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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -41.251551 0.0000000) to (35.721389 41.251551 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4115313 6.3457703 7.0055407 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.251551 0.0000000) to (35.721389 41.251551 7.0055407) create_atoms CPU = 0.004 seconds 629 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4115313 6.3457703 7.0055407 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.251551 0.0000000) to (35.721389 41.251551 7.0055407) create_atoms CPU = 0.003 seconds 629 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 11 25 3 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1234 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4096.5519 0 -4096.5519 4771.7981 95 0 -4126.9279 0 -4126.9279 -2919.4069 Loop time of 18.3427 on 1 procs for 95 steps with 1234 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 = -4096.55185229435 -4126.92404509406 -4126.92785541916 Force two-norm initial, final = 35.437004 0.14801528 Force max component initial, final = 6.7398905 0.042087727 Final line search alpha, max atom move = 0.81482570 0.034294161 Iterations, force evaluations = 95 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.256 | 18.256 | 18.256 | 0.0 | 99.53 Neigh | 0.043156 | 0.043156 | 0.043156 | 0.0 | 0.24 Comm | 0.018008 | 0.018008 | 0.018008 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02562 | | | 0.14 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4006.00 ave 4006 max 4006 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: 94970.0 ave 94970 max 94970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94970 Ave neighs/atom = 76.961102 Neighbor list builds = 3 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -4126.9279 0 -4126.9279 -2919.4069 20646.207 98 0 -4126.9939 0 -4126.9939 -306.57933 20576.828 Loop time of 0.693718 on 1 procs for 3 steps with 1234 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 = -4126.92785541917 -4126.99346486456 -4126.99390407969 Force two-norm initial, final = 54.150333 0.15636490 Force max component initial, final = 41.993926 0.037183966 Final line search alpha, max atom move = 0.00049707368 1.8483171e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69013 | 0.69013 | 0.69013 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062032 | 0.00062032 | 0.00062032 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002972 | | | 0.43 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4000.00 ave 4000 max 4000 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: 95016.0 ave 95016 max 95016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95016 Ave neighs/atom = 76.998379 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4126.9939 0 -4126.9939 -306.57933 Loop time of 8.74e-06 on 1 procs for 0 steps with 1234 atoms 160.2% 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 | | 8.74e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4003.00 ave 4003 max 4003 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: 95036.0 ave 95036 max 95036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95036 Ave neighs/atom = 77.014587 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.722 | 4.722 | 4.722 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 -4126.9939 -4126.9939 35.677897 82.503103 6.9905107 -306.57933 -306.57933 -1.1243281 -919.29082 0.67714636 2.5158303 1057.1474 Loop time of 8.56e-06 on 1 procs for 0 steps with 1234 atoms 233.6% 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 | | 8.56e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4003.00 ave 4003 max 4003 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47518.0 ave 47518 max 47518 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95036.0 ave 95036 max 95036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95036 Ave neighs/atom = 77.014587 Neighbor list builds = 0 Dangerous builds = 0 1234 -4126.99390407969 eV 2.51583031358548 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19