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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -59.771452 0.0000000) to (21.131099 59.771452 5.2021169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7630269 4.5278616 5.2021169 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.771452 0.0000000) to (21.131099 59.771452 5.2021169) create_atoms CPU = 0.001 seconds 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7630269 4.5278616 5.2021169 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.771452 0.0000000) to (21.131099 59.771452 5.2021169) create_atoms CPU = 0.001 seconds 530 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1046 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_024705128470_000#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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.624 | 4.624 | 4.624 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4373.8879 0 -4373.8879 3798.2061 173 0 -4409.8473 0 -4409.8473 -14218.124 Loop time of 0.857672 on 1 procs for 173 steps with 1046 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 = -4373.88793459959 -4409.84325341712 -4409.84733644131 Force two-norm initial, final = 34.225093 0.20021872 Force max component initial, final = 10.940161 0.019435730 Final line search alpha, max atom move = 1.0000000 0.019435730 Iterations, force evaluations = 173 300 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81545 | 0.81545 | 0.81545 | 0.0 | 95.08 Neigh | 0.017501 | 0.017501 | 0.017501 | 0.0 | 2.04 Comm | 0.012755 | 0.012755 | 0.012755 | 0.0 | 1.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01196 | | | 1.39 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5183.00 ave 5183 max 5183 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: 80888.0 ave 80888 max 80888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80888 Ave neighs/atom = 77.330784 Neighbor list builds = 3 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 173 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press Volume 173 0 -4409.8473 0 -4409.8473 -14218.124 13140.927 183 0 -4410.7262 0 -4410.7262 -429.68483 12972.656 Loop time of 0.0358136 on 1 procs for 10 steps with 1046 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 = -4409.84733644132 -4410.72541941132 -4410.72623203726 Force two-norm initial, final = 177.06109 0.85473142 Force max component initial, final = 158.14672 0.69790685 Final line search alpha, max atom move = 0.00021496983 0.00015002891 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033111 | 0.033111 | 0.033111 | 0.0 | 92.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046379 | 0.00046379 | 0.00046379 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002239 | | | 6.25 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5157.00 ave 5157 max 5157 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: 80796.0 ave 80796 max 80796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80796 Ave neighs/atom = 77.242830 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.761 | 4.761 | 4.761 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4410.7262 0 -4410.7262 -429.68483 Loop time of 1.563e-06 on 1 procs for 0 steps with 1046 atoms 128.0% 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 | | 1.563e-06 | | |100.00 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5196.00 ave 5196 max 5196 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: 81024.0 ave 81024 max 81024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81024 Ave neighs/atom = 77.460803 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.761 | 4.761 | 4.761 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 -4410.7262 -4410.7262 20.934263 119.5429 5.1837906 -429.68483 -429.68483 30.1962 -1405.1414 85.890721 2.4212993 701.08169 Loop time of 1.552e-06 on 1 procs for 0 steps with 1046 atoms 193.3% 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 | | 1.552e-06 | | |100.00 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5196.00 ave 5196 max 5196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40512.0 ave 40512 max 40512 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81024.0 ave 81024 max 81024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81024 Ave neighs/atom = 77.460803 Neighbor list builds = 0 Dangerous builds = 0 1046 -4410.72612743726 eV 2.42129927706428 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01