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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -45.966080 0.0000000) to (10.833458 45.966080 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0185877 5.1069410 5.1069410 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -45.966080 0.0000000) to (10.833458 45.966080 5.1069410) create_atoms CPU = 0.001 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0185877 5.1069410 5.1069410 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -45.966080 0.0000000) to (10.833458 45.966080 5.1069410) create_atoms CPU = 0.001 seconds 218 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 = 5 35 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 6 atoms, new total = 430 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_137964310702_004#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 = 5 35 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) = 4.848 | 4.848 | 4.848 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1798.4372 0 -1798.4372 14343.469 55 0 -1819.9387 0 -1819.9387 -1766.4212 Loop time of 2.31467 on 1 procs for 55 steps with 430 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 = -1798.43722223793 -1819.9369932883 -1819.93869863149 Force two-norm initial, final = 38.593931 0.14890039 Force max component initial, final = 14.279111 0.019672720 Final line search alpha, max atom move = 1.0000000 0.019672720 Iterations, force evaluations = 55 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3095 | 2.3095 | 2.3095 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025209 | 0.0025209 | 0.0025209 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002636 | | | 0.11 Nlocal: 430.000 ave 430 max 430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2692.00 ave 2692 max 2692 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: 23068.0 ave 23068 max 23068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23068 Ave neighs/atom = 53.646512 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 35 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.848 | 4.848 | 4.848 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -1819.9387 0 -1819.9387 -1766.4212 5086.2231 56 0 -1819.9399 0 -1819.9399 -2028.3072 5087.0376 Loop time of 0.0693675 on 1 procs for 1 steps with 430 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 = -1819.93869863149 -1819.93869863149 -1819.93987839806 Force two-norm initial, final = 3.9188874 0.68673907 Force max component initial, final = 3.2408115 0.54974443 Final line search alpha, max atom move = 0.00030856469 0.00016963172 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069046 | 0.069046 | 0.069046 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.406e-05 | 6.406e-05 | 6.406e-05 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002572 | | | 0.37 Nlocal: 430.000 ave 430 max 430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2680.00 ave 2680 max 2680 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: 23076.0 ave 23076 max 23076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23076 Ave neighs/atom = 53.665116 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 = 5 35 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) = 4.986 | 4.986 | 4.986 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1819.9399 0 -1819.9399 -2028.3072 Loop time of 1.712e-06 on 1 procs for 0 steps with 430 atoms 116.8% 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 | | 1.712e-06 | | |100.00 Nlocal: 430.000 ave 430 max 430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2680.00 ave 2680 max 2680 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: 23076.0 ave 23076 max 23076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23076 Ave neighs/atom = 53.665116 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 = 5 35 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) = 4.986 | 4.986 | 4.986 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 -1819.9399 -1819.9399 10.838857 91.932161 5.1052147 -2028.3072 -2028.3072 -120.62953 -5791.207 -173.08499 2.351528 134.87093 Loop time of 1.831e-06 on 1 procs for 0 steps with 430 atoms 163.8% 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 | | 1.831e-06 | | |100.00 Nlocal: 430.000 ave 430 max 430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2680.00 ave 2680 max 2680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11538.0 ave 11538 max 11538 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23076.0 ave 23076 max 23076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23076 Ave neighs/atom = 53.665116 Neighbor list builds = 0 Dangerous builds = 0 430 -1819.93987839806 eV 2.35152804582517 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02