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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -73.350753 0.0000000) to (42.349077 73.350753 6.3365399) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6886820 5.8388659 6.3365399 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -73.350753 0.0000000) to (42.349077 73.350753 6.3365399) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6886820 5.8388659 6.3365399 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -73.350753 0.0000000) to (42.349077 73.350753 6.3365399) create_atoms CPU = 0.003 seconds 1610 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 35 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3218 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.35 | 11.35 | 11.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11699.374 0 -11699.374 62830.21 267 0 -12637.796 0 -12637.796 -50711.735 Loop time of 19.6998 on 1 procs for 267 steps with 3218 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11699.3742431772 -12637.7847942993 -12637.7956222411 Force two-norm initial, final = 1277.9964 0.51447941 Force max component initial, final = 370.79850 0.15549664 Final line search alpha, max atom move = 0.96676229 0.15032828 Iterations, force evaluations = 267 497 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.166 | 19.166 | 19.166 | 0.0 | 97.29 Neigh | 0.33009 | 0.33009 | 0.33009 | 0.0 | 1.68 Comm | 0.11143 | 0.11143 | 0.11143 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09262 | | | 0.47 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15277.0 ave 15277 max 15277 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: 660372.0 ave 660372 max 660372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 660372 Ave neighs/atom = 205.21193 Neighbor list builds = 7 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 267 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.35 | 11.35 | 11.35 Mbytes Step Temp E_pair E_mol TotEng Press Volume 267 0 -12637.796 0 -12637.796 -50711.735 39366.853 298 0 -12669.085 0 -12669.085 3.9844276 37895.655 Loop time of 1.6497 on 1 procs for 31 steps with 3218 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 = -12637.795622241 -12669.0795906815 -12669.0849028503 Force two-norm initial, final = 2243.9211 4.3266399 Force max component initial, final = 1641.1962 0.90928679 Final line search alpha, max atom move = 6.4953492e-05 5.9061352e-05 Iterations, force evaluations = 31 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5259 | 1.5259 | 1.5259 | 0.0 | 92.50 Neigh | 0.087077 | 0.087077 | 0.087077 | 0.0 | 5.28 Comm | 0.0060719 | 0.0060719 | 0.0060719 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03066 | | | 1.86 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15463.0 ave 15463 max 15463 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: 697428.0 ave 697428 max 697428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 697428 Ave neighs/atom = 216.72716 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.25 | 11.25 | 11.25 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12669.085 0 -12669.085 3.9844276 Loop time of 2.419e-06 on 1 procs for 0 steps with 3218 atoms 165.4% 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 | | 2.419e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15443.0 ave 15443 max 15443 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: 699088.0 ave 699088 max 699088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 699088 Ave neighs/atom = 217.24301 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.25 | 11.25 | 11.25 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 -12669.085 -12669.085 41.237156 144.54109 6.357837 3.9844276 3.9844276 37.43403 -22.114719 -3.3660279 2.2123941 7927.811 Loop time of 2.779e-06 on 1 procs for 0 steps with 3218 atoms 287.9% 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 | | 2.779e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15443.0 ave 15443 max 15443 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 349544.0 ave 349544 max 349544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 699088.0 ave 699088 max 699088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 699088 Ave neighs/atom = 217.24301 Neighbor list builds = 0 Dangerous builds = 0 3218 -12669.0849028503 eV 2.21239411010755 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22