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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -46.698077 0.0000000) to (28.596615 46.698077 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1993846 5.3065996 5.7481359 Created 1051 atoms using lattice units in orthogonal box = (0.0000000 -46.698077 0.0000000) to (28.596615 46.698077 8.6222039) create_atoms CPU = 0.002 seconds 1051 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1993846 5.3065996 5.7481359 Created 1075 atoms using lattice units in orthogonal box = (0.0000000 -46.698077 0.0000000) to (28.596615 46.698077 8.6222039) create_atoms CPU = 0.002 seconds 1075 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 9 28 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2112 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.572 | 5.572 | 5.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9376.1532 0 -9376.1532 4986.6325 13 0 -9386.4256 0 -9386.4256 6022.6916 Loop time of 0.298935 on 1 procs for 13 steps with 2112 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 = -9376.15324818055 -9386.41853155513 -9386.42558909375 Force two-norm initial, final = 19.111078 0.16089857 Force max component initial, final = 1.9678993 0.0079216696 Final line search alpha, max atom move = 1.0000000 0.0079216696 Iterations, force evaluations = 13 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29491 | 0.29491 | 0.29491 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017486 | 0.0017486 | 0.0017486 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002279 | | | 0.76 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7444.00 ave 7444 max 7444 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: 281760.0 ave 281760 max 281760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281760 Ave neighs/atom = 133.40909 Neighbor list builds = 0 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.572 | 5.572 | 5.572 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -9386.4256 0 -9386.4256 6022.6916 23028.302 19 0 -9386.8394 0 -9386.8394 -12.613527 23106.457 Loop time of 0.101323 on 1 procs for 6 steps with 2112 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 = -9386.42558909369 -9386.83923971014 -9386.83936845047 Force two-norm initial, final = 188.41693 0.89818022 Force max component initial, final = 179.66677 0.71398236 Final line search alpha, max atom move = 0.00032527813 0.00023224284 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.097757 | 0.097757 | 0.097757 | 0.0 | 96.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055119 | 0.00055119 | 0.00055119 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003014 | | | 2.97 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7408.00 ave 7408 max 7408 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: 281088.0 ave 281088 max 281088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281088 Ave neighs/atom = 133.09091 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.710 | 5.710 | 5.710 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9386.8394 0 -9386.8394 -12.613527 Loop time of 1.872e-06 on 1 procs for 0 steps with 2112 atoms 160.3% 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 | | 1.872e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7482.00 ave 7482 max 7482 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: 280992.0 ave 280992 max 280992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280992 Ave neighs/atom = 133.04545 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.710 | 5.710 | 5.710 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 -9386.8394 -9386.8394 28.571478 93.863256 8.6159871 -12.613527 -12.613527 -49.463239 -17.384689 29.007347 2.3777023 626.89847 Loop time of 2.328e-06 on 1 procs for 0 steps with 2112 atoms 171.8% 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 | | 2.328e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7482.00 ave 7482 max 7482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140496.0 ave 140496 max 140496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 280992.0 ave 280992 max 280992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280992 Ave neighs/atom = 133.04545 Neighbor list builds = 0 Dangerous builds = 0 2112 -9386.83936845047 eV 2.37770225107649 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00