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 = 3.9946166 3.9946166 3.9946166 Created orthogonal box = (0.0000000 -48.923862 0.0000000) to (6.9188790 48.923862 5.6492410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9188790 6.5231816 5.6492410 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -48.923862 0.0000000) to (6.9188790 48.923862 5.6492410) create_atoms CPU = 0.002 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9188790 6.5231816 5.6492410 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -48.923862 0.0000000) to (6.9188790 48.923862 5.6492410) create_atoms CPU = 0.002 seconds 122 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 2 26 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 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_115316750986_001#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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 2 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.466 | 4.466 | 4.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -776.25485 0 -776.25485 8396.7307 98 0 -787.05035 0 -787.05035 -929.19184 Loop time of 1.31137 on 1 procs for 98 steps with 240 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 = -776.254848510949 -787.049587696155 -787.050346371618 Force two-norm initial, final = 20.842101 0.060645553 Force max component initial, final = 7.6338685 0.014769915 Final line search alpha, max atom move = 1.0000000 0.014769915 Iterations, force evaluations = 98 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2819 | 1.2819 | 1.2819 | 0.0 | 97.75 Neigh | 0.0046197 | 0.0046197 | 0.0046197 | 0.0 | 0.35 Comm | 0.014245 | 0.014245 | 0.014245 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01063 | | | 0.81 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3156.00 ave 3156 max 3156 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: 31444.0 ave 31444 max 31444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31444 Ave neighs/atom = 131.01667 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 2 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -787.05035 0 -787.05035 -929.19184 3824.5168 102 0 -787.06316 0 -787.06316 -21.750939 3815.3473 Loop time of 0.0429963 on 1 procs for 4 steps with 240 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 = -787.050346371617 -787.062825782217 -787.06316008489 Force two-norm initial, final = 6.8138630 0.18970859 Force max component initial, final = 6.3344148 0.14807826 Final line search alpha, max atom move = 0.0012886581 0.00019082226 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041302 | 0.041302 | 0.041302 | 0.0 | 96.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003938 | 0.0003938 | 0.0003938 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001301 | | | 3.03 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2980.00 ave 2980 max 2980 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: 31500.0 ave 31500 max 31500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31500 Ave neighs/atom = 131.25000 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 2 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -787.06316 0 -787.06316 -21.750939 Loop time of 6.806e-06 on 1 procs for 0 steps with 240 atoms 176.3% 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 | | 6.806e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2973.00 ave 2973 max 2973 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: 31528.0 ave 31528 max 31528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31528 Ave neighs/atom = 131.36667 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 2 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.602 | 4.602 | 4.602 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 -787.06316 -787.06316 6.9288968 97.504852 5.6473377 -21.750939 -21.750939 -62.27245 -28.203047 25.22268 2.6465206 264.87644 Loop time of 6.655e-06 on 1 procs for 0 steps with 240 atoms 240.4% 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 | | 6.655e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2973.00 ave 2973 max 2973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15764.0 ave 15764 max 15764 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31528.0 ave 31528 max 31528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31528 Ave neighs/atom = 131.36667 Neighbor list builds = 0 Dangerous builds = 0 240 -787.06316008489 eV 2.64652060157693 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01