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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -53.604252 0.0000000) to (18.951965 53.604252 5.1580716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9134724 5.9560280 5.1580716 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -53.604252 0.0000000) to (18.951965 53.604252 5.1580716) create_atoms CPU = 0.002 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9134724 5.9560280 5.1580716 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.604252 0.0000000) to (18.951965 53.604252 5.1580716) create_atoms CPU = 0.001 seconds 434 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 41 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 862 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3194.9511 0 -3194.9511 86832.754 65 0 -3563.1554 0 -3563.1554 1589.0319 Loop time of 5.47061 on 1 procs for 65 steps with 862 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3194.95106315111 -3563.15187878027 -3563.15543974578 Force two-norm initial, final = 936.97481 0.23438208 Force max component initial, final = 241.73673 0.032916607 Final line search alpha, max atom move = 1.0000000 0.032916607 Iterations, force evaluations = 65 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4447 | 5.4447 | 5.4447 | 0.0 | 99.53 Neigh | 0.015183 | 0.015183 | 0.015183 | 0.0 | 0.28 Comm | 0.0046266 | 0.0046266 | 0.0046266 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006092 | | | 0.11 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3562.00 ave 3562 max 3562 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: 46304.0 ave 46304 max 46304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46304 Ave neighs/atom = 53.716937 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -3563.1554 0 -3563.1554 1589.0319 10480.231 68 0 -3563.1777 0 -3563.1777 -87.824951 10490.689 Loop time of 0.255038 on 1 procs for 3 steps with 862 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 = -3563.15543974578 -3563.17698045375 -3563.17770483766 Force two-norm initial, final = 27.258363 2.3615888 Force max component initial, final = 27.061636 1.8303536 Final line search alpha, max atom move = 0.00017982682 0.00032914668 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25409 | 0.25409 | 0.25409 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015367 | 0.00015367 | 0.00015367 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007921 | | | 0.31 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3552.00 ave 3552 max 3552 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: 46304.0 ave 46304 max 46304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46304 Ave neighs/atom = 53.716937 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.074 | 5.074 | 5.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3563.1777 0 -3563.1777 -87.824951 Loop time of 3.513e-06 on 1 procs for 0 steps with 862 atoms 170.8% 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 | | 3.513e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3552.00 ave 3552 max 3552 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: 46300.0 ave 46300 max 46300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46300 Ave neighs/atom = 53.712297 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.074 | 5.074 | 5.074 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 -3563.1777 -3563.1777 18.942867 107.39676 5.1566436 -87.824951 -87.824951 -279.40413 -150.05183 165.98111 2.3088233 309.97658 Loop time of 1.756e-06 on 1 procs for 0 steps with 862 atoms 170.8% 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 | | 1.756e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3552.00 ave 3552 max 3552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23150.0 ave 23150 max 23150 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46300.0 ave 46300 max 46300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46300 Ave neighs/atom = 53.712297 Neighbor list builds = 0 Dangerous builds = 0 862 -3563.17770483766 eV 2.30882325576006 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06