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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -31.336337 0.0000000) to (6.3959191 31.336337 7.0063784) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8375515 4.1777969 4.6709189 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -31.336337 0.0000000) to (6.3959191 31.336337 7.0063784) create_atoms CPU = 0.001 seconds 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8375515 4.1777969 4.6709189 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -31.336337 0.0000000) to (6.3959191 31.336337 7.0063784) create_atoms CPU = 0.000 seconds 122 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 = 2 17 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 4 atoms, new total = 240 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 = 2 17 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -988.97831 0 -988.97831 40575.043 79 0 -1040.8968 0 -1040.8968 15390.507 Loop time of 0.323436 on 1 procs for 79 steps with 240 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 = -988.978313114401 -1040.89595908581 -1040.89683448843 Force two-norm initial, final = 51.527010 0.12962040 Force max component initial, final = 13.632479 0.034289409 Final line search alpha, max atom move = 1.0000000 0.034289409 Iterations, force evaluations = 79 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31274 | 0.31274 | 0.31274 | 0.0 | 96.69 Neigh | 0.0052017 | 0.0052017 | 0.0052017 | 0.0 | 1.61 Comm | 0.0035244 | 0.0035244 | 0.0035244 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001967 | | | 0.61 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3054.00 ave 3054 max 3054 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: 39820.0 ave 39820 max 39820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39820 Ave neighs/atom = 165.91667 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 = 2 17 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 : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -1040.8968 0 -1040.8968 15390.507 2808.5023 128 0 -1046.5649 0 -1046.5649 31119.437 2787.0121 Loop time of 0.119281 on 1 procs for 49 steps with 240 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 = -1040.89683448843 -1046.56471692968 -1046.5649153981 Force two-norm initial, final = 210.91287 1.6502376 Force max component initial, final = 180.12895 1.4476337 Final line search alpha, max atom move = 0.0012698761 0.0018383154 Iterations, force evaluations = 49 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11299 | 0.11299 | 0.11299 | 0.0 | 94.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012273 | 0.0012273 | 0.0012273 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00506 | | | 4.24 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3058.00 ave 3058 max 3058 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: 39896.0 ave 39896 max 39896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39896 Ave neighs/atom = 166.23333 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 = 2 17 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) = 4.620 | 4.620 | 4.620 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1046.5649 0 -1046.5649 31119.437 Loop time of 1.502e-06 on 1 procs for 0 steps with 240 atoms 133.2% 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 | | 1.502e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3102.00 ave 3102 max 3102 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: 39340.0 ave 39340 max 39340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39340 Ave neighs/atom = 163.91667 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 = 2 17 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) = 4.620 | 4.620 | 4.620 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 -1046.5649 -1046.5649 6.6140266 62.672674 6.7234888 31119.437 31119.437 23.23722 94133.678 -798.60367 2.3441808 1331.0003 Loop time of 1.392e-06 on 1 procs for 0 steps with 240 atoms 143.7% 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 | | 1.392e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3102.00 ave 3102 max 3102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19670.0 ave 19670 max 19670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39340.0 ave 39340 max 39340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39340 Ave neighs/atom = 163.91667 Neighbor list builds = 0 Dangerous builds = 0 240 -1046.5649153981 eV 2.34418078717634 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00