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 -38.487462 0.0000000) to (27.212197 38.487462 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2514766 6.0763986 5.0973115 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.487462 0.0000000) to (27.212197 38.487462 5.0973115) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2514766 6.0763986 5.0973115 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.487462 0.0000000) to (27.212197 38.487462 5.0973115) create_atoms CPU = 0.001 seconds 458 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 ghost atom cutoff = 6 binsize = 3, bins = 10 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 896 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3765.1829 0 -3765.1829 -5575.9521 46 0 -3787.5306 0 -3787.5306 -22890.754 Loop time of 2.35569 on 1 procs for 46 steps with 896 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 = -3765.18291811827 -3787.52702674839 -3787.53063793292 Force two-norm initial, final = 17.514001 0.17040780 Force max component initial, final = 6.0588898 0.031457022 Final line search alpha, max atom move = 1.0000000 0.031457022 Iterations, force evaluations = 46 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3434 | 2.3434 | 2.3434 | 0.0 | 99.48 Neigh | 0.0049498 | 0.0049498 | 0.0049498 | 0.0 | 0.21 Comm | 0.0032857 | 0.0032857 | 0.0032857 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00406 | | | 0.17 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3934.00 ave 3934 max 3934 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: 68860.0 ave 68860 max 68860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68860 Ave neighs/atom = 76.852679 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -3787.5306 0 -3787.5306 -22890.754 10677.118 68 0 -3789.7865 0 -3789.7865 -72.427103 10520.059 Loop time of 0.732622 on 1 procs for 22 steps with 896 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 = -3787.53063793292 -3789.78562909084 -3789.78653856486 Force two-norm initial, final = 251.21832 0.66880882 Force max component initial, final = 235.94430 0.12212850 Final line search alpha, max atom move = 0.00045136230 5.5124199e-05 Iterations, force evaluations = 22 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72732 | 0.72732 | 0.72732 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082362 | 0.00082362 | 0.00082362 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004477 | | | 0.61 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3948.00 ave 3948 max 3948 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: 68632.0 ave 68632 max 68632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68632 Ave neighs/atom = 76.598214 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 ghost atom cutoff = 6 binsize = 3, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.698 | 4.698 | 4.698 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3789.7865 0 -3789.7865 -72.427103 Loop time of 1.958e-06 on 1 procs for 0 steps with 896 atoms 153.2% 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 | | 1.958e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3990.00 ave 3990 max 3990 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: 68856.0 ave 68856 max 68856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68856 Ave neighs/atom = 76.848214 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 ghost atom cutoff = 6 binsize = 3, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.698 | 4.698 | 4.698 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 -3789.7865 -3789.7865 26.629396 76.974924 5.1322475 -72.427103 -72.427103 12.851401 -211.40539 -18.727319 2.3322582 850.51948 Loop time of 1.744e-06 on 1 procs for 0 steps with 896 atoms 229.4% 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 | | 1.744e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3990.00 ave 3990 max 3990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34428.0 ave 34428 max 34428 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68856.0 ave 68856 max 68856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68856 Ave neighs/atom = 76.848214 Neighbor list builds = 0 Dangerous builds = 0 896 -3789.78653856486 eV 2.33225819513544 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03