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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -62.925696 0.0000000) to (25.689308 62.925696 8.8990373) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1654339 5.4535604 5.9326915 Created 1193 atoms using lattice units in orthogonal box = (0.0000000 -62.925696 0.0000000) to (25.689308 62.925696 8.8990373) create_atoms CPU = 0.002 seconds 1193 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1654339 5.4535604 5.9326915 Created 1201 atoms using lattice units in orthogonal box = (0.0000000 -62.925696 0.0000000) to (25.689308 62.925696 8.8990373) create_atoms CPU = 0.002 seconds 1201 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 33 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2394 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.487 | 6.487 | 6.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9098.228 0 -9098.228 79491.045 118 0 -10214.174 0 -10214.174 -1969.0091 Loop time of 3.69824 on 1 procs for 118 steps with 2394 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9098.22797630183 -10214.1648177785 -10214.1744300943 Force two-norm initial, final = 1430.0564 0.41037953 Force max component initial, final = 252.93266 0.084215840 Final line search alpha, max atom move = 1.0000000 0.084215840 Iterations, force evaluations = 118 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5134 | 3.5134 | 3.5134 | 0.0 | 95.00 Neigh | 0.13647 | 0.13647 | 0.13647 | 0.0 | 3.69 Comm | 0.022099 | 0.022099 | 0.022099 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02624 | | | 0.71 Nlocal: 2394.00 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9315.00 ave 9315 max 9315 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: 382490.0 ave 382490 max 382490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 382490 Ave neighs/atom = 159.77026 Neighbor list builds = 5 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.104 | 6.104 | 6.104 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -10214.174 0 -10214.174 -1969.0091 28770.901 121 0 -10214.262 0 -10214.262 -47.425429 28734.257 Loop time of 0.105963 on 1 procs for 3 steps with 2394 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 = -10214.1744300942 -10214.2613524687 -10214.2617074388 Force two-norm initial, final = 96.195719 2.2712187 Force max component initial, final = 90.154358 2.2019493 Final line search alpha, max atom move = 0.00017236973 0.00037954940 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10282 | 0.10282 | 0.10282 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049355 | 0.00049355 | 0.00049355 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002649 | | | 2.50 Nlocal: 2394.00 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9318.00 ave 9318 max 9318 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: 380544.0 ave 380544 max 380544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 380544 Ave neighs/atom = 158.95739 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.242 | 6.242 | 6.242 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10214.262 0 -10214.262 -47.425429 Loop time of 2.387e-06 on 1 procs for 0 steps with 2394 atoms 167.6% 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 | | 2.387e-06 | | |100.00 Nlocal: 2394.00 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9321.00 ave 9321 max 9321 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: 386074.0 ave 386074 max 386074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 386074 Ave neighs/atom = 161.26734 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.242 | 6.242 | 6.242 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 -10214.262 -10214.262 25.646879 125.95364 8.89518 -47.425429 -47.425429 -0.35422756 -19.198084 -122.72397 2.373654 949.33101 Loop time of 2.623e-06 on 1 procs for 0 steps with 2394 atoms 228.7% 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 | | 2.623e-06 | | |100.00 Nlocal: 2394.00 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9321.00 ave 9321 max 9321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 193037.0 ave 193037 max 193037 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 386074.0 ave 386074 max 386074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 386074 Ave neighs/atom = 161.26734 Neighbor list builds = 0 Dangerous builds = 0 2394 -10214.2617074388 eV 2.3736539573275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04