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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -38.078405 0.0000000) to (12.691628 38.078405 3.5200244) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8813955 4.8813955 3.5200244 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.078405 0.0000000) to (12.691628 38.078405 3.5200244) create_atoms CPU = 0.001 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8813955 4.8813955 3.5200244 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.078405 0.0000000) to (12.691628 38.078405 3.5200244) create_atoms CPU = 0.000 seconds 158 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 4 19 1 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 310 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1358.5451 0 -1358.5451 20460.259 35 0 -1372.7237 0 -1372.7237 -381.1972 Loop time of 0.21807 on 1 procs for 35 steps with 310 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 = -1358.54505869481 -1372.72242337901 -1372.72374029626 Force two-norm initial, final = 32.008132 0.11897093 Force max component initial, final = 14.194938 0.019297591 Final line search alpha, max atom move = 1.0000000 0.019297591 Iterations, force evaluations = 35 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2111 | 0.2111 | 0.2111 | 0.0 | 96.80 Neigh | 0.0038059 | 0.0038059 | 0.0038059 | 0.0 | 1.75 Comm | 0.0020479 | 0.0020479 | 0.0020479 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001117 | | | 0.51 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4536.00 ave 4536 max 4536 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: 69024.0 ave 69024 max 69024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69024 Ave neighs/atom = 222.65806 Neighbor list builds = 1 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -1372.7237 0 -1372.7237 -381.1972 3402.2933 38 0 -1372.7366 0 -1372.7366 544.55948 3400.5111 Loop time of 0.0396755 on 1 procs for 3 steps with 310 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 = -1372.72374029626 -1372.73594727368 -1372.736568249 Force two-norm initial, final = 10.170759 1.5093932 Force max component initial, final = 10.115596 1.4783183 Final line search alpha, max atom move = 0.00045913199 0.00067874323 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.038013 | 0.038013 | 0.038013 | 0.0 | 95.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003478 | 0.0003478 | 0.0003478 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001315 | | | 3.31 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4476.00 ave 4476 max 4476 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: 69044.0 ave 69044 max 69044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69044 Ave neighs/atom = 222.72258 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1372.7366 0 -1372.7366 544.55948 Loop time of 3.269e-06 on 1 procs for 0 steps with 310 atoms 122.4% 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 | | 3.269e-06 | | |100.00 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4476.00 ave 4476 max 4476 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: 69048.0 ave 69048 max 69048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69048 Ave neighs/atom = 222.73548 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 4.612 | 4.612 | 4.612 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 -1372.7366 -1372.7366 12.66497 76.15681 3.5255859 544.55948 544.55948 -695.05782 2459.6723 -130.93602 2.2244042 152.29471 Loop time of 3.082e-06 on 1 procs for 0 steps with 310 atoms 129.8% 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 | | 3.082e-06 | | |100.00 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4476.00 ave 4476 max 4476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34524.0 ave 34524 max 34524 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69048.0 ave 69048 max 69048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69048 Ave neighs/atom = 222.73548 Neighbor list builds = 0 Dangerous builds = 0 310 -1364.285533691 eV 2.22440417245376 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00