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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -41.410754 0.0000000) to (29.281825 41.410754 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4366402 5.6469210 5.0973115 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.410754 0.0000000) to (29.281825 41.410754 5.0973115) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4366402 5.6469210 5.0973115 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.410754 0.0000000) to (29.281825 41.410754 5.0973115) create_atoms CPU = 0.001 seconds 532 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1060 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4243.0857 0 -4243.0857 85196.742 433 0 -4508.1141 0 -4508.1141 3964.8619 Loop time of 28.7136 on 1 procs for 433 steps with 1060 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 = -4243.08574741831 -4508.1095822301 -4508.11408150559 Force two-norm initial, final = 463.50613 0.18361282 Force max component initial, final = 82.998460 0.056248368 Final line search alpha, max atom move = 0.85435191 0.048055900 Iterations, force evaluations = 433 815 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.553 | 28.553 | 28.553 | 0.0 | 99.44 Neigh | 0.078068 | 0.078068 | 0.078068 | 0.0 | 0.27 Comm | 0.040769 | 0.040769 | 0.040769 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04134 | | | 0.14 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4576.00 ave 4576 max 4576 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: 74028.0 ave 74028 max 74028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74028 Ave neighs/atom = 69.837736 Neighbor list builds = 14 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 433 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press Volume 433 0 -4508.1141 0 -4508.1141 3964.8619 12361.821 446 0 -4508.9534 0 -4508.9534 -8.9051795 12391.169 Loop time of 0.497203 on 1 procs for 13 steps with 1060 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 = -4508.11408150559 -4508.95317542578 -4508.95336509901 Force two-norm initial, final = 129.15771 0.93875042 Force max component initial, final = 123.25033 0.43019952 Final line search alpha, max atom move = 0.00096227051 0.00041396831 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4883 | 0.4883 | 0.4883 | 0.0 | 98.21 Neigh | 0.0052459 | 0.0052459 | 0.0052459 | 0.0 | 1.06 Comm | 0.00065461 | 0.00065461 | 0.00065461 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003001 | | | 0.60 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4592.00 ave 4592 max 4592 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: 73920.0 ave 73920 max 73920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73920 Ave neighs/atom = 69.735849 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.738 | 4.738 | 4.738 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4508.9534 0 -4508.9534 -8.9051795 Loop time of 1.748e-06 on 1 procs for 0 steps with 1060 atoms 171.6% 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 | | 1.748e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4592.00 ave 4592 max 4592 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: 73890.0 ave 73890 max 73890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73890 Ave neighs/atom = 69.707547 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.738 | 4.738 | 4.738 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 -4508.9534 -4508.9534 29.162783 83.82612 5.0687858 -8.9051795 -8.9051795 43.655147 -15.057232 -55.313453 2.3854758 4638.2669 Loop time of 2.281e-06 on 1 procs for 0 steps with 1060 atoms 219.2% 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 | | 2.281e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4592.00 ave 4592 max 4592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36945.0 ave 36945 max 36945 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73890.0 ave 73890 max 73890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73890 Ave neighs/atom = 69.707547 Neighbor list builds = 0 Dangerous builds = 0 1060 -4508.95336509901 eV 2.38547575746458 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29