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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -32.091878 0.0000000) to (27.789656 32.091878 5.4500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9878870 4.9367279 5.4500000 Created 318 atoms using lattice units in orthogonal box = (0.0000000 -32.091878 0.0000000) to (27.789656 32.091878 5.4500000) create_atoms CPU = 0.003 seconds 318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9878870 4.9367279 5.4500000 Created 316 atoms using lattice units in orthogonal box = (0.0000000 -32.091878 0.0000000) to (27.789656 32.091878 5.4500000) create_atoms CPU = 0.002 seconds 316 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 23 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 624 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.483 | 4.483 | 4.483 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4186.5378 0 -4186.5378 25164.986 38 0 -4216.1867 0 -4216.1867 13551.083 Loop time of 2.44065 on 1 procs for 38 steps with 624 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 = -4186.53776739564 -4216.18340679729 -4216.18671553755 Force two-norm initial, final = 25.434708 0.20250545 Force max component initial, final = 4.3295458 0.028518941 Final line search alpha, max atom move = 1.0000000 0.028518941 Iterations, force evaluations = 38 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4305 | 2.4305 | 2.4305 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041689 | 0.0041689 | 0.0041689 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005943 | | | 0.24 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2502.00 ave 2502 max 2502 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: 35868.0 ave 35868 max 35868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35868 Ave neighs/atom = 57.480769 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -4216.1867 0 -4216.1867 13551.083 9720.8624 42 0 -4216.3719 0 -4216.3719 2015.7053 9762.9021 Loop time of 0.249336 on 1 procs for 4 steps with 624 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 = -4216.18671553755 -4216.36921499069 -4216.37188003117 Force two-norm initial, final = 113.75372 0.28119270 Force max component initial, final = 92.763122 0.048734683 Final line search alpha, max atom move = 0.00013035681 6.3528978e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24721 | 0.24721 | 0.24721 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040127 | 0.00040127 | 0.00040127 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001729 | | | 0.69 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2555.00 ave 2555 max 2555 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: 35838.0 ave 35838 max 35838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35838 Ave neighs/atom = 57.432692 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4216.3719 0 -4216.3719 2015.7053 Loop time of 6.474e-06 on 1 procs for 0 steps with 624 atoms 169.9% 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 | | 6.474e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2543.00 ave 2543 max 2543 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: 35832.0 ave 35832 max 35832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35832 Ave neighs/atom = 57.423077 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.622 | 4.622 | 4.622 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 -4216.3719 -4216.3719 27.819873 64.183755 5.4676245 2015.7053 2015.7053 -0.56731075 6048.4157 -0.73255111 2.434934 642.95793 Loop time of 6.806e-06 on 1 procs for 0 steps with 624 atoms 264.5% 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 | | 6.806e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2543.00 ave 2543 max 2543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17916.0 ave 17916 max 17916 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35832.0 ave 35832 max 35832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35832 Ave neighs/atom = 57.423077 Neighbor list builds = 0 Dangerous builds = 0 624 -4216.37188003117 eV 2.43493395757997 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03