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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -69.507336 0.0000000) to (40.127982 69.507336 6.2925696) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9205219 5.3172232 6.2925696 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.507336 0.0000000) to (40.127982 69.507336 6.2925696) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9205219 5.3172232 6.2925696 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.507336 0.0000000) to (40.127982 69.507336 6.2925696) create_atoms CPU = 0.002 seconds 1466 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 37 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2906 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_036303866285_000#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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.989 | 6.989 | 6.989 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12282.891 0 -12282.891 9426.3957 87 0 -12389.432 0 -12389.432 -7676.0294 Loop time of 2.99915 on 1 procs for 87 steps with 2906 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 = -12282.8912003078 -12389.4202990882 -12389.4319721638 Force two-norm initial, final = 91.493161 0.45914946 Force max component initial, final = 17.396235 0.047442268 Final line search alpha, max atom move = 1.0000000 0.047442268 Iterations, force evaluations = 87 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9121 | 2.9121 | 2.9121 | 0.0 | 97.10 Neigh | 0.050471 | 0.050471 | 0.050471 | 0.0 | 1.68 Comm | 0.0179 | 0.0179 | 0.0179 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01865 | | | 0.62 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12013.0 ave 12013 max 12013 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: 441108.0 ave 441108 max 441108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441108 Ave neighs/atom = 151.79215 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.608 | 6.608 | 6.608 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -12389.432 0 -12389.432 -7676.0294 35102.334 89 0 -12389.478 0 -12389.478 -5414.742 35049.234 Loop time of 0.092123 on 1 procs for 2 steps with 2906 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 = -12389.4319721639 -12389.4782845947 -12389.4784556098 Force two-norm initial, final = 86.502370 0.48228240 Force max component initial, final = 62.706286 0.093015226 Final line search alpha, max atom move = 0.00032396910 3.0134059e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08969 | 0.08969 | 0.08969 | 0.0 | 97.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042518 | 0.00042518 | 0.00042518 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002008 | | | 2.18 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12050.0 ave 12050 max 12050 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: 444408.0 ave 444408 max 444408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444408 Ave neighs/atom = 152.92774 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.746 | 6.746 | 6.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12389.478 0 -12389.478 -5414.742 Loop time of 1.735e-06 on 1 procs for 0 steps with 2906 atoms 172.9% 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 | | 1.735e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12050.0 ave 12050 max 12050 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: 454244.0 ave 454244 max 454244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 454244 Ave neighs/atom = 156.31246 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.746 | 6.746 | 6.746 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 -12389.478 -12389.478 40.094599 139.01467 6.288282 -5414.742 -5414.742 -1.1781295 -16238.799 -4.2490306 2.3359947 1214.9356 Loop time of 2.252e-06 on 1 procs for 0 steps with 2906 atoms 133.2% 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 | | 2.252e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12050.0 ave 12050 max 12050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 227122.0 ave 227122 max 227122 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 454244.0 ave 454244 max 454244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 454244 Ave neighs/atom = 156.31246 Neighbor list builds = 0 Dangerous builds = 0 2906 -12389.4784556098 eV 2.33599473606629 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03