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 -47.388190 0.0000000) to (33.508511 47.388190 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2341415 6.0612802 5.1100000 Created 683 atoms using lattice units in orthogonal box = (0.0000000 -47.388190 0.0000000) to (33.508511 47.388190 5.1100000) create_atoms CPU = 0.006 seconds 683 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2341415 6.0612802 5.1100000 Created 691 atoms using lattice units in orthogonal box = (0.0000000 -47.388190 0.0000000) to (33.508511 47.388190 5.1100000) create_atoms CPU = 0.005 seconds 691 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 = 12 34 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1374 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 = 12 34 2 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) = 4.661 | 4.661 | 4.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4699.3843 0 -4699.3843 35690.479 58 0 -4847.2278 0 -4847.2278 4273.6033 Loop time of 4.97977 on 1 procs for 58 steps with 1374 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 = -4699.38427703786 -4847.22397603223 -4847.22779638977 Force two-norm initial, final = 166.24567 0.17742455 Force max component initial, final = 30.692803 0.035653508 Final line search alpha, max atom move = 1.0000000 0.035653508 Iterations, force evaluations = 58 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9327 | 4.9327 | 4.9327 | 0.0 | 99.06 Neigh | 0.015164 | 0.015164 | 0.015164 | 0.0 | 0.30 Comm | 0.01522 | 0.01522 | 0.01522 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01664 | | | 0.33 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5338.00 ave 5338 max 5338 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: 81024.0 ave 81024 max 81024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81024 Ave neighs/atom = 58.969432 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 34 2 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.661 | 4.661 | 4.661 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -4847.2278 0 -4847.2278 4273.6033 16228.417 60 0 -4847.2977 0 -4847.2977 -213.03996 16279.887 Loop time of 0.193788 on 1 procs for 2 steps with 1374 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 = -4847.22779638978 -4847.29322496079 -4847.29774396944 Force two-norm initial, final = 76.123819 6.7941992 Force max component initial, final = 53.625148 5.8380004 Final line search alpha, max atom move = 6.2674551e-05 0.00036589405 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19149 | 0.19149 | 0.19149 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050402 | 0.00050402 | 0.00050402 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001791 | | | 0.92 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5360.00 ave 5360 max 5360 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: 81764.0 ave 81764 max 81764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81764 Ave neighs/atom = 59.508006 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 = 12 34 2 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) = 4.799 | 4.799 | 4.799 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4847.2977 0 -4847.2977 -213.03996 Loop time of 6.234e-06 on 1 procs for 0 steps with 1374 atoms 208.5% 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 | | 6.234e-06 | | |100.00 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5360.00 ave 5360 max 5360 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: 79536.0 ave 79536 max 79536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79536 Ave neighs/atom = 57.886463 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 = 12 34 2 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) = 4.799 | 4.799 | 4.799 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 -4847.2977 -4847.2977 33.540726 94.91547 5.1137785 -213.03996 -213.03996 -271.74721 207.59591 -574.96858 2.3806741 1050.8296 Loop time of 6.625e-06 on 1 procs for 0 steps with 1374 atoms 241.5% 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 | | 6.625e-06 | | |100.00 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5360.00 ave 5360 max 5360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39768.0 ave 39768 max 39768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79536.0 ave 79536 max 79536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79536 Ave neighs/atom = 57.886463 Neighbor list builds = 0 Dangerous builds = 0 1374 -4847.29774396944 eV 2.38067411994725 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05