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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7941954 5.5194308 5.9005197 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7941954 5.5194308 5.9005197 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) create_atoms CPU = 0.001 seconds 507 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 35 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1007 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 35 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3463.5836 0 -3463.5836 29094.005 44 0 -3551.3386 0 -3551.3386 5351.9001 Loop time of 1.39136 on 1 procs for 44 steps with 1007 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 = -3463.58362933498 -3551.33661688308 -3551.3386321349 Force two-norm initial, final = 153.17907 0.14362161 Force max component initial, final = 36.016285 0.054441146 Final line search alpha, max atom move = 1.0000000 0.054441146 Iterations, force evaluations = 44 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3827 | 1.3827 | 1.3827 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035111 | 0.0035111 | 0.0035111 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005106 | | | 0.37 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3594.00 ave 3594 max 3594 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: 54886.0 ave 54886 max 54886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54886 Ave neighs/atom = 54.504469 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 35 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3551.3386 0 -3551.3386 5351.9001 11888.259 49 0 -3551.5028 0 -3551.5028 -297.55164 11935.591 Loop time of 0.121423 on 1 procs for 5 steps with 1007 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 = -3551.3386321349 -3551.50081369587 -3551.50278507819 Force two-norm initial, final = 80.046213 4.0562804 Force max component initial, final = 69.484932 2.8122496 Final line search alpha, max atom move = 0.00016227978 0.00045637124 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11972 | 0.11972 | 0.11972 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024173 | 0.00024173 | 0.00024173 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001459 | | | 1.20 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3594.00 ave 3594 max 3594 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: 61882.0 ave 61882 max 61882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61882 Ave neighs/atom = 61.451837 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 36 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.658 | 4.658 | 4.658 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3551.5028 0 -3551.5028 -297.55164 Loop time of 2.38e-06 on 1 procs for 0 steps with 1007 atoms 168.1% 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 | | 2.38e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3594.00 ave 3594 max 3594 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: 57566.0 ave 57566 max 57566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57566 Ave neighs/atom = 57.165839 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 36 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.658 | 4.658 | 4.658 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 -3551.5028 -3551.5028 13.53244 99.802787 8.8374133 -297.55164 -297.55164 -359.55075 -156.17138 -376.93279 2.2926271 425.8462 Loop time of 2.556e-06 on 1 procs for 0 steps with 1007 atoms 195.6% 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 | | 2.556e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3594.00 ave 3594 max 3594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28783.0 ave 28783 max 28783 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57566.0 ave 57566 max 57566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57566 Ave neighs/atom = 57.165839 Neighbor list builds = 0 Dangerous builds = 0 1007 -3551.50278507819 eV 2.29262713959832 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01