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 = 3.6147282 3.6147282 3.6147282 Created orthogonal box = (0.0000000 -41.843504 0.0000000) to (29.587825 41.843504 5.1119976) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7409213 6.2452990 5.1119976 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.843504 0.0000000) to (29.587825 41.843504 5.1119976) create_atoms CPU = 0.006 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7409213 6.2452990 5.1119976 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.843504 0.0000000) to (29.587825 41.843504 5.1119976) create_atoms CPU = 0.005 seconds 538 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 20 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1070 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_942551040047_005#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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3562.2311 0 -3562.2311 42168.034 68 0 -3764.3537 0 -3764.3537 665.87632 Loop time of 3.26798 on 1 procs for 68 steps with 1070 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 = -3562.23110029827 -3764.35076539045 -3764.35372693728 Force two-norm initial, final = 359.17125 0.19944841 Force max component initial, final = 114.81502 0.030312431 Final line search alpha, max atom move = 1.0000000 0.030312431 Iterations, force evaluations = 68 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1937 | 3.1937 | 3.1937 | 0.0 | 97.73 Neigh | 0.033296 | 0.033296 | 0.033296 | 0.0 | 1.02 Comm | 0.023082 | 0.023082 | 0.023082 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01786 | | | 0.55 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8085.00 ave 8085 max 8085 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: 240628.0 ave 240628 max 240628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240628 Ave neighs/atom = 224.88598 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -3764.3537 0 -3764.3537 665.87632 12657.902 74 0 -3764.5525 0 -3764.5525 42.131923 12662.913 Loop time of 0.211259 on 1 procs for 6 steps with 1070 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 = -3764.35372693728 -3764.55181941587 -3764.55249140595 Force two-norm initial, final = 66.671634 0.64063780 Force max component initial, final = 54.622082 0.35933827 Final line search alpha, max atom move = 0.00068881027 0.00024751589 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2055 | 0.2055 | 0.2055 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012874 | 0.0012874 | 0.0012874 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004468 | | | 2.11 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8092.00 ave 8092 max 8092 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: 240444.0 ave 240444 max 240444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240444 Ave neighs/atom = 224.71402 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.579 | 5.579 | 5.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3764.5525 0 -3764.5525 42.131923 Loop time of 6.144e-06 on 1 procs for 0 steps with 1070 atoms 195.3% 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 | | 6.144e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8110.00 ave 8110 max 8110 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: 240220.0 ave 240220 max 240220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240220 Ave neighs/atom = 224.50467 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.579 | 5.579 | 5.579 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 -3764.5525 -3764.5525 29.452659 84.073238 5.1138894 42.131923 42.131923 40.568179 40.345448 45.482141 2.3672393 587.87213 Loop time of 7.448e-06 on 1 procs for 0 steps with 1070 atoms 228.2% 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 | | 7.448e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8110.00 ave 8110 max 8110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120110.0 ave 120110 max 120110 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 240220.0 ave 240220 max 240220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240220 Ave neighs/atom = 224.50467 Neighbor list builds = 0 Dangerous builds = 0 1070 -3764.55249140595 eV 2.36723931320614 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04