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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2390281 5.7351568 5.1068646 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068646) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2390281 5.7351568 5.1068646 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068646) create_atoms CPU = 0.003 seconds 1080 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 40 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2144 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_179158257180_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 40 2 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) = 5.215 | 5.215 | 5.215 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8691.7257 0 -8691.7257 42488.883 679 0 -9112.8018 0 -9112.8018 4682.8012 Loop time of 99.8231 on 1 procs for 679 steps with 2144 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 = -8691.7257271073 -9112.79328506081 -9112.80180035502 Force two-norm initial, final = 425.40272 0.29976839 Force max component initial, final = 53.236877 0.055358659 Final line search alpha, max atom move = 1.0000000 0.055358659 Iterations, force evaluations = 679 1303 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 99.269 | 99.269 | 99.269 | 0.0 | 99.45 Neigh | 0.26502 | 0.26502 | 0.26502 | 0.0 | 0.27 Comm | 0.14109 | 0.14109 | 0.14109 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1479 | | | 0.15 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8013.00 ave 8013 max 8013 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: 146132.0 ave 146132 max 146132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146132 Ave neighs/atom = 68.158582 Neighbor list builds = 21 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 40 2 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 : 679 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.217 | 5.217 | 5.217 Mbytes Step Temp E_pair E_mol TotEng Press Volume 679 0 -9112.8018 0 -9112.8018 4682.8012 25239.62 714 0 -9137.1135 0 -9137.1135 -3.6081607 25266.769 Loop time of 2.7127 on 1 procs for 35 steps with 2144 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 = -9112.80180035503 -9137.11158380492 -9137.11353583097 Force two-norm initial, final = 1162.9181 3.0658734 Force max component initial, final = 985.52006 0.77149498 Final line search alpha, max atom move = 0.00013252712 0.00010224401 Iterations, force evaluations = 35 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6539 | 2.6539 | 2.6539 | 0.0 | 97.83 Neigh | 0.03839 | 0.03839 | 0.03839 | 0.0 | 1.42 Comm | 0.0033149 | 0.0033149 | 0.0033149 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01708 | | | 0.63 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8145.00 ave 8145 max 8145 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: 144530.0 ave 144530 max 144530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144530 Ave neighs/atom = 67.411381 Neighbor list builds = 3 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 41 2 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) = 5.357 | 5.357 | 5.357 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9137.1135 0 -9137.1135 -3.6081607 Loop time of 1.881e-06 on 1 procs for 0 steps with 2144 atoms 159.5% 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 | | 1.881e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8177.00 ave 8177 max 8177 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: 144504.0 ave 144504 max 144504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144504 Ave neighs/atom = 67.399254 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 41 2 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) = 5.357 | 5.357 | 5.357 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 -9137.1135 -9137.1135 41.384465 122.29039 4.9925226 -3.6081607 -3.6081607 33.055282 -50.599863 6.7200983 2.3717955 3791.6413 Loop time of 2.036e-06 on 1 procs for 0 steps with 2144 atoms 196.5% 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 | | 2.036e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8177.00 ave 8177 max 8177 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72252.0 ave 72252 max 72252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 144504.0 ave 144504 max 144504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144504 Ave neighs/atom = 67.399254 Neighbor list builds = 0 Dangerous builds = 0 2144 -9137.11353583097 eV 2.37179554600092 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:43