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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -63.360007 0.0000000) to (44.802290 63.360007 4.9780323) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0842617 5.8666673 4.9780323 Created 1294 atoms using lattice units in orthogonal box = (0.0000000 -63.360007 0.0000000) to (44.802290 63.360007 4.9780323) create_atoms CPU = 0.010 seconds 1294 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0842617 5.8666673 4.9780323 Created 1298 atoms using lattice units in orthogonal box = (0.0000000 -63.360007 0.0000000) to (44.802290 63.360007 4.9780323) create_atoms CPU = 0.012 seconds 1298 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2586 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.537 | 6.537 | 6.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11361.025 0 -11361.025 6334.4375 122 0 -11481.23 0 -11481.23 4569.2944 Loop time of 11.628 on 1 procs for 122 steps with 2586 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 = -11361.0250835497 -11481.2196215985 -11481.2302193898 Force two-norm initial, final = 60.488805 0.36568564 Force max component initial, final = 10.345456 0.074783945 Final line search alpha, max atom move = 1.0000000 0.074783945 Iterations, force evaluations = 122 234 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.432 | 11.432 | 11.432 | 0.0 | 98.31 Neigh | 0.06123 | 0.06123 | 0.06123 | 0.0 | 0.53 Comm | 0.074382 | 0.074382 | 0.074382 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0605 | | | 0.52 Nlocal: 2586.00 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13405.0 ave 13405 max 13405 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: 451244.0 ave 451244 max 451244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451244 Ave neighs/atom = 174.49497 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -11481.23 0 -11481.23 4569.2944 28262.016 125 0 -11481.369 0 -11481.369 1.8706027 28334.87 Loop time of 0.298198 on 1 procs for 3 steps with 2586 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 = -11481.2302193898 -11481.365535821 -11481.3694976789 Force two-norm initial, final = 149.16730 1.9083645 Force max component initial, final = 123.26355 1.3476002 Final line search alpha, max atom move = 6.7608027e-05 9.1108592e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29044 | 0.29044 | 0.29044 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018937 | 0.0018937 | 0.0018937 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005862 | | | 1.97 Nlocal: 2586.00 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13943.0 ave 13943 max 13943 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: 451700.0 ave 451700 max 451700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451700 Ave neighs/atom = 174.67131 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 9.816 | 9.816 | 9.816 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11481.369 0 -11481.369 1.8706027 Loop time of 6.364e-06 on 1 procs for 0 steps with 2586 atoms 204.3% 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 | | 6.364e-06 | | |100.00 Nlocal: 2586.00 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13925.0 ave 13925 max 13925 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: 451512.0 ave 451512 max 451512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451512 Ave neighs/atom = 174.59861 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 9.816 | 9.816 | 9.816 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 -11481.369 -11481.369 44.813957 126.97002 4.9797408 1.8706027 1.8706027 76.219006 2.6106608 -73.217859 2.3048389 1203.739 Loop time of 6.465e-06 on 1 procs for 0 steps with 2586 atoms 278.4% 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 | | 6.465e-06 | | |100.00 Nlocal: 2586.00 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13925.0 ave 13925 max 13925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 225756.0 ave 225756 max 225756 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 451512.0 ave 451512 max 451512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451512 Ave neighs/atom = 174.59861 Neighbor list builds = 0 Dangerous builds = 0 2586 -11481.3694976789 eV 2.30483892564278 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13