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 = 3.1501534 3.1501534 3.1501534 Created orthogonal box = (0.0000000 -33.486590 0.0000000) to (33.486590 33.486590 3.1501534) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4451225 4.4451225 3.1501534 Created 226 atoms using lattice units in orthogonal box = (0.0000000 -33.486590 0.0000000) to (33.486590 33.486590 3.1501534) create_atoms CPU = 0.002 seconds 226 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4451225 4.4451225 3.1501534 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -33.486590 0.0000000) to (33.486590 33.486590 3.1501534) create_atoms CPU = 0.001 seconds 227 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 17 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 8.100217342376709 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 453 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_271256517527_005#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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2959.5217 0 -2959.5217 60004.245 49 0 -3070.0765 0 -3070.0765 12527.963 Loop time of 0.714512 on 1 procs for 49 steps with 453 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 = -2959.52168226968 -3070.07419573912 -3070.07650098828 Force two-norm initial, final = 156.86149 0.19915645 Force max component initial, final = 47.739332 0.059523781 Final line search alpha, max atom move = 1.0000000 0.059523781 Iterations, force evaluations = 49 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68844 | 0.68844 | 0.68844 | 0.0 | 96.35 Neigh | 0.008723 | 0.008723 | 0.008723 | 0.0 | 1.22 Comm | 0.010098 | 0.010098 | 0.010098 | 0.0 | 1.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007254 | | | 1.02 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4605.00 ave 4605 max 4605 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: 63964.0 ave 63964 max 63964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63964 Ave neighs/atom = 141.20088 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.471 | 4.471 | 4.471 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -3070.0765 0 -3070.0765 12527.963 7064.8596 56 0 -3070.3924 0 -3070.3924 -112.39701 7099.384 Loop time of 0.0767727 on 1 procs for 7 steps with 453 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 = -3070.07650098828 -3070.39232407848 -3070.39244956471 Force two-norm initial, final = 115.28856 1.2519925 Force max component initial, final = 104.20665 1.1922209 Final line search alpha, max atom move = 0.00059007702 0.00070350219 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072784 | 0.072784 | 0.072784 | 0.0 | 94.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092654 | 0.00092654 | 0.00092654 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003062 | | | 3.99 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4587.00 ave 4587 max 4587 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: 63642.0 ave 63642 max 63642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63642 Ave neighs/atom = 140.49007 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.609 | 4.609 | 4.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3070.3924 0 -3070.3924 -112.39701 Loop time of 6.074e-06 on 1 procs for 0 steps with 453 atoms 181.1% 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 | | 6.074e-06 | | |100.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4593.00 ave 4593 max 4593 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: 63234.0 ave 63234 max 63234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63234 Ave neighs/atom = 139.58940 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 9 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.609 | 4.609 | 4.609 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 -3070.3924 -3070.3924 33.505805 67.379798 3.1446398 -112.39701 -112.39701 -269.21272 -20.010022 -47.968278 2.4694167 148.42949 Loop time of 6.585e-06 on 1 procs for 0 steps with 453 atoms 288.5% 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 | | 6.585e-06 | | |100.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4593.00 ave 4593 max 4593 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31617.0 ave 31617 max 31617 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63234.0 ave 63234 max 63234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63234 Ave neighs/atom = 139.58940 Neighbor list builds = 0 Dangerous builds = 0 453 -3070.39201755024 eV 2.46941665667183 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01