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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -57.574712 0.0000000) to (40.711469 57.574712 5.7007459) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3861128 5.0801216 5.7007459 Created 814 atoms using lattice units in orthogonal box = (0.0000000 -57.574712 0.0000000) to (40.711469 57.574712 5.7007459) create_atoms CPU = 0.005 seconds 814 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3861128 5.0801216 5.7007459 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -57.574712 0.0000000) to (40.711469 57.574712 5.7007459) create_atoms CPU = 0.004 seconds 822 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 30 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1632 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.513 | 5.513 | 5.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5349.4431 0 -5349.4431 4500.8718 76 0 -5472.7317 0 -5472.7317 2407.9654 Loop time of 2.91908 on 1 procs for 76 steps with 1632 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 = -5349.44309559157 -5472.72654197293 -5472.73169640922 Force two-norm initial, final = 38.236857 0.18667032 Force max component initial, final = 6.0361325 0.027087712 Final line search alpha, max atom move = 1.0000000 0.027087712 Iterations, force evaluations = 76 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8378 | 2.8378 | 2.8378 | 0.0 | 97.22 Neigh | 0.029285 | 0.029285 | 0.029285 | 0.0 | 1.00 Comm | 0.026178 | 0.026178 | 0.026178 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02578 | | | 0.88 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7742.00 ave 7742 max 7742 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: 213612.0 ave 213612 max 213612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213612 Ave neighs/atom = 130.88971 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.518 | 5.518 | 5.518 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -5472.7317 0 -5472.7317 2407.9654 26724.539 79 0 -5472.8081 0 -5472.8081 0.32642105 26810.645 Loop time of 0.121554 on 1 procs for 3 steps with 1632 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 = -5472.73169640924 -5472.80429498354 -5472.80805072025 Force two-norm initial, final = 71.159878 1.1822364 Force max component initial, final = 48.610236 0.93044542 Final line search alpha, max atom move = 0.00010160558 9.4538451e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11696 | 0.11696 | 0.11696 | 0.0 | 96.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010843 | 0.0010843 | 0.0010843 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003513 | | | 2.89 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7913.00 ave 7913 max 7913 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: 215716.0 ave 215716 max 215716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215716 Ave neighs/atom = 132.17892 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.656 | 5.656 | 5.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5472.8081 0 -5472.8081 0.32642105 Loop time of 6.365e-06 on 1 procs for 0 steps with 1632 atoms 188.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7913.00 ave 7913 max 7913 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: 215584.0 ave 215584 max 215584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215584 Ave neighs/atom = 132.09804 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.656 | 5.656 | 5.656 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 -5472.8081 -5472.8081 40.705141 115.38329 5.7084089 0.32642105 0.32642105 19.371198 37.285265 -55.6772 2.6848707 1064.7929 Loop time of 6.876e-06 on 1 procs for 0 steps with 1632 atoms 305.4% 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 | | 6.876e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7913.00 ave 7913 max 7913 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107792.0 ave 107792 max 107792 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 215584.0 ave 215584 max 215584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215584 Ave neighs/atom = 132.09804 Neighbor list builds = 0 Dangerous builds = 0 1632 -5472.80805072024 eV 2.68487069093712 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03