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 = 2.8826503 2.8826503 2.8826503 Created orthogonal box = (0.0000000 -41.972021 0.0000000) to (20.986011 41.972021 2.8826503) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5636622 3.5636622 2.8826503 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -41.972021 0.0000000) to (20.986011 41.972021 2.8826503) create_atoms CPU = 0.003 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5636622 3.5636622 2.8826503 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.972021 0.0000000) to (20.986011 41.972021 2.8826503) create_atoms CPU = 0.001 seconds 213 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 20 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 425 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_331285495617_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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.886 | 4.886 | 4.886 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1414.4101 0 -1414.4101 90269.437 57 0 -1638.5678 0 -1638.5678 13735.333 Loop time of 1.30373 on 1 procs for 57 steps with 425 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 = -1414.41006945449 -1638.56642998757 -1638.5678307518 Force two-norm initial, final = 384.17013 0.16336851 Force max component initial, final = 118.04646 0.020747457 Final line search alpha, max atom move = 1.0000000 0.020747457 Iterations, force evaluations = 57 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.267 | 1.267 | 1.267 | 0.0 | 97.18 Neigh | 0.013319 | 0.013319 | 0.013319 | 0.0 | 1.02 Comm | 0.014781 | 0.014781 | 0.014781 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008652 | | | 0.66 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6127.00 ave 6127 max 6127 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: 103586.0 ave 103586 max 103586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103586 Ave neighs/atom = 243.73176 Neighbor list builds = 1 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.887 | 4.887 | 4.887 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -1638.5678 0 -1638.5678 13735.333 5078.2225 104 0 -1640.7154 0 -1640.7154 540.00064 5117.8109 Loop time of 0.692723 on 1 procs for 47 steps with 425 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 = -1638.5678307518 -1640.71377906132 -1640.71540529217 Force two-norm initial, final = 101.11967 4.4276314 Force max component initial, final = 78.793548 3.8617395 Final line search alpha, max atom move = 0.00029679476 0.0011461440 Iterations, force evaluations = 47 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63781 | 0.63781 | 0.63781 | 0.0 | 92.07 Neigh | 0.026502 | 0.026502 | 0.026502 | 0.0 | 3.83 Comm | 0.0073571 | 0.0073571 | 0.0073571 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02105 | | | 3.04 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5987.00 ave 5987 max 5987 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: 98390.0 ave 98390 max 98390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98390 Ave neighs/atom = 231.50588 Neighbor list builds = 2 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1640.7154 0 -1640.7154 540.00064 Loop time of 6.735e-06 on 1 procs for 0 steps with 425 atoms 178.2% 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 | | 6.735e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5973.00 ave 5973 max 5973 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: 97962.0 ave 97962 max 97962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97962 Ave neighs/atom = 230.49882 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.642 | 4.642 | 4.642 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 -1640.7154 -1640.7154 21.438787 86.108808 2.772276 540.00064 540.00064 205.93895 251.40065 1162.6623 2.3854004 416.96889 Loop time of 7.047e-06 on 1 procs for 0 steps with 425 atoms 255.4% 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 | | 7.047e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5973.00 ave 5973 max 5973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48981.0 ave 48981 max 48981 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97962.0 ave 97962 max 97962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97962 Ave neighs/atom = 230.49882 Neighbor list builds = 0 Dangerous builds = 0 425 -1640.71540529217 eV 2.38540044876275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02