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 = 2.8826503 2.8826503 2.8826503 Created orthogonal box = (0.0000000 -53.153444 0.0000000) to (26.576722 53.153444 2.8826503) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0646752 4.0646752 2.8826503 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -53.153444 0.0000000) to (26.576722 53.153444 2.8826503) create_atoms CPU = 0.002 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0646752 4.0646752 2.8826503 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -53.153444 0.0000000) to (26.576722 53.153444 2.8826503) create_atoms CPU = 0.002 seconds 341 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 25 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 677 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_331285495617_004#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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.974 | 4.974 | 4.974 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2262.3923 0 -2262.3923 63122.855 143 0 -2620.4312 0 -2620.4312 -1767.7605 Loop time of 5.29181 on 1 procs for 143 steps with 677 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 = -2262.39226367927 -2620.42881687051 -2620.43116948448 Force two-norm initial, final = 727.64508 0.20303338 Force max component initial, final = 333.16486 0.019996852 Final line search alpha, max atom move = 1.0000000 0.019996852 Iterations, force evaluations = 143 265 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1695 | 5.1695 | 5.1695 | 0.0 | 97.69 Neigh | 0.040612 | 0.040612 | 0.040612 | 0.0 | 0.77 Comm | 0.051401 | 0.051401 | 0.051401 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0303 | | | 0.57 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8311.00 ave 8311 max 8311 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: 158426.0 ave 158426 max 158426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158426 Ave neighs/atom = 234.01182 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 143 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.973 | 4.973 | 4.973 Mbytes Step Temp E_pair E_mol TotEng Press Volume 143 0 -2620.4312 0 -2620.4312 -1767.7605 8144.3191 177 0 -2622.403 0 -2622.403 318.78141 8140.8993 Loop time of 0.715449 on 1 procs for 34 steps with 677 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 = -2620.43116948448 -2622.40232810179 -2622.40301135914 Force two-norm initial, final = 86.393355 3.5945807 Force max component initial, final = 76.150230 2.3313654 Final line search alpha, max atom move = 0.00027191966 0.00063394409 Iterations, force evaluations = 34 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66997 | 0.66997 | 0.66997 | 0.0 | 93.64 Neigh | 0.018738 | 0.018738 | 0.018738 | 0.0 | 2.62 Comm | 0.006646 | 0.006646 | 0.006646 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0201 | | | 2.81 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8283.00 ave 8283 max 8283 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: 154746.0 ave 154746 max 154746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154746 Ave neighs/atom = 228.57607 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.110 | 5.110 | 5.110 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2622.403 0 -2622.403 318.78141 Loop time of 6.225e-06 on 1 procs for 0 steps with 677 atoms 192.8% 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 | | 6.225e-06 | | |100.00 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8276.00 ave 8276 max 8276 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: 153444.0 ave 153444 max 153444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153444 Ave neighs/atom = 226.65288 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.110 | 5.110 | 5.110 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 -2622.403 -2622.403 27.047567 108.01025 2.7866293 318.78141 318.78141 466.9551 458.02658 31.362566 2.3675061 155.52771 Loop time of 8.45e-06 on 1 procs for 0 steps with 677 atoms 236.7% 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 | | 8.45e-06 | | |100.00 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8276.00 ave 8276 max 8276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76722.0 ave 76722 max 76722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 153444.0 ave 153444 max 153444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153444 Ave neighs/atom = 226.65288 Neighbor list builds = 0 Dangerous builds = 0 677 -2622.40301135914 eV 2.36750608218697 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06