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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -58.908403 0.0000000) to (29.454201 58.908403 3.6533440) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9845571 4.9845571 3.6533440 Created 519 atoms using lattice units in orthogonal box = (0.0000000 -58.908403 0.0000000) to (29.454201 58.908403 3.6533440) create_atoms CPU = 0.003 seconds 519 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9845571 4.9845571 3.6533440 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -58.908403 0.0000000) to (29.454201 58.908403 3.6533440) create_atoms CPU = 0.002 seconds 521 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 27 1 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1040 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_673777079812_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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.451 | 5.451 | 5.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3230.7901 0 -3230.7901 29065.525 58 0 -3386.3332 0 -3386.3332 2989.3321 Loop time of 2.50433 on 1 procs for 58 steps with 1040 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3230.79005562286 -3386.33029260057 -3386.33315670967 Force two-norm initial, final = 198.64189 0.19491629 Force max component initial, final = 41.207525 0.026582778 Final line search alpha, max atom move = 1.0000000 0.026582778 Iterations, force evaluations = 58 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4333 | 2.4333 | 2.4333 | 0.0 | 97.16 Neigh | 0.030914 | 0.030914 | 0.030914 | 0.0 | 1.23 Comm | 0.024867 | 0.024867 | 0.024867 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01523 | | | 0.61 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10201.0 ave 10201 max 10201 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: 232916.0 ave 232916 max 232916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232916 Ave neighs/atom = 223.95769 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.444 | 5.444 | 5.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3386.3332 0 -3386.3332 2989.3321 12677.834 63 0 -3386.4494 0 -3386.4494 198.64554 12704.429 Loop time of 0.167805 on 1 procs for 5 steps with 1040 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 = -3386.33315670968 -3386.44615180274 -3386.4493576407 Force two-norm initial, final = 58.758416 2.8858032 Force max component initial, final = 42.900981 2.2220854 Final line search alpha, max atom move = 0.00014282211 0.00031736293 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16221 | 0.16221 | 0.16221 | 0.0 | 96.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014088 | 0.0014088 | 0.0014088 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004183 | | | 2.49 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9437.00 ave 9437 max 9437 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: 232876.0 ave 232876 max 232876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232876 Ave neighs/atom = 223.91923 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.582 | 5.582 | 5.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3386.4494 0 -3386.4494 198.64554 Loop time of 6.265e-06 on 1 procs for 0 steps with 1040 atoms 191.5% 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 | | 6.265e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9449.00 ave 9449 max 9449 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: 232760.0 ave 232760 max 232760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232760 Ave neighs/atom = 223.80769 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.582 | 5.582 | 5.582 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 -3386.4494 -3386.4494 29.370403 117.92772 3.6680003 198.64554 198.64554 194.8615 119.72005 281.35506 2.3014205 363.67215 Loop time of 6.866e-06 on 1 procs for 0 steps with 1040 atoms 276.7% 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 | | 6.866e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9449.00 ave 9449 max 9449 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116380.0 ave 116380 max 116380 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 232760.0 ave 232760 max 232760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232760 Ave neighs/atom = 223.80769 Neighbor list builds = 0 Dangerous builds = 0 1040 -3386.4493576407 eV 2.30142052245569 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03