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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -63.779241 0.0000000) to (39.056649 63.779241 9.9203987) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2994595 6.1721846 6.6135992 Created 1485 atoms using lattice units in orthogonal box = (0.0000000 -63.779241 0.0000000) to (39.056649 63.779241 9.9203987) create_atoms CPU = 0.003 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2994595 6.1721846 6.6135992 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -63.779241 0.0000000) to (39.056649 63.779241 9.9203987) create_atoms CPU = 0.002 seconds 1491 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 ghost atom cutoff = 6 binsize = 3, bins = 14 43 4 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2976 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_022920256108_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 ghost atom cutoff = 6 binsize = 3, bins = 14 43 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.160 | 5.160 | 5.160 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9742.1275 0 -9742.1275 12053.272 87 0 -9953.7955 0 -9953.7955 2679.6958 Loop time of 7.63693 on 1 procs for 87 steps with 2976 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 = -9742.12746271618 -9953.78581726913 -9953.79548779649 Force two-norm initial, final = 263.80684 0.29112970 Force max component initial, final = 83.900391 0.042821885 Final line search alpha, max atom move = 1.0000000 0.042821885 Iterations, force evaluations = 87 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5692 | 7.5692 | 7.5692 | 0.0 | 99.11 Neigh | 0.029639 | 0.029639 | 0.029639 | 0.0 | 0.39 Comm | 0.013755 | 0.013755 | 0.013755 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02429 | | | 0.32 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6580.00 ave 6580 max 6580 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: 160136.0 ave 160136 max 160136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160136 Ave neighs/atom = 53.809140 Neighbor list builds = 2 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 ghost atom cutoff = 6 binsize = 3, bins = 14 43 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.160 | 5.160 | 5.160 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -9953.7955 0 -9953.7955 2679.6958 49423.494 95 0 -9954.3696 0 -9954.3696 31.830651 49622.507 Loop time of 0.491592 on 1 procs for 8 steps with 2976 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 = -9953.79548779649 -9954.36946932301 -9954.36960805615 Force two-norm initial, final = 184.50228 1.9639437 Force max component initial, final = 177.28173 1.7108465 Final line search alpha, max atom move = 0.00054398353 0.00093067230 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4864 | 0.4864 | 0.4864 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058054 | 0.00058054 | 0.00058054 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004614 | | | 0.94 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6599.00 ave 6599 max 6599 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: 160056.0 ave 160056 max 160056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160056 Ave neighs/atom = 53.782258 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 ghost atom cutoff = 6 binsize = 3, bins = 14 43 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.298 | 5.298 | 5.298 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9954.3696 0 -9954.3696 31.830651 Loop time of 2.527e-06 on 1 procs for 0 steps with 2976 atoms 158.3% 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 | | 2.527e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6596.00 ave 6596 max 6596 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: 159984.0 ave 159984 max 159984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159984 Ave neighs/atom = 53.758065 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 ghost atom cutoff = 6 binsize = 3, bins = 14 43 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.298 | 5.298 | 5.298 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 -9954.3696 -9954.3696 39.010515 128.4569 9.9023801 31.830651 31.830651 18.790721 55.627659 21.073572 2.5532366 1171.0032 Loop time of 2.842e-06 on 1 procs for 0 steps with 2976 atoms 246.3% 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 | | 2.842e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6596.00 ave 6596 max 6596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79992.0 ave 79992 max 79992 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159984.0 ave 159984 max 159984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159984 Ave neighs/atom = 53.758065 Neighbor list builds = 0 Dangerous builds = 0 2976 -9954.36960805615 eV 2.55323656557887 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08