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 = 3.6135806 3.6135806 3.6135806 Created orthogonal box = (0.0000000 -38.412889 0.0000000) to (38.412889 38.412889 3.6135806) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0990560 5.0990560 3.6135806 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -38.412889 0.0000000) to (38.412889 38.412889 3.6135806) create_atoms CPU = 0.001 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0990560 5.0990560 3.6135806 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.412889 0.0000000) to (38.412889 38.412889 3.6135806) create_atoms CPU = 0.000 seconds 454 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 11 21 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 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_426403318662_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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2972.2354 0 -2972.2354 79622.892 78 0 -3200.0055 0 -3200.0055 6316.6029 Loop time of 0.870261 on 1 procs for 78 steps with 906 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 = -2972.23542605658 -3200.00298013715 -3200.00547907838 Force two-norm initial, final = 296.58855 0.17054219 Force max component initial, final = 52.802010 0.043695330 Final line search alpha, max atom move = 1.0000000 0.043695330 Iterations, force evaluations = 78 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84066 | 0.84066 | 0.84066 | 0.0 | 96.60 Neigh | 0.015553 | 0.015553 | 0.015553 | 0.0 | 1.79 Comm | 0.0075647 | 0.0075647 | 0.0075647 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00648 | | | 0.74 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6619.00 ave 6619 max 6619 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: 128844.0 ave 128844 max 128844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128844 Ave neighs/atom = 142.21192 Neighbor list builds = 2 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.976 | 4.976 | 4.976 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -3200.0055 0 -3200.0055 6316.6029 10664.038 83 0 -3200.1912 0 -3200.1912 242.8413 10709.873 Loop time of 0.0446229 on 1 procs for 5 steps with 906 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 = -3200.00547907838 -3200.18947811141 -3200.19124330558 Force two-norm initial, final = 84.749667 3.2525988 Force max component initial, final = 71.486429 2.9438872 Final line search alpha, max atom move = 0.00017534557 0.00051619757 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042853 | 0.042853 | 0.042853 | 0.0 | 96.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003204 | 0.0003204 | 0.0003204 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001449 | | | 3.25 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6649.00 ave 6649 max 6649 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: 128552.0 ave 128552 max 128552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128552 Ave neighs/atom = 141.88962 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 11 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 5.113 | 5.113 | 5.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3200.1912 0 -3200.1912 242.8413 Loop time of 1.926e-06 on 1 procs for 0 steps with 906 atoms 155.8% 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 | | 1.926e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6634.00 ave 6634 max 6634 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: 128272.0 ave 128272 max 128272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128272 Ave neighs/atom = 141.58057 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 11 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 5.113 | 5.113 | 5.113 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 -3200.1912 -3200.1912 38.344466 77.145411 3.6205247 242.8413 242.8413 122.36099 164.91671 441.24621 2.3065105 153.2295 Loop time of 1.779e-06 on 1 procs for 0 steps with 906 atoms 112.4% 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 | | 1.779e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6634.00 ave 6634 max 6634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64136.0 ave 64136 max 64136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128272.0 ave 128272 max 128272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128272 Ave neighs/atom = 141.58057 Neighbor list builds = 0 Dangerous builds = 0 906 -3200.19577330558 eV 2.30651048108212 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01