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 = 2.8169555 2.8169555 2.8169555 Created orthogonal box = (0.0000000 -28.169555 0.0000000) to (3.9837767 28.169555 3.9837767) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9837767 2.8169555 3.9837767 Created 40 atoms using lattice units in orthogonal box = (0.0000000 -28.169555 0.0000000) to (3.9837767 28.169555 3.9837767) create_atoms CPU = 0.001 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9837767 2.8169555 3.9837767 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -28.169555 0.0000000) to (3.9837767 28.169555 3.9837767) create_atoms CPU = 0.000 seconds 42 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 ghost atom cutoff = 8 binsize = 4, bins = 1 15 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 82 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 1 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -155.97699 0 -155.97699 1640451.5 84 0 -327.16215 0 -327.16215 65188.697 Loop time of 0.345867 on 1 procs for 84 steps with 82 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 = -155.976989895038 -327.161854449263 -327.162154551228 Force two-norm initial, final = 400.67253 0.044718016 Force max component initial, final = 144.95138 0.011122936 Final line search alpha, max atom move = 1.0000000 0.011122936 Iterations, force evaluations = 84 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32815 | 0.32815 | 0.32815 | 0.0 | 94.88 Neigh | 0.0023331 | 0.0023331 | 0.0023331 | 0.0 | 0.67 Comm | 0.009902 | 0.009902 | 0.009902 | 0.0 | 2.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005482 | | | 1.59 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2730.00 ave 2730 max 2730 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: 14866.0 ave 14866 max 14866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14866 Ave neighs/atom = 181.29268 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 1 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -327.16215 0 -327.16215 65188.697 894.12855 363 0 -330.98841 0 -330.98841 564.22456 949.55195 Loop time of 0.709141 on 1 procs for 279 steps with 82 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 = -327.162154551229 -330.988217965272 -330.988414382208 Force two-norm initial, final = 73.711226 0.70398448 Force max component initial, final = 57.582565 0.50232637 Final line search alpha, max atom move = 0.0023857319 0.0011984160 Iterations, force evaluations = 279 305 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64363 | 0.64363 | 0.64363 | 0.0 | 90.76 Neigh | 0.0062612 | 0.0062612 | 0.0062612 | 0.0 | 0.88 Comm | 0.015335 | 0.015335 | 0.015335 | 0.0 | 2.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04391 | | | 6.19 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2172.00 ave 2172 max 2172 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: 15136.0 ave 15136 max 15136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15136 Ave neighs/atom = 184.58537 Neighbor list builds = 3 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 ghost atom cutoff = 8 binsize = 4, bins = 2 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -330.98841 0 -330.98841 564.22456 Loop time of 6.295e-06 on 1 procs for 0 steps with 82 atoms 190.6% 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 | | 6.295e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2172.00 ave 2172 max 2172 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: 15064.0 ave 15064 max 15064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15064 Ave neighs/atom = 183.70732 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 ghost atom cutoff = 8 binsize = 4, bins = 2 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.536 | 4.536 | 4.536 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 -330.98841 -330.98841 4.2882844 53.128996 4.167768 564.22456 564.22456 521.10635 284.84803 886.71929 2.4222553 511.98936 Loop time of 6.656e-06 on 1 procs for 0 steps with 82 atoms 225.4% 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 | | 6.656e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2172.00 ave 2172 max 2172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7532.00 ave 7532 max 7532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15064.0 ave 15064 max 15064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15064 Ave neighs/atom = 183.70732 Neighbor list builds = 0 Dangerous builds = 0 82 -330.988414382208 eV 2.42225525872542 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01