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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -39.368621 0.0000000) to (10.714781 39.368621 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5920492 4.3742912 4.6763140 Created 252 atoms using lattice units in orthogonal box = (0.0000000 -39.368621 0.0000000) to (10.714781 39.368621 7.0144710) create_atoms CPU = 0.001 seconds 252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5920492 4.3742912 4.6763140 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.368621 0.0000000) to (10.714781 39.368621 7.0144710) create_atoms CPU = 0.000 seconds 254 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 4 25 3 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 504 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 4 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1570.1358 0 -1570.1358 145949.75 70 0 -2151.0593 0 -2151.0593 8937.8156 Loop time of 4.86871 on 1 procs for 70 steps with 504 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 = -1570.13578637051 -2151.05775941212 -2151.05929890166 Force two-norm initial, final = 1158.1365 0.13772718 Force max component initial, final = 345.85789 0.026620875 Final line search alpha, max atom move = 1.0000000 0.026620875 Iterations, force evaluations = 70 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8514 | 4.8514 | 4.8514 | 0.0 | 99.64 Neigh | 0.0077768 | 0.0077768 | 0.0077768 | 0.0 | 0.16 Comm | 0.004692 | 0.004692 | 0.004692 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004817 | | | 0.10 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3163.00 ave 3163 max 3163 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: 49660.0 ave 49660 max 49660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49660 Ave neighs/atom = 98.531746 Neighbor list builds = 2 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 4 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -2151.0593 0 -2151.0593 8937.8156 5917.7747 78 0 -2151.2841 0 -2151.2841 -50.175454 5948.3734 Loop time of 0.477622 on 1 procs for 8 steps with 504 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 = -2151.05929890166 -2151.284087664 -2151.28410028068 Force two-norm initial, final = 71.699863 0.42321112 Force max component initial, final = 66.233500 0.20394234 Final line search alpha, max atom move = 0.0034048722 0.00069439759 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47561 | 0.47561 | 0.47561 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031421 | 0.00031421 | 0.00031421 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001696 | | | 0.35 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3111.00 ave 3111 max 3111 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: 50068.0 ave 50068 max 50068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50068 Ave neighs/atom = 99.341270 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 4 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.632 | 4.632 | 4.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2151.2841 0 -2151.2841 -50.175454 Loop time of 2.477e-06 on 1 procs for 0 steps with 504 atoms 201.9% 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 | | 2.477e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3127.00 ave 3127 max 3127 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: 48088.0 ave 48088 max 48088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48088 Ave neighs/atom = 95.412698 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 4 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.632 | 4.632 | 4.632 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 -2151.2841 -2151.2841 10.720812 79.274548 6.9990123 -50.175454 -50.175454 -54.962174 -51.907011 -43.657177 2.3071985 510.599 Loop time of 2.852e-06 on 1 procs for 0 steps with 504 atoms 175.3% 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 | | 2.852e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3127.00 ave 3127 max 3127 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24044.0 ave 24044 max 24044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48088.0 ave 48088 max 48088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48088 Ave neighs/atom = 95.412698 Neighbor list builds = 0 Dangerous builds = 0 504 -2151.28410028068 eV 2.30719846821111 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05