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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -41.130024 0.0000000) to (20.147712 41.130024 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3727232 4.9351614 6.0068872 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -41.130024 0.0000000) to (20.147712 41.130024 9.0103308) create_atoms CPU = 0.003 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3727232 4.9351614 6.0068872 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -41.130024 0.0000000) to (20.147712 41.130024 9.0103308) create_atoms CPU = 0.002 seconds 612 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 27 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 1188 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_024705128470_000#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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4958.9188 0 -4958.9188 6686.3198 74 0 -4989.8294 0 -4989.8294 -6537.1141 Loop time of 0.961871 on 1 procs for 74 steps with 1188 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4958.91876811367 -4989.82548631603 -4989.82939270158 Force two-norm initial, final = 23.839007 0.21975609 Force max component initial, final = 4.6249968 0.030026168 Final line search alpha, max atom move = 1.0000000 0.030026168 Iterations, force evaluations = 74 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93162 | 0.93162 | 0.93162 | 0.0 | 96.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012719 | 0.012719 | 0.012719 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01753 | | | 1.82 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4159.00 ave 4159 max 4159 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: 91920.0 ave 91920 max 91920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91920 Ave neighs/atom = 77.373737 Neighbor list builds = 0 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -4989.8294 0 -4989.8294 -6537.1141 14933.288 77 0 -4989.9162 0 -4989.9162 -2487.6234 14876.085 Loop time of 0.0364163 on 1 procs for 3 steps with 1188 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 = -4989.82939270157 -4989.91453325057 -4989.91619734902 Force two-norm initial, final = 62.562716 1.2192353 Force max component initial, final = 51.688111 1.0935247 Final line search alpha, max atom move = 0.00012755945 0.00013948942 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034191 | 0.034191 | 0.034191 | 0.0 | 93.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040593 | 0.00040593 | 0.00040593 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001819 | | | 5.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4012.00 ave 4012 max 4012 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: 92064.0 ave 92064 max 92064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92064 Ave neighs/atom = 77.494949 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.723 | 4.723 | 4.723 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4989.9162 0 -4989.9162 -2487.6234 Loop time of 6.235e-06 on 1 procs for 0 steps with 1188 atoms 176.4% 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 | | 6.235e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4023.00 ave 4023 max 4023 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: 92064.0 ave 92064 max 92064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92064 Ave neighs/atom = 77.494949 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.723 | 4.723 | 4.723 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 -4989.9162 -4989.9162 20.117959 82.260047 8.9890911 -2487.6234 -2487.6234 117.60032 -7529.6497 -50.820967 2.3407872 712.37272 Loop time of 6.916e-06 on 1 procs for 0 steps with 1188 atoms 260.3% 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 | | 6.916e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4023.00 ave 4023 max 4023 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46032.0 ave 46032 max 46032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92064.0 ave 92064 max 92064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92064 Ave neighs/atom = 77.494949 Neighbor list builds = 0 Dangerous builds = 0 1188 -4989.91607854902 eV 2.34078720425349 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01