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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -58.630032 0.0000000) to (20.728847 58.630032 5.1030893) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6533218 4.4416691 5.1030893 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.630032 0.0000000) to (20.728847 58.630032 5.1030893) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6533218 4.4416691 5.1030893 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.630032 0.0000000) to (20.728847 58.630032 5.1030893) create_atoms CPU = 0.001 seconds 530 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 = 7 40 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 6 atoms, new total = 1052 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_549900287421_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 = 7 40 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) = 4.624 | 4.624 | 4.624 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4172.7949 0 -4172.7949 76894.366 106 0 -4469.789 0 -4469.789 -4546.8759 Loop time of 8.10792 on 1 procs for 106 steps with 1052 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4172.7948749905 -4469.78481016608 -4469.78902698872 Force two-norm initial, final = 1026.7026 0.17983502 Force max component initial, final = 354.30623 0.047697750 Final line search alpha, max atom move = 1.0000000 0.047697750 Iterations, force evaluations = 106 196 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0677 | 8.0677 | 8.0677 | 0.0 | 99.50 Neigh | 0.013263 | 0.013263 | 0.013263 | 0.0 | 0.16 Comm | 0.014009 | 0.014009 | 0.014009 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01299 | | | 0.16 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4908.00 ave 4908 max 4908 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: 81128.0 ave 81128 max 81128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81128 Ave neighs/atom = 77.117871 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 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 : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -4469.789 0 -4469.789 -4546.8759 12403.905 114 0 -4470.128 0 -4470.128 -145.37371 12370.939 Loop time of 0.408169 on 1 procs for 8 steps with 1052 atoms 94.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4469.78902698872 -4470.12420589467 -4470.12801910655 Force two-norm initial, final = 96.589319 2.1605084 Force max component initial, final = 96.259746 1.7930531 Final line search alpha, max atom move = 0.00017935398 0.00032159122 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4053 | 0.4053 | 0.4053 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045324 | 0.00045324 | 0.00045324 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002413 | | | 0.59 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5083.00 ave 5083 max 5083 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: 80508.0 ave 80508 max 80508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80508 Ave neighs/atom = 76.528517 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 = 7 40 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) = 4.760 | 4.760 | 4.760 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4470.128 0 -4470.128 -145.37371 Loop time of 2.502e-06 on 1 procs for 0 steps with 1052 atoms 199.8% 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 | | 2.502e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5083.00 ave 5083 max 5083 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: 80616.0 ave 80616 max 80616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80616 Ave neighs/atom = 76.631179 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 = 7 40 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) = 4.760 | 4.760 | 4.760 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 -4470.128 -4470.128 20.579282 117.73882 5.1056701 -145.37371 -145.37371 -230.54512 -126.45185 -79.124161 2.3687018 1049.2204 Loop time of 2.796e-06 on 1 procs for 0 steps with 1052 atoms 250.4% 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 | | 2.796e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5083.00 ave 5083 max 5083 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40308.0 ave 40308 max 40308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80616.0 ave 80616 max 80616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80616 Ave neighs/atom = 76.631179 Neighbor list builds = 0 Dangerous builds = 0 1052 -4470.12801910655 eV 2.36870180752176 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08