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 = 2.8675702 2.8675702 2.8675702 Created orthogonal box = (0.0000000 -30.617271 0.0000000) to (21.649680 30.617271 4.0553566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9376463 4.8343060 4.0553566 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.617271 0.0000000) to (21.649680 30.617271 4.0553566) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9376463 4.8343060 4.0553566 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.617271 0.0000000) to (21.649680 30.617271 4.0553566) create_atoms CPU = 0.001 seconds 230 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 18 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 456 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_427873955970_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1585.325 0 -1585.325 195328.01 54 0 -1941.2571 0 -1941.2571 6746.5686 Loop time of 4.24556 on 1 procs for 54 steps with 456 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 = -1585.32499809342 -1941.25523416478 -1941.25707958205 Force two-norm initial, final = 1146.1190 0.15127736 Force max component initial, final = 398.15486 0.030589129 Final line search alpha, max atom move = 1.0000000 0.030589129 Iterations, force evaluations = 54 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2314 | 4.2314 | 4.2314 | 0.0 | 99.67 Neigh | 0.0077726 | 0.0077726 | 0.0077726 | 0.0 | 0.18 Comm | 0.0035232 | 0.0035232 | 0.0035232 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002907 | | | 0.07 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3647.00 ave 3647 max 3647 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: 54516.0 ave 54516 max 54516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54516 Ave neighs/atom = 119.55263 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1941.2571 0 -1941.2571 6746.5686 5376.2197 59 0 -1941.3421 0 -1941.3421 -8.9572616 5397.8599 Loop time of 0.353765 on 1 procs for 5 steps with 456 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 = -1941.25707958206 -1941.34196445838 -1941.34206075963 Force two-norm initial, final = 45.555724 0.24336589 Force max component initial, final = 39.283783 0.10599054 Final line search alpha, max atom move = 0.00079934856 8.4723384e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35274 | 0.35274 | 0.35274 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019471 | 0.00019471 | 0.00019471 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008332 | | | 0.24 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3236.00 ave 3236 max 3236 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: 53784.0 ave 53784 max 53784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53784 Ave neighs/atom = 117.94737 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1941.3421 0 -1941.3421 -8.9572616 Loop time of 1.762e-06 on 1 procs for 0 steps with 456 atoms 170.3% 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 | | 1.762e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3224.00 ave 3224 max 3224 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: 53324.0 ave 53324 max 53324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53324 Ave neighs/atom = 116.93860 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.599 | 4.599 | 4.599 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 -1941.3421 -1941.3421 21.679535 61.46453 4.0508587 -8.9572616 -8.9572616 29.649765 -31.57795 -24.9436 2.2507895 327.57677 Loop time of 3.093e-06 on 1 procs for 0 steps with 456 atoms 161.7% 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 | | 3.093e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3224.00 ave 3224 max 3224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26662.0 ave 26662 max 26662 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53324.0 ave 53324 max 53324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53324 Ave neighs/atom = 116.93860 Neighbor list builds = 0 Dangerous builds = 0 456 -1941.34206075963 eV 2.25078945394861 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05