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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -39.102483 0.0000000) to (39.102483 39.102483 3.6784521) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1905950 5.1905950 3.6784521 Created 451 atoms using lattice units in orthogonal box = (0.0000000 -39.102483 0.0000000) to (39.102483 39.102483 3.6784521) create_atoms CPU = 0.002 seconds 451 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1905950 5.1905950 3.6784521 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -39.102483 0.0000000) to (39.102483 39.102483 3.6784521) create_atoms CPU = 0.001 seconds 453 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 26 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 904 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.557 | 4.557 | 4.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3540.4811 0 -3540.4811 39439.346 58 0 -3811.2296 0 -3811.2296 -2505.2471 Loop time of 0.625546 on 1 procs for 58 steps with 904 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 = -3540.48107830415 -3811.22594874721 -3811.22964556635 Force two-norm initial, final = 254.73811 0.19462416 Force max component initial, final = 60.539755 0.044740295 Final line search alpha, max atom move = 1.0000000 0.044740295 Iterations, force evaluations = 58 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58946 | 0.58946 | 0.58946 | 0.0 | 94.23 Neigh | 0.011802 | 0.011802 | 0.011802 | 0.0 | 1.89 Comm | 0.012181 | 0.012181 | 0.012181 | 0.0 | 1.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01211 | | | 1.94 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5296.00 ave 5296 max 5296 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: 70050.0 ave 70050 max 70050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70050 Ave neighs/atom = 77.488938 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3811.2296 0 -3811.2296 -2505.2471 11248.737 85 0 -3812.6702 0 -3812.6702 0.69404702 11196.575 Loop time of 0.197757 on 1 procs for 27 steps with 904 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 = -3811.22964556633 -3812.66775013787 -3812.67018743994 Force two-norm initial, final = 83.230476 1.1461552 Force max component initial, final = 68.011767 0.21523602 Final line search alpha, max atom move = 0.00037110582 7.9875338e-05 Iterations, force evaluations = 27 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16994 | 0.16994 | 0.16994 | 0.0 | 85.93 Neigh | 0.011732 | 0.011732 | 0.011732 | 0.0 | 5.93 Comm | 0.0034466 | 0.0034466 | 0.0034466 | 0.0 | 1.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01264 | | | 6.39 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5323.00 ave 5323 max 5323 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: 70328.0 ave 70328 max 70328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70328 Ave neighs/atom = 77.796460 Neighbor list builds = 1 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.696 | 4.696 | 4.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3812.6702 0 -3812.6702 0.69404702 Loop time of 4.4554e-05 on 1 procs for 0 steps with 904 atoms 24.7% 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 | | 4.455e-05 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5333.00 ave 5333 max 5333 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: 70336.0 ave 70336 max 70336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70336 Ave neighs/atom = 77.805310 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.696 | 4.696 | 4.696 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 -3812.6702 -3812.6702 38.422621 77.186505 3.7753466 0.69404702 0.69404702 17.216981 16.475694 -31.610534 2.3333409 162.3214 Loop time of 7.167e-06 on 1 procs for 0 steps with 904 atoms 307.0% 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 | | 7.167e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5333.00 ave 5333 max 5333 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35168.0 ave 35168 max 35168 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70336.0 ave 70336 max 70336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70336 Ave neighs/atom = 77.805310 Neighbor list builds = 0 Dangerous builds = 0 904 -3812.67009703994 eV 2.33334094761654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01