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 = 3.5878716 3.5878716 3.5878716 Created orthogonal box = (0.0000000 -38.139598 0.0000000) to (38.139598 38.139598 3.5878716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0627785 5.0627785 3.5878716 Created 451 atoms using lattice units in orthogonal box = (0.0000000 -38.139598 0.0000000) to (38.139598 38.139598 3.5878716) create_atoms CPU = 0.002 seconds 451 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0627785 5.0627785 3.5878716 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -38.139598 0.0000000) to (38.139598 38.139598 3.5878716) create_atoms CPU = 0.002 seconds 453 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 10 19 1 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 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 904 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_228059236215_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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.002 | 5.002 | 5.002 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3011.4693 0 -3011.4693 57790.763 61 0 -3175.5452 0 -3175.5452 4516.3725 Loop time of 4.45994 on 1 procs for 61 steps with 904 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 = -3011.46930378005 -3175.54274738885 -3175.54523684199 Force two-norm initial, final = 167.74967 0.14986001 Force max component initial, final = 29.946480 0.027410948 Final line search alpha, max atom move = 1.0000000 0.027410948 Iterations, force evaluations = 61 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4042 | 4.4042 | 4.4042 | 0.0 | 98.75 Neigh | 0.022542 | 0.022542 | 0.022542 | 0.0 | 0.51 Comm | 0.018791 | 0.018791 | 0.018791 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01438 | | | 0.32 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7751.00 ave 7751 max 7751 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: 180426.0 ave 180426 max 180426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180426 Ave neighs/atom = 199.58628 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.002 | 5.002 | 5.002 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -3175.5452 0 -3175.5452 4516.3725 10438.044 66 0 -3175.6528 0 -3175.6528 244.16712 10469.152 Loop time of 0.330611 on 1 procs for 5 steps with 904 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 = -3175.54523684199 -3175.65156688481 -3175.65275947619 Force two-norm initial, final = 60.881788 3.9508187 Force max component initial, final = 48.344352 2.9096762 Final line search alpha, max atom move = 0.00020422140 0.00059421817 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32524 | 0.32524 | 0.32524 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012546 | 0.0012546 | 0.0012546 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004117 | | | 1.25 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7728.00 ave 7728 max 7728 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: 180232.0 ave 180232 max 180232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180232 Ave neighs/atom = 199.37168 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.140 | 5.140 | 5.140 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3175.6528 0 -3175.6528 244.16712 Loop time of 6.395e-06 on 1 procs for 0 steps with 904 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7724.00 ave 7724 max 7724 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: 180054.0 ave 180054 max 180054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180054 Ave neighs/atom = 199.17478 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.140 | 5.140 | 5.140 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 -3175.6528 -3175.6528 38.049907 76.453685 3.5988148 244.16712 244.16712 444.24341 -106.89001 395.14795 2.2992881 145.9629 Loop time of 6.726e-06 on 1 procs for 0 steps with 904 atoms 282.5% 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 | | 6.726e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7724.00 ave 7724 max 7724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90027.0 ave 90027 max 90027 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180054.0 ave 180054 max 180054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180054 Ave neighs/atom = 199.17478 Neighbor list builds = 0 Dangerous builds = 0 904 -3175.65275947619 eV 2.29928813119375 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05