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 -36.506965 0.0000000) to (25.814322 36.506965 5.1119976) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5554687 5.7265827 5.1119976 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.506965 0.0000000) to (25.814322 36.506965 5.1119976) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5554687 5.7265827 5.1119976 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.506965 0.0000000) to (25.814322 36.506965 5.1119976) create_atoms CPU = 0.002 seconds 410 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 = 6 17 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 6 atoms, new total = 812 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 = 6 17 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) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2635.1627 0 -2635.1627 55201.542 100 0 -2848.772 0 -2848.772 2630.6077 Loop time of 3.80959 on 1 procs for 100 steps with 812 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 = -2635.16272957262 -2848.76924682007 -2848.77199479764 Force two-norm initial, final = 394.29418 0.18279087 Force max component initial, final = 106.93442 0.034982518 Final line search alpha, max atom move = 0.94541294 0.033072925 Iterations, force evaluations = 100 190 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7076 | 3.7076 | 3.7076 | 0.0 | 97.32 Neigh | 0.051123 | 0.051123 | 0.051123 | 0.0 | 1.34 Comm | 0.02906 | 0.02906 | 0.02906 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02176 | | | 0.57 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6293.00 ave 6293 max 6293 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: 181708.0 ave 181708 max 181708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181708 Ave neighs/atom = 223.77833 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 17 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 : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.986 | 4.986 | 4.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -2848.772 0 -2848.772 2630.6077 9635.1192 102 0 -2848.7857 0 -2848.7857 -3.363646 9653.3916 Loop time of 0.101019 on 1 procs for 2 steps with 812 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 = -2848.77199479765 -2848.78490356083 -2848.78568446294 Force two-norm initial, final = 27.528435 0.37389576 Force max component initial, final = 17.969419 0.25721286 Final line search alpha, max atom move = 0.00053932021 0.00013872010 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.098381 | 0.098381 | 0.098381 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068598 | 0.00068598 | 0.00068598 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001952 | | | 1.93 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6301.00 ave 6301 max 6301 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: 181812.0 ave 181812 max 181812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181812 Ave neighs/atom = 223.90640 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 = 6 17 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) = 5.124 | 5.124 | 5.124 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2848.7857 0 -2848.7857 -3.363646 Loop time of 6.525e-06 on 1 procs for 0 steps with 812 atoms 199.2% 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 | | 6.525e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6301.00 ave 6301 max 6301 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: 181724.0 ave 181724 max 181724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181724 Ave neighs/atom = 223.79803 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 = 6 17 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) = 5.124 | 5.124 | 5.124 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 -2848.7857 -2848.7857 25.847073 73.040921 5.1133122 -3.363646 -3.363646 -0.38287342 -42.705483 32.997418 2.3764813 656.13866 Loop time of 7.507e-06 on 1 procs for 0 steps with 812 atoms 226.5% 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 | | 7.507e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6301.00 ave 6301 max 6301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90862.0 ave 90862 max 90862 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181724.0 ave 181724 max 181724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181724 Ave neighs/atom = 223.79803 Neighbor list builds = 0 Dangerous builds = 0 812 -2848.78568446294 eV 2.37648127890029 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04