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 = 3.1501534 3.1501534 3.1501534 Created orthogonal box = (0.0000000 -47.566273 0.0000000) to (33.634434 47.566273 4.4549896) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3107001 4.5897281 4.4549896 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.566273 0.0000000) to (33.634434 47.566273 4.4549896) create_atoms CPU = 0.004 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3107001 4.5897281 4.4549896 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.566273 0.0000000) to (33.634434 47.566273 4.4549896) create_atoms CPU = 0.003 seconds 458 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 24 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 8.100217342376709 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_271256517527_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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.977 | 4.977 | 4.977 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6012.0793 0 -6012.0793 46578.506 68 0 -6185.7412 0 -6185.7412 22001.592 Loop time of 1.81235 on 1 procs for 68 steps with 914 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 = -6012.07931785009 -6185.73616427242 -6185.74118972829 Force two-norm initial, final = 281.21609 0.25902899 Force max component initial, final = 111.38324 0.044217285 Final line search alpha, max atom move = 1.0000000 0.044217285 Iterations, force evaluations = 68 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7792 | 1.7792 | 1.7792 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017847 | 0.017847 | 0.017847 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01532 | | | 0.85 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6214.00 ave 6214 max 6214 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: 124924.0 ave 124924 max 124924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124924 Ave neighs/atom = 136.67834 Neighbor list builds = 0 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -6185.7412 0 -6185.7412 22001.592 14254.761 81 0 -6187.9769 0 -6187.9769 232.94349 14373.741 Loop time of 0.257022 on 1 procs for 13 steps with 914 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 = -6185.74118972828 -6187.97683194951 -6187.97694791429 Force two-norm initial, final = 424.55998 3.7793547 Force max component initial, final = 402.73065 2.4448872 Final line search alpha, max atom move = 0.0037248343 0.0091067997 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.229 | 0.229 | 0.229 | 0.0 | 89.10 Neigh | 0.017977 | 0.017977 | 0.017977 | 0.0 | 6.99 Comm | 0.00249 | 0.00249 | 0.00249 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007559 | | | 2.94 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6200.00 ave 6200 max 6200 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: 124656.0 ave 124656 max 124656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124656 Ave neighs/atom = 136.38512 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 5.120 | 5.120 | 5.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6187.9769 0 -6187.9769 232.94349 Loop time of 6.535e-06 on 1 procs for 0 steps with 914 atoms 183.6% 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 | | 6.535e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6200.00 ave 6200 max 6200 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: 124652.0 ave 124652 max 124652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124652 Ave neighs/atom = 136.38074 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 5.120 | 5.120 | 5.120 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 -6187.9769 -6187.9769 33.606352 96.259703 4.4432827 232.94349 232.94349 272.29308 218.62832 207.90908 2.4400839 837.65847 Loop time of 6.755e-06 on 1 procs for 0 steps with 914 atoms 296.1% 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 | | 6.755e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6200.00 ave 6200 max 6200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62326.0 ave 62326 max 62326 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 124652.0 ave 124652 max 124652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124652 Ave neighs/atom = 136.38074 Neighbor list builds = 0 Dangerous builds = 0 914 -6187.97607625596 eV 2.44008385884989 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02