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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -57.524922 0.0000000) to (28.760677 57.524922 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9822476 3.9822476 3.5673230 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -57.524922 0.0000000) to (28.760677 57.524922 3.5673230) create_atoms CPU = 0.002 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9822476 3.9822476 3.5673230 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -57.524922 0.0000000) to (28.760677 57.524922 3.5673230) create_atoms CPU = 0.002 seconds 522 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1040 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4317.4522 0 -4317.4522 23371.128 40 0 -4384.2399 0 -4384.2399 28891.889 Loop time of 5.0989 on 1 procs for 40 steps with 1040 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 = -4317.4521835233 -4384.23670180315 -4384.23990487988 Force two-norm initial, final = 63.807055 0.30597262 Force max component initial, final = 12.593298 0.074871316 Final line search alpha, max atom move = 1.0000000 0.074871316 Iterations, force evaluations = 40 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0791 | 5.0791 | 5.0791 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010082 | 0.010082 | 0.010082 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009748 | | | 0.19 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6075.00 ave 6075 max 6075 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: 56508.0 ave 56508 max 56508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56508 Ave neighs/atom = 54.334615 Neighbor list builds = 0 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -4384.2399 0 -4384.2399 28891.889 11803.956 81 0 -4391.8371 0 -4391.8371 -4408.4196 12178.33 Loop time of 2.85881 on 1 procs for 41 steps with 1040 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 = -4384.23990487988 -4391.83591665879 -4391.83708586757 Force two-norm initial, final = 241.88920 2.8525339 Force max component initial, final = 220.40565 1.4414609 Final line search alpha, max atom move = 0.00025596015 0.00036895654 Iterations, force evaluations = 41 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8182 | 2.8182 | 2.8182 | 0.0 | 98.58 Neigh | 0.012393 | 0.012393 | 0.012393 | 0.0 | 0.43 Comm | 0.0058527 | 0.0058527 | 0.0058527 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02236 | | | 0.78 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6003.00 ave 6003 max 6003 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: 58596.0 ave 58596 max 58596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58596 Ave neighs/atom = 56.342308 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.743 | 4.743 | 4.743 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4391.8371 0 -4391.8371 -4408.4196 Loop time of 6.084e-06 on 1 procs for 0 steps with 1040 atoms 180.8% 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 | | 6.084e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5980.00 ave 5980 max 5980 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: 61200.0 ave 61200 max 61200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61200 Ave neighs/atom = 58.846154 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.743 | 4.743 | 4.743 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 -4391.8371 -4391.8371 29.922906 115.04984 3.5375121 -4408.4196 -4408.4196 -197.30139 -13064.247 36.290082 2.2847575 228.84937 Loop time of 7.197e-06 on 1 procs for 0 steps with 1040 atoms 250.1% 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 | | 7.197e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5980.00 ave 5980 max 5980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30600.0 ave 30600 max 30600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61200.0 ave 61200 max 61200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61200 Ave neighs/atom = 58.846154 Neighbor list builds = 0 Dangerous builds = 0 1040 -4391.83708586757 eV 2.28475748505424 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08