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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -40.935624 0.0000000) to (23.634193 40.935624 5.4702528) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0644700 4.8732885 5.4702528 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -40.935624 0.0000000) to (23.634193 40.935624 5.4702528) create_atoms CPU = 0.003 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0644700 4.8732885 5.4702528 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -40.935624 0.0000000) to (23.634193 40.935624 5.4702528) create_atoms CPU = 0.002 seconds 339 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 675 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_228581001644_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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2776.7141 0 -2776.7141 305363.26 320 0 -4309.5089 0 -4309.5089 17217.344 Loop time of 6.88863 on 1 procs for 320 steps with 675 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 = -2776.71413315361 -4309.50507759715 -4309.50888479057 Force two-norm initial, final = 2304.6733 0.36701720 Force max component initial, final = 605.58155 0.10887928 Final line search alpha, max atom move = 0.35183829 0.038307900 Iterations, force evaluations = 320 609 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5989 | 6.5989 | 6.5989 | 0.0 | 95.79 Neigh | 0.15776 | 0.15776 | 0.15776 | 0.0 | 2.29 Comm | 0.073421 | 0.073421 | 0.073421 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05855 | | | 0.85 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5243.00 ave 5243 max 5243 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: 106186.0 ave 106186 max 106186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106186 Ave neighs/atom = 157.31259 Neighbor list builds = 10 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 320 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.928 | 4.928 | 4.928 Mbytes Step Temp E_pair E_mol TotEng Press Volume 320 0 -4309.5089 0 -4309.5089 17217.344 10584.725 341 0 -4319.6606 0 -4319.6606 -67.887083 10630.025 Loop time of 0.280119 on 1 procs for 21 steps with 675 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 = -4309.50888479057 -4319.65770279797 -4319.66058733356 Force two-norm initial, final = 780.03659 7.2354382 Force max component initial, final = 599.44889 2.9509539 Final line search alpha, max atom move = 0.00015669996 0.00046241435 Iterations, force evaluations = 21 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25275 | 0.25275 | 0.25275 | 0.0 | 90.23 Neigh | 0.015525 | 0.015525 | 0.015525 | 0.0 | 5.54 Comm | 0.0028444 | 0.0028444 | 0.0028444 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009 | | | 3.21 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5066.00 ave 5066 max 5066 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: 106456.0 ave 106456 max 106456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106456 Ave neighs/atom = 157.71259 Neighbor list builds = 1 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4319.6606 0 -4319.6606 -67.887083 Loop time of 6.576e-06 on 1 procs for 0 steps with 675 atoms 182.5% 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 | | 6.576e-06 | | |100.00 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5030.00 ave 5030 max 5030 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: 106900.0 ave 106900 max 106900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106900 Ave neighs/atom = 158.37037 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 5.064 | 5.064 | 5.064 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 -4319.6606 -4319.6606 23.786645 80.28082 5.5665909 -67.887083 -67.887083 -282.00898 436.13292 -357.78519 2.4920148 4094.2345 Loop time of 6.465e-06 on 1 procs for 0 steps with 675 atoms 263.0% 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 | | 6.465e-06 | | |100.00 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5030.00 ave 5030 max 5030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53450.0 ave 53450 max 53450 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106900.0 ave 106900 max 106900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106900 Ave neighs/atom = 158.37037 Neighbor list builds = 0 Dangerous builds = 0 675 -4319.66058733357 eV 2.49201483870116 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07