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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -53.053085 0.0000000) to (37.514196 53.053085 5.7208612) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9793853 6.7858597 5.7208612 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -53.053085 0.0000000) to (37.514196 53.053085 5.7208612) create_atoms CPU = 0.004 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9793853 6.7858597 5.7208612 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -53.053085 0.0000000) to (37.514196 53.053085 5.7208612) create_atoms CPU = 0.003 seconds 690 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 = 9 25 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 10 atoms, new total = 1362 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_106969701023_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 = 9 25 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) = 5.101 | 5.101 | 5.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4601.1726 0 -4601.1726 4002.7805 88 0 -4632.654 0 -4632.654 -3519.0564 Loop time of 3.88562 on 1 procs for 88 steps with 1362 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 = -4601.17262017251 -4632.64991912318 -4632.65401708852 Force two-norm initial, final = 44.899143 0.14881819 Force max component initial, final = 7.4369289 0.031339886 Final line search alpha, max atom move = 1.0000000 0.031339886 Iterations, force evaluations = 88 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8197 | 3.8197 | 3.8197 | 0.0 | 98.30 Neigh | 0.024626 | 0.024626 | 0.024626 | 0.0 | 0.63 Comm | 0.021601 | 0.021601 | 0.021601 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01967 | | | 0.51 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7696.00 ave 7696 max 7696 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: 192340.0 ave 192340 max 192340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192340 Ave neighs/atom = 141.21880 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 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 : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -4632.654 0 -4632.654 -3519.0564 22771.817 93 0 -4632.8071 0 -4632.8071 -8.4038103 22668.209 Loop time of 0.185918 on 1 procs for 5 steps with 1362 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 = -4632.65401708858 -4632.80581711629 -4632.8071319627 Force two-norm initial, final = 90.341700 0.41612662 Force max component initial, final = 70.699133 0.35579320 Final line search alpha, max atom move = 0.00010366246 3.6882399e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18095 | 0.18095 | 0.18095 | 0.0 | 97.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089105 | 0.00089105 | 0.00089105 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004079 | | | 2.19 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7280.00 ave 7280 max 7280 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: 191808.0 ave 191808 max 191808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191808 Ave neighs/atom = 140.82819 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 = 9 25 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) = 5.236 | 5.236 | 5.236 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4632.8071 0 -4632.8071 -8.4038103 Loop time of 3.192e-06 on 1 procs for 0 steps with 1362 atoms 156.6% 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 | | 3.192e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7401.00 ave 7401 max 7401 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: 192200.0 ave 192200 max 192200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192200 Ave neighs/atom = 141.11601 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 = 9 25 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) = 5.236 | 5.236 | 5.236 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 -4632.8071 -4632.8071 37.512259 105.69034 5.7175329 -8.4038103 -8.4038103 -25.145969 -4.3286379 4.2631759 2.6749236 977.01957 Loop time of 3.914e-06 on 1 procs for 0 steps with 1362 atoms 178.8% 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 | | 3.914e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7401.00 ave 7401 max 7401 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96100.0 ave 96100 max 96100 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192200.0 ave 192200 max 192200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192200 Ave neighs/atom = 141.11601 Neighbor list builds = 0 Dangerous builds = 0 1362 -4632.8071319627 eV 2.67492355706948 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04