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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -58.148854 0.0000000) to (41.114571 58.148854 5.7571914) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4493444 5.1304221 5.7571914 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -58.148854 0.0000000) to (41.114571 58.148854 5.7571914) create_atoms CPU = 0.005 seconds 822 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4493444 5.1304221 5.7571914 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -58.148854 0.0000000) to (41.114571 58.148854 5.7571914) create_atoms CPU = 0.004 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1630 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5435.7407 0 -5435.7407 6643.9014 26 0 -5475.1399 0 -5475.1399 1642.0434 Loop time of 5.37662 on 1 procs for 26 steps with 1630 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 = -5435.74066803431 -5475.13580456337 -5475.13987769512 Force two-norm initial, final = 30.427783 0.14290541 Force max component initial, final = 4.9510369 0.020829881 Final line search alpha, max atom move = 1.0000000 0.020829881 Iterations, force evaluations = 26 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3449 | 5.3449 | 5.3449 | 0.0 | 99.41 Neigh | 0.015936 | 0.015936 | 0.015936 | 0.0 | 0.30 Comm | 0.0070578 | 0.0070578 | 0.0070578 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008689 | | | 0.16 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5964.00 ave 5964 max 5964 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: 87736.0 ave 87736 max 87736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87736 Ave neighs/atom = 53.825767 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -5475.1399 0 -5475.1399 1642.0434 27528.186 27 0 -5475.1411 0 -5475.1411 1340.5907 27536.566 Loop time of 0.3626 on 1 procs for 1 steps with 1630 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 = -5475.13987769515 -5475.13987769515 -5475.14113378497 Force two-norm initial, final = 7.8912474 5.3427326 Force max component initial, final = 7.8844352 5.3382084 Final line search alpha, max atom move = 0.00012683217 0.00067705654 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36082 | 0.36082 | 0.36082 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038633 | 0.00038633 | 0.00038633 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001391 | | | 0.38 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5964.00 ave 5964 max 5964 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: 87726.0 ave 87726 max 87726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87726 Ave neighs/atom = 53.819632 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.860 | 4.860 | 4.860 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5475.1411 0 -5475.1411 1340.5907 Loop time of 6.746e-06 on 1 procs for 0 steps with 1630 atoms 177.9% 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 | | 6.746e-06 | | |100.00 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5960.00 ave 5960 max 5960 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: 87726.0 ave 87726 max 87726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87726 Ave neighs/atom = 53.819632 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.860 | 4.860 | 4.860 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 -5475.1411 -5475.1411 41.127573 116.29771 5.7571233 1340.5907 1340.5907 -9.5842958 4341.949 -310.5925 2.6080018 825.20902 Loop time of 6.886e-06 on 1 procs for 0 steps with 1630 atoms 275.9% 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 | | 6.886e-06 | | |100.00 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5960.00 ave 5960 max 5960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43863.0 ave 43863 max 43863 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87726.0 ave 87726 max 87726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87726 Ave neighs/atom = 53.819632 Neighbor list builds = 0 Dangerous builds = 0 1630 -5475.14113378497 eV 2.60800179714521 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06