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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -69.126799 0.0000000) to (39.910376 69.126799 6.2584463) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8884161 5.2883890 6.2584463 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -69.126799 0.0000000) to (39.910376 69.126799 6.2584463) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8884161 5.2883890 6.2584463 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.126799 0.0000000) to (39.910376 69.126799 6.2584463) create_atoms CPU = 0.002 seconds 1465 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 43 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2923 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.808 | 5.808 | 5.808 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10022.257 0 -10022.257 28206.673 52 0 -10313.332 0 -10313.332 3148.5731 Loop time of 7.29424 on 1 procs for 52 steps with 2923 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10022.2567415398 -10313.3229558697 -10313.3318685885 Force two-norm initial, final = 327.91504 0.32762103 Force max component initial, final = 59.601767 0.11763775 Final line search alpha, max atom move = 1.0000000 0.11763775 Iterations, force evaluations = 52 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2417 | 7.2417 | 7.2417 | 0.0 | 99.28 Neigh | 0.021059 | 0.021059 | 0.021059 | 0.0 | 0.29 Comm | 0.015628 | 0.015628 | 0.015628 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01589 | | | 0.22 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11187.0 ave 11187 max 11187 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: 252374.0 ave 252374 max 252374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252374 Ave neighs/atom = 86.340746 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.808 | 5.808 | 5.808 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -10313.332 0 -10313.332 3148.5731 34532.562 55 0 -10313.452 0 -10313.452 5.4077437 34609.305 Loop time of 0.4307 on 1 procs for 3 steps with 2923 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 = -10313.3318685884 -10313.4470814898 -10313.4523261036 Force two-norm initial, final = 128.21804 2.1618792 Force max component initial, final = 109.27592 1.7571603 Final line search alpha, max atom move = 4.1968588e-05 7.3745539e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42757 | 0.42757 | 0.42757 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050353 | 0.00050353 | 0.00050353 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002629 | | | 0.61 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11172.0 ave 11172 max 11172 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: 252226.0 ave 252226 max 252226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252226 Ave neighs/atom = 86.290113 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.946 | 5.946 | 5.946 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10313.452 0 -10313.452 5.4077437 Loop time of 2.229e-06 on 1 procs for 0 steps with 2923 atoms 179.5% 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 | | 2.229e-06 | | |100.00 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11163.0 ave 11163 max 11163 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: 252154.0 ave 252154 max 252154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252154 Ave neighs/atom = 86.265481 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.946 | 5.946 | 5.946 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 -10313.452 -10313.452 39.902174 138.55297 6.2600888 5.4077437 5.4077437 -55.130059 -10.012686 81.365976 2.2545544 960.37092 Loop time of 2.152e-06 on 1 procs for 0 steps with 2923 atoms 232.3% 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 | | 2.152e-06 | | |100.00 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11163.0 ave 11163 max 11163 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126077.0 ave 126077 max 126077 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 252154.0 ave 252154 max 252154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252154 Ave neighs/atom = 86.265481 Neighbor list builds = 0 Dangerous builds = 0 2923 -10313.4523261036 eV 2.25455438396696 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08