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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -41.519939 0.0000000) to (14.678257 41.519939 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0439880 6.1053498 5.0346005 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.519939 0.0000000) to (14.678257 41.519939 5.0346005) create_atoms CPU = 0.001 seconds 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0439880 6.1053498 5.0346005 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.519939 0.0000000) to (14.678257 41.519939 5.0346005) create_atoms CPU = 0.001 seconds 274 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 540 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2340.0179 0 -2340.0179 6385.0923 98 0 -2368.0912 0 -2368.0912 1289.7461 Loop time of 0.949665 on 1 procs for 98 steps with 540 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 = -2340.01792102672 -2368.08907289898 -2368.09121707928 Force two-norm initial, final = 37.615942 0.23934395 Force max component initial, final = 12.337014 0.074913183 Final line search alpha, max atom move = 1.0000000 0.074913183 Iterations, force evaluations = 98 192 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92535 | 0.92535 | 0.92535 | 0.0 | 97.44 Neigh | 0.011847 | 0.011847 | 0.011847 | 0.0 | 1.25 Comm | 0.0075089 | 0.0075089 | 0.0075089 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004956 | | | 0.52 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5068.00 ave 5068 max 5068 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: 94368.0 ave 94368 max 94368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94368 Ave neighs/atom = 174.75556 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -2368.0912 0 -2368.0912 1289.7461 6136.577 102 0 -2368.1299 0 -2368.1299 -444.46684 6142.0757 Loop time of 0.0296953 on 1 procs for 4 steps with 540 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 = -2368.09121707929 -2368.12970065435 -2368.12988256604 Force two-norm initial, final = 22.213673 0.99314760 Force max component initial, final = 21.246761 0.93454925 Final line search alpha, max atom move = 0.00050508767 0.00047202930 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02865 | 0.02865 | 0.02865 | 0.0 | 96.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021835 | 0.00021835 | 0.00021835 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008274 | | | 2.79 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5068.00 ave 5068 max 5068 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: 94324.0 ave 94324 max 94324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94324 Ave neighs/atom = 174.67407 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.674 | 4.674 | 4.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2368.1299 0 -2368.1299 -444.46684 Loop time of 1.483e-06 on 1 procs for 0 steps with 540 atoms 202.3% 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 | | 1.483e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5060.00 ave 5060 max 5060 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: 94316.0 ave 94316 max 94316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94316 Ave neighs/atom = 174.65926 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.674 | 4.674 | 4.674 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 -2368.1299 -2368.1299 14.721293 83.039878 5.0243803 -444.46684 -444.46684 -2.0485393 -1088.0672 -243.28474 2.3677092 357.3974 Loop time of 1.541e-06 on 1 procs for 0 steps with 540 atoms 129.8% 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 | | 1.541e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5060.00 ave 5060 max 5060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47158.0 ave 47158 max 47158 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94316.0 ave 94316 max 94316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94316 Ave neighs/atom = 174.65926 Neighbor list builds = 0 Dangerous builds = 0 540 -2368.12988256604 eV 2.36770919879893 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01