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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -60.563890 0.0000000) to (30.280185 60.563890 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9103002 4.9103002 3.5200000 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.563890 0.0000000) to (30.280185 60.563890 3.5200000) create_atoms CPU = 0.001 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9103002 4.9103002 3.5200000 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.563890 0.0000000) to (30.280185 60.563890 3.5200000) create_atoms CPU = 0.001 seconds 594 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 28 1 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1180 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.488 | 5.488 | 5.488 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5207.7918 0 -5207.7918 5679.6294 73 0 -5236.4921 0 -5236.4921 -218.36786 Loop time of 2.2278 on 1 procs for 73 steps with 1180 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5207.79182105904 -5236.48796064602 -5236.49207866878 Force two-norm initial, final = 19.411297 0.21718610 Force max component initial, final = 4.9200049 0.032293216 Final line search alpha, max atom move = 1.0000000 0.032293216 Iterations, force evaluations = 73 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.191 | 2.191 | 2.191 | 0.0 | 98.35 Neigh | 0.016856 | 0.016856 | 0.016856 | 0.0 | 0.76 Comm | 0.01199 | 0.01199 | 0.01199 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008006 | | | 0.36 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10507.0 ave 10507 max 10507 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: 291904.0 ave 291904 max 291904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291904 Ave neighs/atom = 247.37627 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.489 | 5.489 | 5.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -5236.4921 0 -5236.4921 -218.36786 12910.556 76 0 -5236.5215 0 -5236.5215 543.87229 12905.038 Loop time of 0.0880577 on 1 procs for 3 steps with 1180 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 = -5236.49207866878 -5236.5200898927 -5236.5214807235 Force two-norm initial, final = 28.124141 2.5748589 Force max component initial, final = 27.288371 2.5396357 Final line search alpha, max atom move = 0.00011525523 0.00029270629 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086207 | 0.086207 | 0.086207 | 0.0 | 97.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038737 | 0.00038737 | 0.00038737 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001463 | | | 1.66 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10525.0 ave 10525 max 10525 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: 291736.0 ave 291736 max 291736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291736 Ave neighs/atom = 247.23390 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.627 | 5.627 | 5.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5236.5215 0 -5236.5215 543.87229 Loop time of 1.746e-06 on 1 procs for 0 steps with 1180 atoms 171.8% 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 | | 1.746e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10525.0 ave 10525 max 10525 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: 291744.0 ave 291744 max 291744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291744 Ave neighs/atom = 247.24068 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.627 | 5.627 | 5.627 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 -5236.5215 -5236.5215 30.227905 121.12778 3.524581 543.87229 543.87229 44.739158 1271.1685 315.70926 2.232293 300.21003 Loop time of 1.657e-06 on 1 procs for 0 steps with 1180 atoms 241.4% 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 | | 1.657e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10525.0 ave 10525 max 10525 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145872.0 ave 145872 max 145872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 291744.0 ave 291744 max 291744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291744 Ave neighs/atom = 247.24068 Neighbor list builds = 0 Dangerous builds = 0 1180 -5236.5214807235 eV 2.23229296811043 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02