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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -42.037112 0.0000000) to (14.861089 42.037112 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1192719 6.1813981 5.0973115 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.037112 0.0000000) to (14.861089 42.037112 5.0973115) create_atoms CPU = 0.001 seconds 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1192719 6.1813981 5.0973115 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.037112 0.0000000) to (14.861089 42.037112 5.0973115) create_atoms CPU = 0.001 seconds 274 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 = 5 28 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 12 atoms, new total = 536 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 = 5 28 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) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2257.6841 0 -2257.6841 -6392.6269 634 0 -2281.4373 0 -2281.4373 -31905.085 Loop time of 26.3558 on 1 procs for 634 steps with 536 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 = -2257.68408361235 -2281.43507300883 -2281.43727075459 Force two-norm initial, final = 7.7380167 0.13940325 Force max component initial, final = 1.8033414 0.033853052 Final line search alpha, max atom move = 1.0000000 0.033853052 Iterations, force evaluations = 634 1225 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.237 | 26.237 | 26.237 | 0.0 | 99.55 Neigh | 0.053398 | 0.053398 | 0.053398 | 0.0 | 0.20 Comm | 0.03585 | 0.03585 | 0.03585 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02916 | | | 0.11 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3254.00 ave 3254 max 3254 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: 35684.0 ave 35684 max 35684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35684 Ave neighs/atom = 66.574627 Neighbor list builds = 17 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 = 5 28 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 : 634 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 634 0 -2281.4373 0 -2281.4373 -31905.085 6368.7568 665 0 -2286.0793 0 -2286.0793 -8713.5143 6268.9476 Loop time of 0.875573 on 1 procs for 31 steps with 536 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 = -2281.43727075459 -2286.07878013833 -2286.07925748823 Force two-norm initial, final = 283.87279 2.6730974 Force max component initial, final = 281.23296 2.4537124 Final line search alpha, max atom move = 0.0055037233 0.013504554 Iterations, force evaluations = 31 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87069 | 0.87069 | 0.87069 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084135 | 0.00084135 | 0.00084135 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004043 | | | 0.46 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3256.00 ave 3256 max 3256 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: 35632.0 ave 35632 max 35632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35632 Ave neighs/atom = 66.477612 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 = 5 28 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2286.0793 0 -2286.0793 -8713.5143 Loop time of 2.13e-06 on 1 procs for 0 steps with 536 atoms 187.8% 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 | | 2.13e-06 | | |100.00 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3298.00 ave 3298 max 3298 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: 35724.0 ave 35724 max 35724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35724 Ave neighs/atom = 66.649254 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 = 5 28 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) = 4.633 | 4.633 | 4.633 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 -2286.0793 -2286.0793 15.077735 84.074223 4.9453343 -8713.5143 -8713.5143 -636.24569 -25697.075 192.77778 2.332554 1211.1599 Loop time of 1.783e-06 on 1 procs for 0 steps with 536 atoms 168.3% 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 | | 1.783e-06 | | |100.00 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3298.00 ave 3298 max 3298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17862.0 ave 17862 max 17862 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35724.0 ave 35724 max 35724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35724 Ave neighs/atom = 66.649254 Neighbor list builds = 0 Dangerous builds = 0 536 -2286.07925748823 eV 2.33255399207445 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27