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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -44.226744 0.0000000) to (6.2546062 44.226744 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2546062 5.8968993 5.1068646 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -44.226744 0.0000000) to (6.2546062 44.226744 5.1068646) create_atoms CPU = 0.001 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2546062 5.8968993 5.1068646 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.226744 0.0000000) to (6.2546062 44.226744 5.1068646) create_atoms CPU = 0.001 seconds 122 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 = 3 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 242 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_162036141261_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 = 3 30 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) = 4.427 | 4.427 | 4.427 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -906.68421 0 -906.68421 106818.04 234 0 -1026.6794 0 -1026.6794 18450.824 Loop time of 3.83929 on 1 procs for 234 steps with 242 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 = -906.684208755375 -1026.67851488903 -1026.67941125999 Force two-norm initial, final = 225.60879 0.082501798 Force max component initial, final = 111.49440 0.015911933 Final line search alpha, max atom move = 1.0000000 0.015911933 Iterations, force evaluations = 234 438 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8153 | 3.8153 | 3.8153 | 0.0 | 99.37 Neigh | 0.0091447 | 0.0091447 | 0.0091447 | 0.0 | 0.24 Comm | 0.008812 | 0.008812 | 0.008812 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006046 | | | 0.16 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2397.00 ave 2397 max 2397 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: 18104.0 ave 18104 max 18104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18104 Ave neighs/atom = 74.809917 Neighbor list builds = 7 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 = 3 30 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 : 234 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.427 | 4.427 | 4.427 Mbytes Step Temp E_pair E_mol TotEng Press Volume 234 0 -1026.6794 0 -1026.6794 18450.824 2825.3306 253 0 -1027.2967 0 -1027.2967 14.635845 2853.1132 Loop time of 0.176802 on 1 procs for 19 steps with 242 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 = -1026.67941125999 -1027.2966326071 -1027.29673940696 Force two-norm initial, final = 75.993829 0.30514254 Force max component initial, final = 73.876786 0.092126962 Final line search alpha, max atom move = 0.0025108824 0.00023131997 Iterations, force evaluations = 19 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17485 | 0.17485 | 0.17485 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036581 | 0.00036581 | 0.00036581 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001588 | | | 0.90 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2402.00 ave 2402 max 2402 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: 18020.0 ave 18020 max 18020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18020 Ave neighs/atom = 74.462810 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 = 3 30 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) = 4.565 | 4.565 | 4.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1027.2967 0 -1027.2967 14.635845 Loop time of 1.592e-06 on 1 procs for 0 steps with 242 atoms 125.6% 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 | | 1.592e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2376.00 ave 2376 max 2376 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: 17464.0 ave 17464 max 17464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17464 Ave neighs/atom = 72.165289 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 = 3 30 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) = 4.565 | 4.565 | 4.565 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 -1027.2967 -1027.2967 6.3670599 87.818921 5.1026052 14.635845 14.635845 51.05796 44.540669 -51.691095 2.4090659 898.51974 Loop time of 1.567e-06 on 1 procs for 0 steps with 242 atoms 191.4% 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 | | 1.567e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2376.00 ave 2376 max 2376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8732.00 ave 8732 max 8732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17464.0 ave 17464 max 17464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17464 Ave neighs/atom = 72.165289 Neighbor list builds = 0 Dangerous builds = 0 242 -1027.29673940696 eV 2.40906588813429 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04