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 -70.055407 0.0000000) to (28.600000 70.055407 9.9073307) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8640001 6.0714686 6.6048871 Created 1193 atoms using lattice units in orthogonal box = (0.0000000 -70.055407 0.0000000) to (28.600000 70.055407 9.9073307) create_atoms CPU = 0.002 seconds 1193 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8640001 6.0714686 6.6048871 Created 1201 atoms using lattice units in orthogonal box = (0.0000000 -70.055407 0.0000000) to (28.600000 70.055407 9.9073307) create_atoms CPU = 0.002 seconds 1201 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 41 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 2385 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_478967255435_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.162 | 5.162 | 5.162 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7789.6817 0 -7789.6817 12282.252 67 0 -7995.9674 0 -7995.9674 -2470.3925 Loop time of 10.9895 on 1 procs for 67 steps with 2385 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7789.6816558689 -7995.96099584494 -7995.96738929863 Force two-norm initial, final = 232.25252 0.26805406 Force max component initial, final = 39.215870 0.12573615 Final line search alpha, max atom move = 0.56722700 0.071320938 Iterations, force evaluations = 67 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.902 | 10.902 | 10.902 | 0.0 | 99.20 Neigh | 0.061667 | 0.061667 | 0.061667 | 0.0 | 0.56 Comm | 0.010644 | 0.010644 | 0.010644 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01561 | | | 0.14 Nlocal: 2385.00 ave 2385 max 2385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6890.00 ave 6890 max 6890 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: 188916.0 ave 188916 max 188916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188916 Ave neighs/atom = 79.210063 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.161 | 5.161 | 5.161 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -7995.9674 0 -7995.9674 -2470.3925 39700.352 70 0 -7996.085 0 -7996.085 -1.0630091 39575.287 Loop time of 0.665 on 1 procs for 3 steps with 2385 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7995.96738929863 -7996.07912255766 -7996.08498085469 Force two-norm initial, final = 109.01525 0.30998981 Force max component initial, final = 74.580201 0.12710893 Final line search alpha, max atom move = 5.9437032e-05 7.5549773e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66237 | 0.66237 | 0.66237 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036434 | 0.00036434 | 0.00036434 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002267 | | | 0.34 Nlocal: 2385.00 ave 2385 max 2385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6849.00 ave 6849 max 6849 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: 188164.0 ave 188164 max 188164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188164 Ave neighs/atom = 78.894759 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.299 | 5.299 | 5.299 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7996.085 0 -7996.085 -1.0630091 Loop time of 2.037e-06 on 1 procs for 0 steps with 2385 atoms 196.4% 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 | | 2.037e-06 | | |100.00 Nlocal: 2385.00 ave 2385 max 2385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6969.00 ave 6969 max 6969 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: 193522.0 ave 193522 max 193522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193522 Ave neighs/atom = 81.141300 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.299 | 5.299 | 5.299 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 -7996.085 -7996.085 28.607491 139.9001 9.8884059 -1.0630091 -1.0630091 -1.9437799 2.8817508 -4.1269983 2.4643434 722.04247 Loop time of 2.447e-06 on 1 procs for 0 steps with 2385 atoms 286.1% 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 | | 2.447e-06 | | |100.00 Nlocal: 2385.00 ave 2385 max 2385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6969.00 ave 6969 max 6969 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96761.0 ave 96761 max 96761 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193522.0 ave 193522 max 193522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193522 Ave neighs/atom = 81.141300 Neighbor list builds = 0 Dangerous builds = 0 2385 -7996.08498085469 eV 2.46434344522789 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12