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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -40.256446 0.0000000) to (28.465606 40.256446 4.4455807) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8599815 5.4002549 4.4455807 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -40.256446 0.0000000) to (28.465606 40.256446 4.4455807) create_atoms CPU = 0.001 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8599815 5.4002549 4.4455807 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -40.256446 0.0000000) to (28.465606 40.256446 4.4455807) create_atoms CPU = 0.001 seconds 330 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 652 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3726.0195 0 -3726.0195 134055.38 122 0 -4341.9895 0 -4341.9895 -5716.1464 Loop time of 1.53249 on 1 procs for 122 steps with 652 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 = -3726.01946341909 -4341.98546008131 -4341.98946202847 Force two-norm initial, final = 1163.7201 0.34206247 Force max component initial, final = 394.73757 0.033291359 Final line search alpha, max atom move = 0.72697530 0.024201996 Iterations, force evaluations = 122 209 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4583 | 1.4583 | 1.4583 | 0.0 | 95.16 Neigh | 0.055267 | 0.055267 | 0.055267 | 0.0 | 3.61 Comm | 0.011756 | 0.011756 | 0.011756 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007163 | | | 0.47 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7187.00 ave 7187 max 7187 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: 179444.0 ave 179444 max 179444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179444 Ave neighs/atom = 275.22086 Neighbor list builds = 6 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.961 | 4.961 | 4.961 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -4341.9895 0 -4341.9895 -5716.1464 10188.596 133 0 -4343.5614 0 -4343.5614 4.2678493 10165.701 Loop time of 0.0950614 on 1 procs for 11 steps with 652 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 = -4341.98946202848 -4343.56001164133 -4343.56142049666 Force two-norm initial, final = 252.66509 1.5068439 Force max component initial, final = 224.50924 0.29227805 Final line search alpha, max atom move = 0.00017266545 5.0466322e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091428 | 0.091428 | 0.091428 | 0.0 | 96.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073359 | 0.00073359 | 0.00073359 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0029 | | | 3.05 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7682.00 ave 7682 max 7682 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: 179816.0 ave 179816 max 179816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179816 Ave neighs/atom = 275.79141 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4343.5614 0 -4343.5614 4.2678493 Loop time of 1.777e-06 on 1 procs for 0 steps with 652 atoms 168.8% 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 | | 1.777e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6303.00 ave 6303 max 6303 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: 179336.0 ave 179336 max 179336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179336 Ave neighs/atom = 275.05521 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.088 | 5.088 | 5.088 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 -4343.5614 -4343.5614 28.172715 80.620222 4.4757378 4.2678493 4.2678493 45.59083 -17.540706 -15.246577 2.5731676 861.72607 Loop time of 2.288e-06 on 1 procs for 0 steps with 652 atoms 262.2% 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 | | 2.288e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6303.00 ave 6303 max 6303 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89668.0 ave 89668 max 89668 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179336.0 ave 179336 max 179336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179336 Ave neighs/atom = 275.05521 Neighbor list builds = 0 Dangerous builds = 0 652 -4343.56142049666 eV 2.57316759118473 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01