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 -63.169636 0.0000000) to (31.582860 63.169636 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3730113 4.3730113 3.9173716 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -63.169636 0.0000000) to (31.582860 63.169636 3.9173716) create_atoms CPU = 0.002 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3730113 4.3730113 3.9173716 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -63.169636 0.0000000) to (31.582860 63.169636 3.9173716) create_atoms CPU = 0.001 seconds 522 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 = 10 39 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 5 atoms, new total = 1039 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_070797404269_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 = 10 39 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) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5893.9312 0 -5893.9312 22644.235 35 0 -5976.7821 0 -5976.7821 4933.2778 Loop time of 2.52224 on 1 procs for 35 steps with 1039 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 = -5893.9311599251 -5976.77764695616 -5976.78210596582 Force two-norm initial, final = 96.122920 0.25919404 Force max component initial, final = 23.317172 0.057197735 Final line search alpha, max atom move = 1.0000000 0.057197735 Iterations, force evaluations = 35 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5055 | 2.5055 | 2.5055 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0084509 | 0.0084509 | 0.0084509 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008302 | | | 0.33 Nlocal: 1039.00 ave 1039 max 1039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6250.00 ave 6250 max 6250 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: 80916.0 ave 80916 max 80916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80916 Ave neighs/atom = 77.878730 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 = 10 39 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -5976.7821 0 -5976.7821 4933.2778 15630.922 38 0 -5976.8404 0 -5976.8404 853.15625 15666.042 Loop time of 0.263006 on 1 procs for 3 steps with 1039 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 = -5976.78210596581 -5976.83593755993 -5976.84039419991 Force two-norm initial, final = 61.784155 0.26310450 Force max component initial, final = 51.528104 0.059151819 Final line search alpha, max atom move = 0.00012559117 7.4289463e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25946 | 0.25946 | 0.25946 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090296 | 0.00090296 | 0.00090296 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002639 | | | 1.00 Nlocal: 1039.00 ave 1039 max 1039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6238.00 ave 6238 max 6238 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: 80520.0 ave 80520 max 80520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80520 Ave neighs/atom = 77.497594 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 = 10 39 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) = 4.748 | 4.748 | 4.748 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5976.8404 0 -5976.8404 853.15625 Loop time of 6.465e-06 on 1 procs for 0 steps with 1039 atoms 170.1% 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 | | 6.465e-06 | | |100.00 Nlocal: 1039.00 ave 1039 max 1039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6233.00 ave 6233 max 6233 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: 80498.0 ave 80498 max 80498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80498 Ave neighs/atom = 77.476420 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 = 10 39 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) = 4.748 | 4.748 | 4.748 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 -5976.8404 -5976.8404 31.655749 126.33927 3.917133 853.15625 853.15625 -1.9167863 2561.8349 -0.44932515 2.5125443 279.24509 Loop time of 6.716e-06 on 1 procs for 0 steps with 1039 atoms 268.0% 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 | | 6.716e-06 | | |100.00 Nlocal: 1039.00 ave 1039 max 1039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6233.00 ave 6233 max 6233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40249.0 ave 40249 max 40249 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80498.0 ave 80498 max 80498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80498 Ave neighs/atom = 77.476420 Neighbor list builds = 0 Dangerous builds = 0 1039 -5976.84039419991 eV 2.51254426530414 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03