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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -53.865396 0.0000000) to (38.088586 53.865396 5.0449565) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0139873 5.1975382 5.0449565 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -53.865396 0.0000000) to (38.088586 53.865396 5.0449565) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0139873 5.1975382 5.0449565 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.865396 0.0000000) to (38.088586 53.865396 5.0449565) create_atoms CPU = 0.002 seconds 916 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1820 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.143 | 5.143 | 5.143 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7459.4463 0 -7459.4463 29082.573 75 0 -7681.2503 0 -7681.2503 37502.15 Loop time of 7.63343 on 1 procs for 75 steps with 1820 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7459.44626250502 -7681.24411396759 -7681.25032156521 Force two-norm initial, final = 295.12209 0.40452885 Force max component initial, final = 66.555776 0.076860341 Final line search alpha, max atom move = 1.0000000 0.076860341 Iterations, force evaluations = 75 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5953 | 7.5953 | 7.5953 | 0.0 | 99.50 Neigh | 0.0087237 | 0.0087237 | 0.0087237 | 0.0 | 0.11 Comm | 0.013278 | 0.013278 | 0.013278 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01615 | | | 0.21 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6603.00 ave 6603 max 6603 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: 102624.0 ave 102624 max 102624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102624 Ave neighs/atom = 56.386813 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.143 | 5.143 | 5.143 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -7681.2503 0 -7681.2503 37502.15 20701.039 82 0 -7683.972 0 -7683.972 -183.74026 20923.257 Loop time of 0.496553 on 1 procs for 7 steps with 1820 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7681.2503215652 -7683.97082173398 -7683.97197270555 Force two-norm initial, final = 847.28191 5.8022225 Force max component initial, final = 574.73911 4.8515693 Final line search alpha, max atom move = 7.0807427e-05 0.00034352714 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49168 | 0.49168 | 0.49168 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00070194 | 0.00070194 | 0.00070194 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004171 | | | 0.84 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6597.00 ave 6597 max 6597 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: 105792.0 ave 105792 max 105792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105792 Ave neighs/atom = 58.127473 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.281 | 5.281 | 5.281 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7683.972 0 -7683.972 -183.74026 Loop time of 2.738e-06 on 1 procs for 0 steps with 1820 atoms 182.6% 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 | | 2.738e-06 | | |100.00 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6578.00 ave 6578 max 6578 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: 102808.0 ave 102808 max 102808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102808 Ave neighs/atom = 56.487912 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.281 | 5.281 | 5.281 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 -7683.972 -7683.972 38.20792 108.37878 5.0527942 -183.74026 -183.74026 -183.87171 4.7319455 -372.08101 2.3609217 849.92898 Loop time of 2.858e-06 on 1 procs for 0 steps with 1820 atoms 244.9% 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 | | 2.858e-06 | | |100.00 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6578.00 ave 6578 max 6578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51404.0 ave 51404 max 51404 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102808.0 ave 102808 max 102808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102808 Ave neighs/atom = 56.487912 Neighbor list builds = 0 Dangerous builds = 0 1820 -7683.97197270555 eV 2.36092171498873 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08