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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247506 71.442777 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3457702 6.4115312 7.0055406 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247506 71.442777 7.0055406) create_atoms CPU = 0.009 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3457702 6.4115312 7.0055406 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247506 71.442777 7.0055406) create_atoms CPU = 0.008 seconds 1251 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2498 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_616482358807_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.201 | 5.201 | 5.201 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7938.0676 0 -7938.0676 26003.114 109 0 -8370.7925 0 -8370.7925 4145.231 Loop time of 35.4461 on 1 procs for 109 steps with 2498 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 = -7938.06757540987 -8370.78425589355 -8370.79246570613 Force two-norm initial, final = 403.53065 0.24172379 Force max component initial, final = 71.294293 0.026060495 Final line search alpha, max atom move = 1.0000000 0.026060495 Iterations, force evaluations = 109 177 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 35.252 | 35.252 | 35.252 | 0.0 | 99.45 Neigh | 0.11252 | 0.11252 | 0.11252 | 0.0 | 0.32 Comm | 0.031799 | 0.031799 | 0.031799 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04941 | | | 0.14 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7053.00 ave 7053 max 7053 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: 191896.0 ave 191896 max 191896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191896 Ave neighs/atom = 76.819856 Neighbor list builds = 4 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.201 | 5.201 | 5.201 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -8370.7925 0 -8370.7925 4145.231 41288.364 117 0 -8371.4012 0 -8371.4012 11.15404 41502.227 Loop time of 2.12457 on 1 procs for 8 steps with 2498 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 = -8370.79246570614 -8371.40107653369 -8371.40123833166 Force two-norm initial, final = 212.04610 1.2937554 Force max component initial, final = 190.87326 1.1734163 Final line search alpha, max atom move = 0.00031733495 0.00037236600 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0851 | 2.0851 | 2.0851 | 0.0 | 98.14 Neigh | 0.028135 | 0.028135 | 0.028135 | 0.0 | 1.32 Comm | 0.0021239 | 0.0021239 | 0.0021239 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009228 | | | 0.43 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7049.00 ave 7049 max 7049 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: 191882.0 ave 191882 max 191882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191882 Ave neighs/atom = 76.814251 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 45 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.340 | 5.340 | 5.340 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8371.4012 0 -8371.4012 11.15404 Loop time of 7.267e-06 on 1 procs for 0 steps with 2498 atoms 178.9% 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 | | 7.267e-06 | | |100.00 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7049.00 ave 7049 max 7049 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: 191882.0 ave 191882 max 191882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191882 Ave neighs/atom = 76.814251 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 45 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.340 | 5.340 | 5.340 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 -8371.4012 -8371.4012 41.226413 143.88325 6.9965767 11.15404 11.15404 -14.858387 45.615558 2.7049478 2.5411527 1120.6701 Loop time of 7.047e-06 on 1 procs for 0 steps with 2498 atoms 269.6% 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 | | 7.047e-06 | | |100.00 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7049.00 ave 7049 max 7049 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95941.0 ave 95941 max 95941 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191882.0 ave 191882 max 191882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191882 Ave neighs/atom = 76.814251 Neighbor list builds = 0 Dangerous builds = 0 2498 -8371.40123833166 eV 2.54115271449621 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:38