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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -42.191383 0.0000000) to (21.095692 42.191383 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0920635 5.0920635 3.9173716 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -42.191383 0.0000000) to (21.095692 42.191383 3.9173716) create_atoms CPU = 0.003 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0920635 5.0920635 3.9173716 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -42.191383 0.0000000) to (21.095692 42.191383 3.9173716) create_atoms CPU = 0.002 seconds 233 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 463 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.455 | 4.455 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2508.4557 0 -2508.4557 58567.47 25 0 -2652.9311 0 -2652.9311 13421.151 Loop time of 0.964896 on 1 procs for 25 steps with 463 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2508.45568311307 -2652.92873618883 -2652.93108461539 Force two-norm initial, final = 284.29231 0.18184017 Force max component initial, final = 101.97980 0.026356269 Final line search alpha, max atom move = 1.0000000 0.026356269 Iterations, force evaluations = 25 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95715 | 0.95715 | 0.95715 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038823 | 0.0038823 | 0.0038823 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003859 | | | 0.40 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3379.00 ave 3379 max 3379 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: 35956.0 ave 35956 max 35956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35956 Ave neighs/atom = 77.658747 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.455 | 4.455 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -2652.9311 0 -2652.9311 13421.151 6973.3633 36 0 -2653.4095 0 -2653.4095 150.67347 7025.5857 Loop time of 0.283182 on 1 procs for 11 steps with 463 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 = -2652.93108461539 -2653.4093721579 -2653.40953155422 Force two-norm initial, final = 117.95647 1.3878613 Force max component initial, final = 107.78336 0.98926497 Final line search alpha, max atom move = 0.00076265973 0.00075447255 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27812 | 0.27812 | 0.27812 | 0.0 | 98.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011171 | 0.0011171 | 0.0011171 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003941 | | | 1.39 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3383.00 ave 3383 max 3383 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: 35696.0 ave 35696 max 35696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35696 Ave neighs/atom = 77.097192 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2653.4095 0 -2653.4095 150.67347 Loop time of 6.415e-06 on 1 procs for 0 steps with 463 atoms 218.2% 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 | | 6.415e-06 | | |100.00 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3387.00 ave 3387 max 3387 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: 35636.0 ave 35636 max 35636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35636 Ave neighs/atom = 76.967603 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.594 | 4.594 | 4.594 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 -2653.4095 -2653.4095 21.090442 85.202767 3.9096976 150.67347 150.67347 225.54456 88.049739 138.42611 2.4487857 388.52616 Loop time of 7.076e-06 on 1 procs for 0 steps with 463 atoms 212.0% 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 | | 7.076e-06 | | |100.00 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3387.00 ave 3387 max 3387 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17818.0 ave 17818 max 17818 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35636.0 ave 35636 max 35636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35636 Ave neighs/atom = 76.967603 Neighbor list builds = 0 Dangerous builds = 0 463 -2653.40953155422 eV 2.44878565522127 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01