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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -69.619797 0.0000000) to (40.195009 69.619797 6.3030803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9304111 5.3261047 6.3030803 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -69.619797 0.0000000) to (40.195009 69.619797 6.3030803) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9304111 5.3261047 6.3030803 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.619797 0.0000000) to (40.195009 69.619797 6.3030803) create_atoms CPU = 0.003 seconds 1465 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2928 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_120596890176_005#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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.50 | 12.50 | 12.50 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8965.7162 0 -8965.7162 61227.277 67 0 -9582.521 0 -9582.521 4149.2558 Loop time of 4.70583 on 1 procs for 67 steps with 2928 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 = -8965.71615489524 -9582.51262882311 -9582.520965261 Force two-norm initial, final = 1123.4424 0.22494685 Force max component initial, final = 302.93620 0.029994885 Final line search alpha, max atom move = 0.69050658 0.020711666 Iterations, force evaluations = 67 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4744 | 4.4744 | 4.4744 | 0.0 | 95.08 Neigh | 0.19247 | 0.19247 | 0.19247 | 0.0 | 4.09 Comm | 0.021398 | 0.021398 | 0.021398 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01757 | | | 0.37 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16768.0 ave 16768 max 16768 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: 931768.0 ave 931768 max 931768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 931768 Ave neighs/atom = 318.22678 Neighbor list builds = 4 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.50 | 12.50 | 12.50 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -9582.521 0 -9582.521 4149.2558 35276.681 70 0 -9582.6729 0 -9582.6729 1.1596338 35378.832 Loop time of 0.282569 on 1 procs for 3 steps with 2928 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 = -9582.520965261 -9582.67007001884 -9582.67294603566 Force two-norm initial, final = 162.61437 1.6368608 Force max component initial, final = 115.07530 1.2873516 Final line search alpha, max atom move = 6.2281907e-05 8.0178710e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27843 | 0.27843 | 0.27843 | 0.0 | 98.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076158 | 0.00076158 | 0.00076158 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003375 | | | 1.19 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16768.0 ave 16768 max 16768 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: 931870.0 ave 931870 max 931870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 931870 Ave neighs/atom = 318.26161 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.01 | 12.01 | 12.01 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9582.6729 0 -9582.6729 1.1596338 Loop time of 2.131e-06 on 1 procs for 0 steps with 2928 atoms 187.7% 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 | | 2.131e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16744.0 ave 16744 max 16744 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: 931486.0 ave 931486 max 931486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 931486 Ave neighs/atom = 318.13046 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.01 | 12.01 | 12.01 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 -9582.6729 -9582.6729 40.237933 139.47006 6.3041544 1.1596338 1.1596338 -58.36165 36.65405 25.186501 2.2315488 1185.3531 Loop time of 2.409e-06 on 1 procs for 0 steps with 2928 atoms 249.1% 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 | | 2.409e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16744.0 ave 16744 max 16744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 465743.0 ave 465743 max 465743 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 931486.0 ave 931486 max 931486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 931486 Ave neighs/atom = 318.13046 Neighbor list builds = 0 Dangerous builds = 0 2928 -9582.67294603566 eV 2.23154879708183 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05