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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -44.697859 0.0000000) to (21.069070 44.697859 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1967852 6.1345044 5.1100000 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.697859 0.0000000) to (21.069070 44.697859 5.1100000) create_atoms CPU = 0.004 seconds 412 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1967852 6.1345044 5.1100000 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.697859 0.0000000) to (21.069070 44.697859 5.1100000) create_atoms CPU = 0.003 seconds 412 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 32 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 816 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_849011491644_001#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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2834.3699 0 -2834.3699 22185.225 50 0 -2878.9485 0 -2878.9485 5614.41 Loop time of 2.79571 on 1 procs for 50 steps with 816 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 = -2834.36985190776 -2878.94594266042 -2878.94853826994 Force two-norm initial, final = 58.879108 0.14432699 Force max component initial, final = 13.562470 0.026677024 Final line search alpha, max atom move = 1.0000000 0.026677024 Iterations, force evaluations = 50 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7688 | 2.7688 | 2.7688 | 0.0 | 99.04 Neigh | 0.0088005 | 0.0088005 | 0.0088005 | 0.0 | 0.31 Comm | 0.0084906 | 0.0084906 | 0.0084906 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009645 | | | 0.34 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3748.00 ave 3748 max 3748 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: 48344.0 ave 48344 max 48344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48344 Ave neighs/atom = 59.245098 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2878.9485 0 -2878.9485 5614.41 9624.6064 52 0 -2878.9856 0 -2878.9856 1741.6964 9650.8419 Loop time of 0.127086 on 1 procs for 2 steps with 816 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 = -2878.94853826994 -2878.98293560212 -2878.98564638643 Force two-norm initial, final = 38.694304 0.56206801 Force max component initial, final = 27.573197 0.42564790 Final line search alpha, max atom move = 0.00012999465 5.5331948e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12552 | 0.12552 | 0.12552 | 0.0 | 98.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032174 | 0.00032174 | 0.00032174 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001247 | | | 0.98 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3784.00 ave 3784 max 3784 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: 48512.0 ave 48512 max 48512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48512 Ave neighs/atom = 59.450980 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.685 | 4.685 | 4.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2878.9856 0 -2878.9856 1741.6964 Loop time of 7.136e-06 on 1 procs for 0 steps with 816 atoms 168.2% 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 | | 7.136e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3784.00 ave 3784 max 3784 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: 47776.0 ave 47776 max 47776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47776 Ave neighs/atom = 58.549020 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.685 | 4.685 | 4.685 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 -2878.9856 -2878.9856 21.097559 89.395719 5.11701 1741.6964 1741.6964 -70.759134 5239.9931 55.855114 2.4028945 525.4417 Loop time of 7.137e-06 on 1 procs for 0 steps with 816 atoms 252.2% 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 | | 7.137e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3784.00 ave 3784 max 3784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23888.0 ave 23888 max 23888 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47776.0 ave 47776 max 47776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47776 Ave neighs/atom = 58.549020 Neighbor list builds = 0 Dangerous builds = 0 816 -2878.98564638643 eV 2.40289445642902 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03