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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -49.863918 0.0000000) to (11.752115 49.863918 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5289527 5.5400000 5.5400000 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -49.863918 0.0000000) to (11.752115 49.863918 5.5400000) create_atoms CPU = 0.003 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5289527 5.5400000 5.5400000 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -49.863918 0.0000000) to (11.752115 49.863918 5.5400000) create_atoms CPU = 0.002 seconds 218 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 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_070797404269_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2439.9141 0 -2439.9141 6652.8222 57 0 -2459.9993 0 -2459.9993 -7205.3786 Loop time of 2.13847 on 1 procs for 57 steps with 428 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 = -2439.91412893757 -2459.99701281064 -2459.99928509612 Force two-norm initial, final = 40.442078 0.16192714 Force max component initial, final = 15.778698 0.034825055 Final line search alpha, max atom move = 1.0000000 0.034825055 Iterations, force evaluations = 57 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1216 | 2.1216 | 2.1216 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.008791 | 0.008791 | 0.008791 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008071 | | | 0.38 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3051.00 ave 3051 max 3051 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: 33016.0 ave 33016 max 33016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33016 Ave neighs/atom = 77.140187 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -2459.9993 0 -2459.9993 -7205.3786 6492.9519 60 0 -2460.0486 0 -2460.0486 -1001.0804 6470.3386 Loop time of 0.131125 on 1 procs for 3 steps with 428 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 = -2459.99928509611 -2460.0485007017 -2460.04864724934 Force two-norm initial, final = 39.440858 0.19264190 Force max component initial, final = 30.130462 0.031975148 Final line search alpha, max atom move = 0.00083976806 2.6851708e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12884 | 0.12884 | 0.12884 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049149 | 0.00049149 | 0.00049149 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001789 | | | 1.36 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3142.00 ave 3142 max 3142 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: 33080.0 ave 33080 max 33080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33080 Ave neighs/atom = 77.289720 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2460.0486 0 -2460.0486 -1001.0804 Loop time of 6.796e-06 on 1 procs for 0 steps with 428 atoms 191.3% 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 | | 6.796e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3142.00 ave 3142 max 3142 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: 33080.0 ave 33080 max 33080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33080 Ave neighs/atom = 77.289720 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.612 | 4.612 | 4.612 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 -2460.0486 -2460.0486 11.735506 99.727836 5.5285188 -1001.0804 -1001.0804 -4.1298673 -3002.6502 3.5388292 2.5850475 242.98733 Loop time of 9.161e-06 on 1 procs for 0 steps with 428 atoms 251.1% 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 | | 9.161e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3142.00 ave 3142 max 3142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16540.0 ave 16540 max 16540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33080.0 ave 33080 max 33080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33080 Ave neighs/atom = 77.289720 Neighbor list builds = 0 Dangerous builds = 0 428 -2460.04864724934 eV 2.58504748981214 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02