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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -46.804569 0.0000000) to (27.022631 46.804569 6.2545236) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7905637 5.5719725 6.2545236 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -46.804569 0.0000000) to (27.022631 46.804569 6.2545236) create_atoms CPU = 0.004 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7905637 5.5719725 6.2545236 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.804569 0.0000000) to (27.022631 46.804569 6.2545236) create_atoms CPU = 0.004 seconds 676 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1348 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.737 | 6.737 | 6.737 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4886.2295 0 -4886.2295 87424.769 102 0 -5568.046 0 -5568.046 12399.245 Loop time of 11.3794 on 1 procs for 102 steps with 1348 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4886.22945690862 -5568.04093128103 -5568.04603302967 Force two-norm initial, final = 736.42756 0.31596555 Force max component initial, final = 154.75939 0.041688078 Final line search alpha, max atom move = 1.0000000 0.041688078 Iterations, force evaluations = 102 186 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.115 | 11.115 | 11.115 | 0.0 | 97.68 Neigh | 0.18359 | 0.18359 | 0.18359 | 0.0 | 1.61 Comm | 0.048556 | 0.048556 | 0.048556 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03199 | | | 0.28 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11198.0 ave 11198 max 11198 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: 512968.0 ave 512968 max 512968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 512968 Ave neighs/atom = 380.54006 Neighbor list builds = 3 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.737 | 6.737 | 6.737 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -5568.046 0 -5568.046 12399.245 15821.225 109 0 -5568.6532 0 -5568.6532 -6.7992914 15934.671 Loop time of 0.601584 on 1 procs for 7 steps with 1348 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5568.04603302967 -5568.65287429755 -5568.65323224681 Force two-norm initial, final = 229.93851 0.62989512 Force max component initial, final = 194.66859 0.25692603 Final line search alpha, max atom move = 0.00019296406 4.9577491e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59183 | 0.59183 | 0.59183 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023174 | 0.0023174 | 0.0023174 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007436 | | | 1.24 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11194.0 ave 11194 max 11194 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: 513136.0 ave 513136 max 513136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513136 Ave neighs/atom = 380.66469 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.875 | 6.875 | 6.875 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5568.6532 0 -5568.6532 -6.7992914 Loop time of 6.585e-06 on 1 procs for 0 steps with 1348 atoms 182.2% 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 | | 6.585e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11190.0 ave 11190 max 11190 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: 512112.0 ave 512112 max 512112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 512112 Ave neighs/atom = 379.90504 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.875 | 6.875 | 6.875 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 -5568.6532 -5568.6532 27.031206 94.126809 6.2627395 -6.7992914 -6.7992914 -25.841229 -17.374009 22.817364 2.332761 854.58034 Loop time of 6.896e-06 on 1 procs for 0 steps with 1348 atoms 319.0% 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 | | 6.896e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11190.0 ave 11190 max 11190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 256056.0 ave 256056 max 256056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 512112.0 ave 512112 max 512112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 512112 Ave neighs/atom = 379.90504 Neighbor list builds = 0 Dangerous builds = 0 1348 -5568.65323224681 eV 2.33276102472182 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12