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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -63.363794 0.0000000) to (25.866667 63.363794 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2080001 5.4912118 5.9736509 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -63.363794 0.0000000) to (25.866667 63.363794 8.9604763) create_atoms CPU = 0.002 seconds 1203 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2080001 5.4912118 5.9736509 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -63.363794 0.0000000) to (25.866667 63.363794 8.9604763) create_atoms CPU = 0.002 seconds 1203 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 35 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 2366 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_634187028437_000#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.037 | 6.037 | 6.037 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9159.3609 0 -9159.3609 -4870.2016 865 0 -9298.5015 0 -9298.5015 -67100.994 Loop time of 29.6433 on 1 procs for 865 steps with 2366 atoms 92.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9159.36086469928 -9298.49383169085 -9298.50151266232 Force two-norm initial, final = 7.7577833 0.23299835 Force max component initial, final = 1.3950641 0.044159243 Final line search alpha, max atom move = 0.84081790 0.037129882 Iterations, force evaluations = 865 1714 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.986 | 28.986 | 28.986 | 0.0 | 97.78 Neigh | 0.3157 | 0.3157 | 0.3157 | 0.0 | 1.06 Comm | 0.15136 | 0.15136 | 0.15136 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1903 | | | 0.64 Nlocal: 2366.00 ave 2366 max 2366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8641.00 ave 8641 max 8641 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: 322828.0 ave 322828 max 322828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322828 Ave neighs/atom = 136.44463 Neighbor list builds = 15 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 865 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.040 | 6.040 | 6.040 Mbytes Step Temp E_pair E_mol TotEng Press Volume 865 0 -9298.5015 0 -9298.5015 -67100.994 29372.624 921 0 -9350.6706 0 -9350.6706 -20845.446 28424.814 Loop time of 0.925192 on 1 procs for 56 steps with 2366 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 = -9298.50151266234 -9350.66450299511 -9350.67064866364 Force two-norm initial, final = 1979.5503 9.1024560 Force max component initial, final = 1972.9123 6.2270297 Final line search alpha, max atom move = 0.00014311818 0.00089120113 Iterations, force evaluations = 56 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87548 | 0.87548 | 0.87548 | 0.0 | 94.63 Neigh | 0.019446 | 0.019446 | 0.019446 | 0.0 | 2.10 Comm | 0.0041971 | 0.0041971 | 0.0041971 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02607 | | | 2.82 Nlocal: 2366.00 ave 2366 max 2366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8547.00 ave 8547 max 8547 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: 332268.0 ave 332268 max 332268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332268 Ave neighs/atom = 140.43449 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.175 | 6.175 | 6.175 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9350.6706 0 -9350.6706 -20845.446 Loop time of 1.467e-06 on 1 procs for 0 steps with 2366 atoms 136.3% 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 | | 1.467e-06 | | |100.00 Nlocal: 2366.00 ave 2366 max 2366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8446.00 ave 8446 max 8446 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: 334072.0 ave 334072 max 334072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334072 Ave neighs/atom = 141.19696 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.175 | 6.175 | 6.175 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 -9350.6706 -9350.6706 24.522221 126.72759 9.1467472 -20845.446 -20845.446 -273.78052 -62620.844 358.2855 2.3726433 5741.9506 Loop time of 1.962e-06 on 1 procs for 0 steps with 2366 atoms 254.8% 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 | | 1.962e-06 | | |100.00 Nlocal: 2366.00 ave 2366 max 2366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8446.00 ave 8446 max 8446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167036.0 ave 167036 max 167036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 334072.0 ave 334072 max 334072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334072 Ave neighs/atom = 141.19696 Neighbor list builds = 0 Dangerous builds = 0 2366 -9016.06708648491 eV 2.37264329358186 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31