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 = 3.6131481 3.6131481 3.6131481 Created orthogonal box = (0.0000000 -59.149784 0.0000000) to (41.825213 59.149784 5.1097631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2425692 5.7384119 5.1097631 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.149784 0.0000000) to (41.825213 59.149784 5.1097631) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2425692 5.7384119 5.1097631 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.149784 0.0000000) to (41.825213 59.149784 5.1097631) 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 23 1 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 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2152 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_173787283511_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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 11.98 | 11.98 | 11.98 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6916.5189 0 -6916.5189 55386.649 111 0 -7497.7426 0 -7497.7426 7042.2159 Loop time of 7.35689 on 1 procs for 111 steps with 2152 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6916.51892245158 -7497.73600937376 -7497.7426484112 Force two-norm initial, final = 307.43788 0.30775840 Force max component initial, final = 33.791278 0.016808374 Final line search alpha, max atom move = 1.0000000 0.016808374 Iterations, force evaluations = 111 199 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1895 | 7.1895 | 7.1895 | 0.0 | 97.72 Neigh | 0.099317 | 0.099317 | 0.099317 | 0.0 | 1.35 Comm | 0.041047 | 0.041047 | 0.041047 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02707 | | | 0.37 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17687.0 ave 17687 max 17687 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: 837216.0 ave 837216 max 837216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 837216 Ave neighs/atom = 389.04089 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -7497.7426 0 -7497.7426 7042.2159 25282.621 116 0 -7498.2527 0 -7498.2527 89.664632 25412.183 Loop time of 0.273846 on 1 procs for 5 steps with 2152 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 = -7497.74264841119 -7498.24938407244 -7498.25273308213 Force two-norm initial, final = 229.84538 4.7861708 Force max component initial, final = 197.60578 4.4473084 Final line search alpha, max atom move = 5.6855952e-05 0.00025285595 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26828 | 0.26828 | 0.26828 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092403 | 0.00092403 | 0.00092403 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004641 | | | 1.69 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16859.0 ave 16859 max 16859 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: 835248.0 ave 835248 max 835248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 835248 Ave neighs/atom = 388.12639 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 9 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 11.49 | 11.49 | 11.49 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7498.2527 0 -7498.2527 89.664632 Loop time of 2.272e-06 on 1 procs for 0 steps with 2152 atoms 176.1% 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 | | 2.272e-06 | | |100.00 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16879.0 ave 16879 max 16879 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: 832960.0 ave 832960 max 832960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 832960 Ave neighs/atom = 387.06320 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 9 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 11.49 | 11.49 | 11.49 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 -7498.2527 -7498.2527 41.988093 118.57702 5.1040542 89.664632 89.664632 -83.270737 281.04963 71.215002 2.4148059 1192.5698 Loop time of 2.841e-06 on 1 procs for 0 steps with 2152 atoms 246.4% 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 | | 2.841e-06 | | |100.00 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16879.0 ave 16879 max 16879 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 416480.0 ave 416480 max 416480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 832960.0 ave 832960 max 832960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 832960 Ave neighs/atom = 387.06320 Neighbor list builds = 0 Dangerous builds = 0 2152 -7498.25273308212 eV 2.4148059104946 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08