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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -70.342281 0.0000000) to (28.717116 70.342281 9.9479008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8921078 6.0963310 6.6319338 Created 1196 atoms using lattice units in orthogonal box = (0.0000000 -70.342281 0.0000000) to (28.717116 70.342281 9.9479008) create_atoms CPU = 0.002 seconds 1196 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8921078 6.0963310 6.6319338 Created 1204 atoms using lattice units in orthogonal box = (0.0000000 -70.342281 0.0000000) to (28.717116 70.342281 9.9479008) create_atoms CPU = 0.001 seconds 1204 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 6 29 3 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2400 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 6 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 6.976 | 6.976 | 6.976 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6031.9189 0 -6031.9189 17833.921 146 0 -6462.0799 0 -6462.0799 2331.8168 Loop time of 5.07484 on 1 procs for 146 steps with 2400 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 = -6031.91890955095 -6462.07409958463 -6462.07988539349 Force two-norm initial, final = 392.89620 0.21886021 Force max component initial, final = 65.735796 0.025151947 Final line search alpha, max atom move = 1.0000000 0.025151947 Iterations, force evaluations = 146 225 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7513 | 4.7513 | 4.7513 | 0.0 | 93.62 Neigh | 0.26887 | 0.26887 | 0.26887 | 0.0 | 5.30 Comm | 0.025507 | 0.025507 | 0.025507 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02914 | | | 0.57 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11370.0 ave 11370 max 11370 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: 539450.0 ave 539450 max 539450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 539450 Ave neighs/atom = 224.77083 Neighbor list builds = 8 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 6 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 146 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.976 | 6.976 | 6.976 Mbytes Step Temp E_pair E_mol TotEng Press Volume 146 0 -6462.0799 0 -6462.0799 2331.8168 40190.065 152 0 -6462.5145 0 -6462.5145 32.577909 40312.43 Loop time of 0.1697 on 1 procs for 6 steps with 2400 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 = -6462.07988539349 -6462.51214342629 -6462.5145116942 Force two-norm initial, final = 166.36850 1.4729993 Force max component initial, final = 165.80453 0.99457341 Final line search alpha, max atom move = 0.00013176818 0.00013105313 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16551 | 0.16551 | 0.16551 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066129 | 0.00066129 | 0.00066129 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003529 | | | 2.08 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11370.0 ave 11370 max 11370 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: 539400.0 ave 539400 max 539400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 539400 Ave neighs/atom = 224.75000 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 7.114 | 7.114 | 7.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6462.5145 0 -6462.5145 32.577909 Loop time of 2.218e-06 on 1 procs for 0 steps with 2400 atoms 135.3% 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 | | 2.218e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11370.0 ave 11370 max 11370 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: 538948.0 ave 538948 max 538948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 538948 Ave neighs/atom = 224.56167 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 7.114 | 7.114 | 7.114 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 -6462.5145 -6462.5145 28.686032 141.43306 9.9361367 32.577909 32.577909 39.485522 30.715909 27.532296 2.7364392 1389.1174 Loop time of 2.267e-06 on 1 procs for 0 steps with 2400 atoms 308.8% 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 | | 2.267e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11370.0 ave 11370 max 11370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 269474.0 ave 269474 max 269474 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 538948.0 ave 538948 max 538948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 538948 Ave neighs/atom = 224.56167 Neighbor list builds = 0 Dangerous builds = 0 2400 -6462.5145116942 eV 2.73643915119024 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05