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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -56.410774 0.0000000) to (28.203581 56.410774 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0858917 5.0858917 3.6110986 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.410774 0.0000000) to (28.203581 56.410774 3.6110986) create_atoms CPU = 0.003 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0858917 5.0858917 3.6110986 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.410774 0.0000000) to (28.203581 56.410774 3.6110986) create_atoms CPU = 0.002 seconds 490 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 974 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_179158257180_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4070.5839 0 -4070.5839 18645.806 138 0 -4124.523 0 -4124.523 -276.7082 Loop time of 20.2199 on 1 procs for 138 steps with 974 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 = -4070.58390312184 -4124.51910199733 -4124.52295934563 Force two-norm initial, final = 41.383999 0.21809143 Force max component initial, final = 11.532142 0.051726271 Final line search alpha, max atom move = 1.0000000 0.051726271 Iterations, force evaluations = 138 243 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.121 | 20.121 | 20.121 | 0.0 | 99.51 Neigh | 0.03582 | 0.03582 | 0.03582 | 0.0 | 0.18 Comm | 0.031462 | 0.031462 | 0.031462 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03179 | | | 0.16 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5182.00 ave 5182 max 5182 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: 75468.0 ave 75468 max 75468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75468 Ave neighs/atom = 77.482546 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 138 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press Volume 138 0 -4124.523 0 -4124.523 -276.7082 11490.414 146 0 -4124.7277 0 -4124.7277 -2219.5259 11503.352 Loop time of 0.812689 on 1 procs for 8 steps with 974 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 = -4124.52295934563 -4124.72755433879 -4124.7277121834 Force two-norm initial, final = 42.688443 0.36803792 Force max component initial, final = 31.256818 0.086659468 Final line search alpha, max atom move = 0.0011315129 9.8056304e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80725 | 0.80725 | 0.80725 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011214 | 0.0011214 | 0.0011214 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004319 | | | 0.53 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5182.00 ave 5182 max 5182 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: 75572.0 ave 75572 max 75572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75572 Ave neighs/atom = 77.589322 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.723 | 4.723 | 4.723 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4124.7277 0 -4124.7277 -2219.5259 Loop time of 8.47e-06 on 1 procs for 0 steps with 974 atoms 165.3% 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 | | 8.47e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5182.00 ave 5182 max 5182 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: 75596.0 ave 75596 max 75596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75596 Ave neighs/atom = 77.613963 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.723 | 4.723 | 4.723 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 -4124.7277 -4124.7277 28.033567 112.82155 3.6370895 -2219.5259 -2219.5259 7.1171057 -6653.5382 -12.156726 2.3192887 158.45578 Loop time of 6.886e-06 on 1 procs for 0 steps with 974 atoms 275.9% 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 | | 6.886e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5182.00 ave 5182 max 5182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37798.0 ave 37798 max 37798 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75596.0 ave 75596 max 75596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75596 Ave neighs/atom = 77.613963 Neighbor list builds = 0 Dangerous builds = 0 974 -4124.7277121834 eV 2.31928866778367 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21