm initial, final = 23.175052 0.80907679 Force max component initial, final = 17.299559 0.60919792 Final line search alpha, max atom move = 0.0010656319 0.00064918076 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04394 | 0.04394 | 0.04394 | 0.0 | 96.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030159 | 0.00030159 | 0.00030159 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00133 | | | 2.92 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5974.00 ave 5974 max 5974 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: 137016.0 ave 137016 max 137016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137016 Ave neighs/atom = 168.73892 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.095 | 5.095 | 5.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3339.1579 0 -3339.1579 -68.028458 Loop time of 2.382e-06 on 1 procs for 0 steps with 812 atoms 125.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5974.00 ave 5974 max 5974 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: 137024.0 ave 137024 max 137024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137024 Ave neighs/atom = 168.74877 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.095 | 5.095 | 5.095 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 -3339.1579 -3339.1579 28.809513 81.642596 4.033412 -68.028458 -68.028458 -83.440746 -17.877163 -102.76747 2.2815534 433.41345 Loop time of 2.888e-06 on 1 procs for 0 steps with 812 atoms 207.8% 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 | | 2.888e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5974.00 ave 5974 max 5974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68512.0 ave 68512 max 68512 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137024.0 ave 137024 max 137024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137024 Ave neighs/atom = 168.74877 Neighbor list builds = 0 Dangerous builds = 0 812 -3339.15789085341 eV 2.28155344920721 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01