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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -73.249320 0.0000000) to (42.290515 73.249320 6.3277775) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6808154 5.8307917 6.3277775 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -73.249320 0.0000000) to (42.290515 73.249320 6.3277775) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6808154 5.8307917 6.3277775 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -73.249320 0.0000000) to (42.290515 73.249320 6.3277775) create_atoms CPU = 0.004 seconds 1610 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 10 34 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3212 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_673777079812_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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 11.74 | 11.74 | 11.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10092.731 0 -10092.731 21351.895 143 0 -10473.218 0 -10473.218 -631.12915 Loop time of 5.98115 on 1 procs for 143 steps with 3212 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10092.7305871293 -10473.209222035 -10473.2180795101 Force two-norm initial, final = 374.65678 0.38925339 Force max component initial, final = 126.00942 0.091351920 Final line search alpha, max atom move = 1.0000000 0.091351920 Iterations, force evaluations = 143 255 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6298 | 5.6298 | 5.6298 | 0.0 | 94.13 Neigh | 0.2519 | 0.2519 | 0.2519 | 0.0 | 4.21 Comm | 0.054536 | 0.054536 | 0.054536 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04495 | | | 0.75 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15468.0 ave 15468 max 15468 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: 720816.0 ave 720816 max 720816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720816 Ave neighs/atom = 224.41345 Neighbor list builds = 6 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 11.74 | 11.74 | 11.74 Mbytes Step Temp E_pair E_mol TotEng Press Volume 143 0 -10473.218 0 -10473.218 -631.12915 39203.764 144 0 -10473.229 0 -10473.229 235.2705 39178.085 Loop time of 0.063355 on 1 procs for 1 steps with 3212 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 = -10473.2180795101 -10473.2180795101 -10473.2285213615 Force two-norm initial, final = 38.582146 13.878104 Force max component initial, final = 29.998840 13.606761 Final line search alpha, max atom move = 3.3334622e-05 0.00045357624 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061711 | 0.061711 | 0.061711 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034274 | 0.00034274 | 0.00034274 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001301 | | | 2.05 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15475.0 ave 15475 max 15475 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: 720780.0 ave 720780 max 720780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720780 Ave neighs/atom = 224.40224 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 11.26 | 11.26 | 11.26 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10473.229 0 -10473.229 235.2705 Loop time of 2.117e-06 on 1 procs for 0 steps with 3212 atoms 188.9% 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 | | 2.117e-06 | | |100.00 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15475.0 ave 15475 max 15475 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: 720824.0 ave 720824 max 720824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720824 Ave neighs/atom = 224.41594 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 11.26 | 11.26 | 11.26 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 -10473.229 -10473.229 42.276611 146.51298 6.3250934 235.2705 235.2705 51.668001 556.49904 97.644465 2.2761488 1110.8356 Loop time of 2.566e-06 on 1 procs for 0 steps with 3212 atoms 272.8% 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 | | 2.566e-06 | | |100.00 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15475.0 ave 15475 max 15475 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 360412.0 ave 360412 max 360412 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 720824.0 ave 720824 max 720824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720824 Ave neighs/atom = 224.41594 Neighbor list builds = 0 Dangerous builds = 0 3212 -10473.2285213615 eV 2.27614884718635 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06