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 = 4.0515263 4.0515263 4.0515263 Created orthogonal box = (0.0000000 -73.376262 0.0000000) to (25.942426 73.376262 5.7297234) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9601631 6.2638272 5.7297234 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -73.376262 0.0000000) to (25.942426 73.376262 5.7297234) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9601631 6.2638272 5.7297234 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -73.376262 0.0000000) to (25.942426 73.376262 5.7297234) create_atoms CPU = 0.002 seconds 658 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 37 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.101 | 5.101 | 5.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3736.3501 0 -3736.3501 94498.292 86 0 -4402.352 0 -4402.352 3955.96 Loop time of 2.72754 on 1 procs for 86 steps with 1312 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3736.35014109253 -4402.34818012169 -4402.3519774245 Force two-norm initial, final = 1554.5428 0.18749896 Force max component initial, final = 472.42647 0.025250393 Final line search alpha, max atom move = 1.0000000 0.025250393 Iterations, force evaluations = 86 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.647 | 2.647 | 2.647 | 0.0 | 97.05 Neigh | 0.04231 | 0.04231 | 0.04231 | 0.0 | 1.55 Comm | 0.020289 | 0.020289 | 0.020289 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01793 | | | 0.66 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7427.00 ave 7427 max 7427 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: 174860.0 ave 174860 max 174860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174860 Ave neighs/atom = 133.27744 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.109 | 5.109 | 5.109 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -4402.352 0 -4402.352 3955.96 21813.725 89 0 -4402.485 0 -4402.485 6.8019273 21901.739 Loop time of 0.107395 on 1 procs for 3 steps with 1312 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 = -4402.3519774245 -4402.48150190302 -4402.48500851197 Force two-norm initial, final = 98.059417 1.9855955 Force max component initial, final = 66.365190 1.4507971 Final line search alpha, max atom move = 8.8681190e-05 0.00012865841 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10361 | 0.10361 | 0.10361 | 0.0 | 96.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075345 | 0.00075345 | 0.00075345 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003027 | | | 2.82 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8040.00 ave 8040 max 8040 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: 175076.0 ave 175076 max 175076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175076 Ave neighs/atom = 133.44207 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.247 | 5.247 | 5.247 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4402.485 0 -4402.485 6.8019273 Loop time of 3.136e-06 on 1 procs for 0 steps with 1312 atoms 127.6% 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 | | 3.136e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8040.00 ave 8040 max 8040 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: 174916.0 ave 174916 max 174916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174916 Ave neighs/atom = 133.32012 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.247 | 5.247 | 5.247 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 -4402.485 -4402.485 25.990592 147.07187 5.7297126 6.8019273 6.8019273 -106.32711 91.852894 34.879997 2.6866122 597.48108 Loop time of 3.44e-06 on 1 procs for 0 steps with 1312 atoms 174.4% 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 | | 3.44e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8040.00 ave 8040 max 8040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87458.0 ave 87458 max 87458 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174916.0 ave 174916 max 174916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174916 Ave neighs/atom = 133.32012 Neighbor list builds = 0 Dangerous builds = 0 1312 -4402.48500849986 eV 2.68661220772395 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03