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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -50.299056 0.0000000) to (35.564313 50.299056 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5787158 4.4378413 4.9800000 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -50.299056 0.0000000) to (35.564313 50.299056 4.9800000) create_atoms CPU = 0.002 seconds 822 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5787158 4.4378413 4.9800000 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -50.299056 0.0000000) to (35.564313 50.299056 4.9800000) create_atoms CPU = 0.001 seconds 822 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 33 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1624 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.131 | 5.131 | 5.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7124.7467 0 -7124.7467 16485.036 60 0 -7200.3411 0 -7200.3411 -1182.434 Loop time of 6.28128 on 1 procs for 60 steps with 1624 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7124.74674672838 -7200.33395205507 -7200.34105744214 Force two-norm initial, final = 77.678410 0.28900777 Force max component initial, final = 11.370287 0.024944922 Final line search alpha, max atom move = 1.0000000 0.024944922 Iterations, force evaluations = 60 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2485 | 6.2485 | 6.2485 | 0.0 | 99.48 Neigh | 0.010867 | 0.010867 | 0.010867 | 0.0 | 0.17 Comm | 0.011249 | 0.011249 | 0.011249 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01069 | | | 0.17 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7608.00 ave 7608 max 7608 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: 139584.0 ave 139584 max 139584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139584 Ave neighs/atom = 85.950739 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.131 | 5.131 | 5.131 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -7200.3411 0 -7200.3411 -1182.434 17816.96 61 0 -7200.3428 0 -7200.3428 -790.80926 17813.201 Loop time of 0.180604 on 1 procs for 1 steps with 1624 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 = -7200.34105744213 -7200.34105744213 -7200.34279909163 Force two-norm initial, final = 10.611089 2.2544531 Force max component initial, final = 10.096515 2.1362775 Final line search alpha, max atom move = 9.9044076e-05 0.00021158563 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17952 | 0.17952 | 0.17952 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021358 | 0.00021358 | 0.00021358 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000868 | | | 0.48 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7615.00 ave 7615 max 7615 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: 139568.0 ave 139568 max 139568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139568 Ave neighs/atom = 85.940887 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.269 | 5.269 | 5.269 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7200.3428 0 -7200.3428 -790.80926 Loop time of 2.229e-06 on 1 procs for 0 steps with 1624 atoms 179.5% 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 | | 2.229e-06 | | |100.00 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7615.00 ave 7615 max 7615 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: 139568.0 ave 139568 max 139568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139568 Ave neighs/atom = 85.940887 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.269 | 5.269 | 5.269 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 -7200.3428 -7200.3428 35.567877 100.59811 4.9784505 -790.80926 -790.80926 192.16291 -2623.8132 59.222493 2.3315716 686.07035 Loop time of 2.39e-06 on 1 procs for 0 steps with 1624 atoms 251.0% 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 | | 2.39e-06 | | |100.00 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7615.00 ave 7615 max 7615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69784.0 ave 69784 max 69784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139568.0 ave 139568 max 139568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139568 Ave neighs/atom = 85.940887 Neighbor list builds = 0 Dangerous builds = 0 1624 -7200.34279909163 eV 2.33157156107282 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06