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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2390280 5.7351567 5.1068645 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068645) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2390280 5.7351567 5.1068645 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068645) create_atoms CPU = 0.003 seconds 1080 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 35 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2128 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_260546967793_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8952.3976 0 -8952.3976 2804.2051 427 0 -9044.1704 0 -9044.1704 -7725.6076 Loop time of 123.122 on 1 procs for 427 steps with 2128 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 = -8952.39759509511 -9044.1621048847 -9044.1704478974 Force two-norm initial, final = 67.002793 0.29549102 Force max component initial, final = 12.027468 0.046685723 Final line search alpha, max atom move = 0.85224516 0.039787681 Iterations, force evaluations = 427 808 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 122.75 | 122.75 | 122.75 | 0.0 | 99.69 Neigh | 0.19082 | 0.19082 | 0.19082 | 0.0 | 0.15 Comm | 0.098251 | 0.098251 | 0.098251 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08647 | | | 0.07 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9363.00 ave 9363 max 9363 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: 241882.0 ave 241882 max 241882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241882 Ave neighs/atom = 113.66635 Neighbor list builds = 11 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 427 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press Volume 427 0 -9044.1704 0 -9044.1704 -7725.6076 25239.62 456 0 -9064.3223 0 -9064.3223 -5.0080033 25088.847 Loop time of 5.56406 on 1 procs for 29 steps with 2128 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 = -9044.17044789739 -9064.31820415524 -9064.32231744384 Force two-norm initial, final = 1056.1306 2.9884568 Force max component initial, final = 745.81109 0.59277690 Final line search alpha, max atom move = 8.4735937e-05 5.0229506e-05 Iterations, force evaluations = 29 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5016 | 5.5016 | 5.5016 | 0.0 | 98.88 Neigh | 0.045953 | 0.045953 | 0.045953 | 0.0 | 0.83 Comm | 0.0030695 | 0.0030695 | 0.0030695 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01343 | | | 0.24 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9520.00 ave 9520 max 9520 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: 240484.0 ave 240484 max 240484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240484 Ave neighs/atom = 113.00940 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.772 | 5.772 | 5.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9064.3223 0 -9064.3223 -5.0080033 Loop time of 1.937e-06 on 1 procs for 0 steps with 2128 atoms 154.9% 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 | | 1.937e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9533.00 ave 9533 max 9533 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: 240492.0 ave 240492 max 240492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240492 Ave neighs/atom = 113.01316 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.772 | 5.772 | 5.772 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 -9064.3223 -9064.3223 41.377691 121.56564 4.9877377 -5.0080033 -5.0080033 0.53111261 -38.92199 23.366867 2.3615741 5101.6187 Loop time of 2.042e-06 on 1 procs for 0 steps with 2128 atoms 195.9% 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 | | 2.042e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9533.00 ave 9533 max 9533 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120246.0 ave 120246 max 120246 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 240492.0 ave 240492 max 240492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240492 Ave neighs/atom = 113.01316 Neighbor list builds = 0 Dangerous builds = 0 2128 -9064.32231744384 eV 2.36157409411145 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:09