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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -62.238130 0.0000000) to (38.112915 62.238130 7.6999717) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4076161 4.4455807 5.1333145 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -62.238130 0.0000000) to (38.112915 62.238130 7.6999717) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4076161 4.4455807 5.1333145 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -62.238130 0.0000000) to (38.112915 62.238130 7.6999717) create_atoms CPU = 0.001 seconds 1182 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 8 25 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2340 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 7.318 | 7.318 | 7.318 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14284.008 0 -14284.008 81011.991 118 0 -15569.571 0 -15569.571 -1187.7792 Loop time of 5.16856 on 1 procs for 118 steps with 2340 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 = -14284.0081335573 -15569.5568974297 -15569.5710392322 Force two-norm initial, final = 1560.6805 0.70665437 Force max component initial, final = 303.06319 0.093364591 Final line search alpha, max atom move = 0.83878546 0.078312862 Iterations, force evaluations = 118 225 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0432 | 5.0432 | 5.0432 | 0.0 | 97.57 Neigh | 0.067898 | 0.067898 | 0.067898 | 0.0 | 1.31 Comm | 0.031354 | 0.031354 | 0.031354 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02609 | | | 0.50 Nlocal: 2340.00 ave 2340 max 2340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12153.0 ave 12153 max 12153 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: 651516.0 ave 651516 max 651516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651516 Ave neighs/atom = 278.42564 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.318 | 7.318 | 7.318 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -15569.571 0 -15569.571 -1187.7792 36529.845 123 0 -15570.335 0 -15570.335 -54.527297 36514.586 Loop time of 0.154368 on 1 procs for 5 steps with 2340 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 = -15569.5710392322 -15570.334683152 -15570.334959581 Force two-norm initial, final = 322.22332 3.1728437 Force max component initial, final = 226.61742 2.0396806 Final line search alpha, max atom move = 0.00018270446 0.00037265874 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15076 | 0.15076 | 0.15076 | 0.0 | 97.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063301 | 0.00063301 | 0.00063301 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002978 | | | 1.93 Nlocal: 2340.00 ave 2340 max 2340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12149.0 ave 12149 max 12149 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: 650304.0 ave 650304 max 650304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 650304 Ave neighs/atom = 277.90769 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 7.456 | 7.456 | 7.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15570.335 0 -15570.335 -54.527297 Loop time of 2.108e-06 on 1 procs for 0 steps with 2340 atoms 142.3% 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 | | 2.108e-06 | | |100.00 Nlocal: 2340.00 ave 2340 max 2340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12153.0 ave 12153 max 12153 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: 650532.0 ave 650532 max 650532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 650532 Ave neighs/atom = 278.00513 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 7.456 | 7.456 | 7.456 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 -15570.335 -15570.335 38.029428 124.97079 7.6831279 -54.527297 -54.527297 -89.300474 8.5519912 -82.833409 2.5250166 1474.8652 Loop time of 2.198e-06 on 1 procs for 0 steps with 2340 atoms 318.5% 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 | | 2.198e-06 | | |100.00 Nlocal: 2340.00 ave 2340 max 2340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12153.0 ave 12153 max 12153 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325266.0 ave 325266 max 325266 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 650532.0 ave 650532 max 650532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 650532 Ave neighs/atom = 278.00513 Neighbor list builds = 0 Dangerous builds = 0 2340 -15570.334959581 eV 2.5250165954916 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05