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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -64.618572 0.0000000) to (37.305438 64.618572 6.3360136) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7392981 5.7987743 6.3360136 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -64.618572 0.0000000) to (37.305438 64.618572 6.3360136) create_atoms CPU = 0.012 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7392981 5.7987743 6.3360136 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -64.618572 0.0000000) to (37.305438 64.618572 6.3360136) create_atoms CPU = 0.003 seconds 1251 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 2471 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.123 | 6.123 | 6.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9562.4013 0 -9562.4013 -1649.8102 560 0 -9710.4672 0 -9710.4672 -63643.204 Loop time of 19.2212 on 1 procs for 560 steps with 2471 atoms 95.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9562.4013040376 -9710.45891501505 -9710.46723509974 Force two-norm initial, final = 27.135488 0.37468682 Force max component initial, final = 5.5913300 0.090858281 Final line search alpha, max atom move = 0.86838375 0.078899855 Iterations, force evaluations = 560 1088 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.782 | 18.782 | 18.782 | 0.0 | 97.72 Neigh | 0.20492 | 0.20492 | 0.20492 | 0.0 | 1.07 Comm | 0.11738 | 0.11738 | 0.11738 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1165 | | | 0.61 Nlocal: 2471.00 ave 2471 max 2471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10208.0 ave 10208 max 10208 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: 332826.0 ave 332826 max 332826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332826 Ave neighs/atom = 134.69284 Neighbor list builds = 10 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 560 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.123 | 6.123 | 6.123 Mbytes Step Temp E_pair E_mol TotEng Press Volume 560 0 -9710.4672 0 -9710.4672 -63643.204 30547.494 601 0 -9744.1198 0 -9744.1198 -10626.002 29316.68 Loop time of 0.962441 on 1 procs for 41 steps with 2471 atoms 88.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9710.46723509977 -9744.11217327105 -9744.11980314525 Force two-norm initial, final = 1775.3280 4.4621505 Force max component initial, final = 1601.8459 1.3289311 Final line search alpha, max atom move = 4.2088838e-05 5.5933167e-05 Iterations, force evaluations = 41 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9087 | 0.9087 | 0.9087 | 0.0 | 94.42 Neigh | 0.023758 | 0.023758 | 0.023758 | 0.0 | 2.47 Comm | 0.0042408 | 0.0042408 | 0.0042408 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02575 | | | 2.68 Nlocal: 2471.00 ave 2471 max 2471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10377.0 ave 10377 max 10377 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: 346080.0 ave 346080 max 346080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346080 Ave neighs/atom = 140.05666 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.261 | 6.261 | 6.261 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9744.1198 0 -9744.1198 -10626.002 Loop time of 1.895e-06 on 1 procs for 0 steps with 2471 atoms 211.1% 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 | | 1.895e-06 | | |100.00 Nlocal: 2471.00 ave 2471 max 2471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10351.0 ave 10351 max 10351 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: 346642.0 ave 346642 max 346642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346642 Ave neighs/atom = 140.28410 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.261 | 6.261 | 6.261 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 -9744.1198 -9744.1198 35.848173 129.23714 6.3279117 -10626.002 -10626.002 14.512615 -31819.986 -72.534123 2.2285075 5687.4575 Loop time of 2.275e-06 on 1 procs for 0 steps with 2471 atoms 219.8% 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 | | 2.275e-06 | | |100.00 Nlocal: 2471.00 ave 2471 max 2471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10351.0 ave 10351 max 10351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173321.0 ave 173321 max 173321 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346642.0 ave 346642 max 346642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346642 Ave neighs/atom = 140.28410 Neighbor list builds = 0 Dangerous builds = 0 2471 -9394.66697045563 eV 2.22850749822617 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20