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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -71.540000 0.0000000) to (43.809124 71.540000 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0663613 5.1100000 5.9005197 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.540000 0.0000000) to (43.809124 71.540000 8.8507796) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0663613 5.1100000 5.9005197 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.540000 0.0000000) to (43.809124 71.540000 8.8507796) create_atoms CPU = 0.003 seconds 2358 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 4704 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_087820130586_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 6.250 | 6.250 | 6.250 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15882.584 0 -15882.584 36175.56 31 0 -16604.121 0 -16604.121 5927.7713 Loop time of 4.14098 on 1 procs for 31 steps with 4704 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15882.5841761557 -16604.1105107435 -16604.1208473543 Force two-norm initial, final = 626.49918 0.35174176 Force max component initial, final = 113.53221 0.044325054 Final line search alpha, max atom move = 1.0000000 0.044325054 Iterations, force evaluations = 31 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1171 | 4.1171 | 4.1171 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0087973 | 0.0087973 | 0.0087973 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01504 | | | 0.36 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10957.0 ave 10957 max 10957 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: 366552.0 ave 366552 max 366552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366552 Ave neighs/atom = 77.923469 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.250 | 6.250 | 6.250 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -16604.121 0 -16604.121 5927.7713 55478.54 37 0 -16605.064 0 -16605.064 -384.36992 55724.234 Loop time of 0.610584 on 1 procs for 6 steps with 4704 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16604.1208473542 -16605.0525580399 -16605.0636306807 Force two-norm initial, final = 408.59196 24.483213 Force max component initial, final = 364.51231 19.185051 Final line search alpha, max atom move = 3.5006187e-05 0.00067159547 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60404 | 0.60404 | 0.60404 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081932 | 0.00081932 | 0.00081932 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005726 | | | 0.94 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10972.0 ave 10972 max 10972 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: 364704.0 ave 364704 max 364704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 364704 Ave neighs/atom = 77.530612 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 6.388 | 6.388 | 6.388 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16605.064 0 -16605.064 -384.36992 Loop time of 2.301e-06 on 1 procs for 0 steps with 4704 atoms 173.8% 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 | | 2.301e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10936.0 ave 10936 max 10936 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: 364512.0 ave 364512 max 364512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 364512 Ave neighs/atom = 77.489796 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 6.388 | 6.388 | 6.388 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 -16605.064 -16605.064 43.795671 143.89004 8.8426449 -384.36992 -384.36992 -551.4369 -228.85825 -372.81461 2.2616482 1810.9913 Loop time of 2.461e-06 on 1 procs for 0 steps with 4704 atoms 243.8% 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 | | 2.461e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10936.0 ave 10936 max 10936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 182256.0 ave 182256 max 182256 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 364512.0 ave 364512 max 364512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 364512 Ave neighs/atom = 77.489796 Neighbor list builds = 0 Dangerous builds = 0 4704 -16605.0636306807 eV 2.26164821385486 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05