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 -64.083562 0.0000000) to (45.311404 64.083562 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1534006 5.9333335 5.0346005 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -64.083562 0.0000000) to (45.311404 64.083562 5.0346005) create_atoms CPU = 0.011 seconds 1299 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1534006 5.9333335 5.0346005 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -64.083562 0.0000000) to (45.311404 64.083562 5.0346005) create_atoms CPU = 0.010 seconds 1299 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 = 12 33 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 30 atoms, new total = 2568 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_820335782779_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 = 12 33 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) = 6.539 | 6.539 | 6.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11204.983 0 -11204.983 -3863.1824 67 0 -11271.618 0 -11271.618 -5740.6435 Loop time of 5.9812 on 1 procs for 67 steps with 2568 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11204.9829674077 -11271.6079280517 -11271.6180268415 Force two-norm initial, final = 41.556624 0.47491801 Force max component initial, final = 10.441374 0.083944084 Final line search alpha, max atom move = 1.0000000 0.083944084 Iterations, force evaluations = 67 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.852 | 5.852 | 5.852 | 0.0 | 97.84 Neigh | 0.059757 | 0.059757 | 0.059757 | 0.0 | 1.00 Comm | 0.036844 | 0.036844 | 0.036844 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03263 | | | 0.55 Nlocal: 2568.00 ave 2568 max 2568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12880.0 ave 12880 max 12880 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: 449020.0 ave 449020 max 449020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449020 Ave neighs/atom = 174.85202 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 33 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.539 | 6.539 | 6.539 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -11271.618 0 -11271.618 -5740.6435 29238.102 72 0 -11271.934 0 -11271.934 -2635.9265 29186.764 Loop time of 0.347883 on 1 procs for 5 steps with 2568 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11271.6180268416 -11271.9336189849 -11271.9337067203 Force two-norm initial, final = 145.74685 0.57299396 Force max component initial, final = 143.91089 0.090982570 Final line search alpha, max atom move = 0.00035088187 3.1924134e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33895 | 0.33895 | 0.33895 | 0.0 | 97.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019484 | 0.0019484 | 0.0019484 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006982 | | | 2.01 Nlocal: 2568.00 ave 2568 max 2568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12920.0 ave 12920 max 12920 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: 448876.0 ave 448876 max 448876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448876 Ave neighs/atom = 174.79595 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 = 12 33 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) = 6.677 | 6.677 | 6.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11271.934 0 -11271.934 -2635.9265 Loop time of 6.585e-06 on 1 procs for 0 steps with 2568 atoms 182.2% 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 | | 6.585e-06 | | |100.00 Nlocal: 2568.00 ave 2568 max 2568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12920.0 ave 12920 max 12920 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: 449156.0 ave 449156 max 449156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449156 Ave neighs/atom = 174.90498 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 = 12 33 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) = 6.677 | 6.677 | 6.677 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 -11271.934 -11271.934 45.410617 128.16712 5.0147803 -2635.9265 -2635.9265 1.9980729 -7909.8413 0.063675351 2.3946442 1223.5408 Loop time of 7.156e-06 on 1 procs for 0 steps with 2568 atoms 279.5% 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 | | 7.156e-06 | | |100.00 Nlocal: 2568.00 ave 2568 max 2568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12920.0 ave 12920 max 12920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224578.0 ave 224578 max 224578 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 449156.0 ave 449156 max 449156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449156 Ave neighs/atom = 174.90498 Neighbor list builds = 0 Dangerous builds = 0 2568 -11271.9337067203 eV 2.39464421288637 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07