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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -30.037155 0.0000000) to (36.784345 30.037155 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6816439 4.3686242 4.6763329 Created 663 atoms using lattice units in orthogonal box = (0.0000000 -30.037155 0.0000000) to (36.784345 30.037155 7.0144993) create_atoms CPU = 0.004 seconds 663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6816439 4.3686242 4.6763329 Created 663 atoms using lattice units in orthogonal box = (0.0000000 -30.037155 0.0000000) to (36.784345 30.037155 7.0144993) create_atoms CPU = 0.003 seconds 663 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 22 3 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1302 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5391.0159 0 -5391.0159 23586.113 50 0 -5550.7469 0 -5550.7469 -11997.662 Loop time of 5.27774 on 1 procs for 50 steps with 1302 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 = -5391.01589978178 -5550.74211540566 -5550.7469435073 Force two-norm initial, final = 178.31643 0.30196610 Force max component initial, final = 34.493013 0.10255078 Final line search alpha, max atom move = 1.0000000 0.10255078 Iterations, force evaluations = 50 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2432 | 5.2432 | 5.2432 | 0.0 | 99.35 Neigh | 0.014862 | 0.014862 | 0.014862 | 0.0 | 0.28 Comm | 0.0073719 | 0.0073719 | 0.0073719 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01226 | | | 0.23 Nlocal: 1302.00 ave 1302 max 1302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4049.00 ave 4049 max 4049 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: 75722.0 ave 75722 max 75722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75722 Ave neighs/atom = 58.158218 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -5550.7469 0 -5550.7469 -11997.662 15500.599 55 0 -5551.045 0 -5551.045 -3167.9434 15419.458 Loop time of 0.564606 on 1 procs for 5 steps with 1302 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5550.74694350731 -5551.04391524521 -5551.04496835476 Force two-norm initial, final = 146.84329 0.37634608 Force max component initial, final = 126.26509 0.085641779 Final line search alpha, max atom move = 0.00014381098 1.2316228e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56061 | 0.56061 | 0.56061 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068732 | 0.00068732 | 0.00068732 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00331 | | | 0.59 Nlocal: 1302.00 ave 1302 max 1302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4050.00 ave 4050 max 4050 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: 75980.0 ave 75980 max 75980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75980 Ave neighs/atom = 58.356375 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.730 | 4.730 | 4.730 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5551.045 0 -5551.045 -3167.9434 Loop time of 6.515e-06 on 1 procs for 0 steps with 1302 atoms 184.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 1302.00 ave 1302 max 1302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4053.00 ave 4053 max 4053 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: 76064.0 ave 76064 max 76064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76064 Ave neighs/atom = 58.420891 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.730 | 4.730 | 4.730 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 -5551.045 -5551.045 36.735164 60.07431 6.987122 -3167.9434 -3167.9434 -4.603226 -9498.6256 -0.60130972 2.3237813 1930.4648 Loop time of 6.886e-06 on 1 procs for 0 steps with 1302 atoms 275.9% 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 | | 6.886e-06 | | |100.00 Nlocal: 1302.00 ave 1302 max 1302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4053.00 ave 4053 max 4053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38032.0 ave 38032 max 38032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76064.0 ave 76064 max 76064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76064 Ave neighs/atom = 58.420891 Neighbor list builds = 0 Dangerous builds = 0 1302 -5551.04496835476 eV 2.32378130530356 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06