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 = 2.4599767 2.4599767 2.4599767 Created orthogonal box = (0.0000000 -36.156586 0.0000000) to (12.782414 36.156586 3.4789324) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.3139591 4.0171251 3.4789324 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -36.156586 0.0000000) to (12.782414 36.156586 3.4789324) create_atoms CPU = 0.001 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.3139591 4.0171251 3.4789324 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -36.156586 0.0000000) to (12.782414 36.156586 3.4789324) create_atoms CPU = 0.001 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 20 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 7.5466 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_677328661525_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.908 | 4.908 | 4.908 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5276.252 0 -5276.252 105668.91 61 0 -5399.4265 0 -5399.4265 6914.424 Loop time of 3.19368 on 1 procs for 61 steps with 428 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 = -5276.25199021556 -5399.42135593011 -5399.42645948655 Force two-norm initial, final = 344.43599 0.59712773 Force max component initial, final = 122.38945 0.066169017 Final line search alpha, max atom move = 0.28200795 0.018660189 Iterations, force evaluations = 61 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1801 | 3.1801 | 3.1801 | 0.0 | 99.57 Neigh | 0.0055762 | 0.0055762 | 0.0055762 | 0.0 | 0.17 Comm | 0.005131 | 0.005131 | 0.005131 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00291 | | | 0.09 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5727.00 ave 5727 max 5727 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: 108156.0 ave 108156 max 108156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108156 Ave neighs/atom = 252.70093 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.908 | 4.908 | 4.908 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -5399.4265 0 -5399.4265 6914.424 3215.7055 63 0 -5399.441 0 -5399.441 14862.492 3212.1002 Loop time of 0.135952 on 1 procs for 2 steps with 428 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 = -5399.42645948657 -5399.43773143075 -5399.44103363038 Force two-norm initial, final = 25.772449 0.62805722 Force max component initial, final = 23.706891 0.068469937 Final line search alpha, max atom move = 0.00013339542 9.1335761e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13498 | 0.13498 | 0.13498 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019905 | 0.00019905 | 0.00019905 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007704 | | | 0.57 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5751.00 ave 5751 max 5751 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: 108304.0 ave 108304 max 108304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108304 Ave neighs/atom = 253.04673 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.046 | 5.046 | 5.046 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5399.441 0 -5399.441 14862.492 Loop time of 1.703e-06 on 1 procs for 0 steps with 428 atoms 176.2% 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 | | 1.703e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5751.00 ave 5751 max 5751 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: 108340.0 ave 108340 max 108340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108340 Ave neighs/atom = 253.13084 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.046 | 5.046 | 5.046 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 -5399.441 -5399.441 12.765772 72.313172 3.479562 14862.492 14862.492 14.852922 44581.146 -8.5222969 2.007808 437.4208 Loop time of 1.361e-06 on 1 procs for 0 steps with 428 atoms 220.4% 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 | | 1.361e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5751.00 ave 5751 max 5751 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54170.0 ave 54170 max 54170 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108340.0 ave 108340 max 108340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108340 Ave neighs/atom = 253.13084 Neighbor list builds = 0 Dangerous builds = 0 428 -5399.44103363038 eV 2.00780797888645 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03