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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -55.009419 0.0000000) to (27.502949 55.009419 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9595481 4.9595481 3.5213917 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.009419 0.0000000) to (27.502949 55.009419 3.5213917) create_atoms CPU = 0.003 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9595481 4.9595481 3.5213917 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.009419 0.0000000) to (27.502949 55.009419 3.5213917) create_atoms CPU = 0.002 seconds 490 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 34 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 972 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_008996216289_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.616 | 4.616 | 4.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4265.7851 0 -4265.7851 18781.471 64 0 -4314.3696 0 -4314.3696 -2136.673 Loop time of 12.9419 on 1 procs for 64 steps with 972 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 = -4265.7850517396 -4314.36545791431 -4314.36961496887 Force two-norm initial, final = 48.929699 0.24158232 Force max component initial, final = 14.228099 0.045164522 Final line search alpha, max atom move = 1.0000000 0.045164522 Iterations, force evaluations = 64 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.91 | 12.91 | 12.91 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017413 | 0.017413 | 0.017413 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01474 | | | 0.11 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7023.00 ave 7023 max 7023 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: 84356.0 ave 84356 max 84356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84356 Ave neighs/atom = 86.786008 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -4314.3696 0 -4314.3696 -2136.673 10655.177 66 0 -4314.377 0 -4314.377 -278.57339 10644.529 Loop time of 0.574355 on 1 procs for 2 steps with 972 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4314.36961496888 -4314.37689682427 -4314.37695364118 Force two-norm initial, final = 20.829459 0.25815122 Force max component initial, final = 15.442245 0.078365715 Final line search alpha, max atom move = 0.0013246625 0.00010380812 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57138 | 0.57138 | 0.57138 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069307 | 0.00069307 | 0.00069307 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002282 | | | 0.40 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6983.00 ave 6983 max 6983 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: 85360.0 ave 85360 max 85360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85360 Ave neighs/atom = 87.818930 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.753 | 4.753 | 4.753 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4314.377 0 -4314.377 -278.57339 Loop time of 6.545e-06 on 1 procs for 0 steps with 972 atoms 198.6% 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 | | 6.545e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6983.00 ave 6983 max 6983 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: 85456.0 ave 85456 max 85456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85456 Ave neighs/atom = 87.917695 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.753 | 4.753 | 4.753 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 -4314.377 -4314.377 27.490654 110.01884 3.5194462 -278.57339 -278.57339 -11.790054 -826.98089 3.050782 2.2477776 147.91927 Loop time of 7.046e-06 on 1 procs for 0 steps with 972 atoms 269.7% 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 | | 7.046e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6983.00 ave 6983 max 6983 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42728.0 ave 42728 max 42728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85456.0 ave 85456 max 85456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85456 Ave neighs/atom = 87.917695 Neighbor list builds = 0 Dangerous builds = 0 972 -4314.37695364118 eV 2.24777763757478 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14