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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -53.171849 0.0000000) to (37.598175 53.171849 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9365540 5.1306170 4.9800000 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -53.171849 0.0000000) to (37.598175 53.171849 4.9800000) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9365540 5.1306170 4.9800000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.171849 0.0000000) to (37.598175 53.171849 4.9800000) create_atoms CPU = 0.002 seconds 916 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_876687166519_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.177 | 5.177 | 5.177 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7429.5049 0 -7429.5049 73454.918 78 0 -8094.2029 0 -8094.2029 6626.2027 Loop time of 13.1049 on 1 procs for 78 steps with 1824 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7429.50486624458 -8094.1966225146 -8094.20291914908 Force two-norm initial, final = 796.20043 0.27137619 Force max component initial, final = 177.69365 0.040061837 Final line search alpha, max atom move = 1.0000000 0.040061837 Iterations, force evaluations = 78 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.042 | 13.042 | 13.042 | 0.0 | 99.52 Neigh | 0.028308 | 0.028308 | 0.028308 | 0.0 | 0.22 Comm | 0.018226 | 0.018226 | 0.018226 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01646 | | | 0.13 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8462.00 ave 8462 max 8462 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: 161736.0 ave 161736 max 161736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161736 Ave neighs/atom = 88.671053 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.177 | 5.177 | 5.177 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -8094.2029 0 -8094.2029 6626.2027 19911.678 84 0 -8094.6429 0 -8094.6429 -244.25629 19984.298 Loop time of 0.769851 on 1 procs for 6 steps with 1824 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 = -8094.20291914904 -8094.64125962503 -8094.6428559108 Force two-norm initial, final = 184.18437 5.7402956 Force max component initial, final = 173.77644 4.0155407 Final line search alpha, max atom move = 0.00011158449 0.00044807205 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76593 | 0.76593 | 0.76593 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060994 | 0.00060994 | 0.00060994 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003309 | | | 0.43 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8510.00 ave 8510 max 8510 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: 161264.0 ave 161264 max 161264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161264 Ave neighs/atom = 88.412281 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.315 | 5.315 | 5.315 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8094.6429 0 -8094.6429 -244.25629 Loop time of 2.369e-06 on 1 procs for 0 steps with 1824 atoms 211.1% 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 | | 2.369e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8489.00 ave 8489 max 8489 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: 160352.0 ave 160352 max 160352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160352 Ave neighs/atom = 87.912281 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.315 | 5.315 | 5.315 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 -8094.6429 -8094.6429 37.547733 106.90934 4.9783967 -244.25629 -244.25629 -311.29842 -99.641078 -321.82936 2.2998099 672.50124 Loop time of 2.518e-06 on 1 procs for 0 steps with 1824 atoms 317.7% 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 | | 2.518e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8489.00 ave 8489 max 8489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80176.0 ave 80176 max 80176 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160352.0 ave 160352 max 160352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160352 Ave neighs/atom = 87.912281 Neighbor list builds = 0 Dangerous builds = 0 1824 -8094.6428559108 eV 2.29980990688832 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14