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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -45.251969 0.0000000) to (21.331983 45.251969 5.1737657) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2741125 6.2110545 5.1737657 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -45.251969 0.0000000) to (21.331983 45.251969 5.1737657) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2741125 6.2110545 5.1737657 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -45.251969 0.0000000) to (21.331983 45.251969 5.1737657) create_atoms CPU = 0.001 seconds 412 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 25 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 820 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.966 | 4.966 | 4.966 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2706.3978 0 -2706.3978 127930.32 259 0 -3214.2163 0 -3214.2163 -40140.739 Loop time of 3.27338 on 1 procs for 259 steps with 820 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2706.39778262766 -3214.21349546902 -3214.21634100262 Force two-norm initial, final = 1266.4543 0.17101815 Force max component initial, final = 390.87835 0.018422484 Final line search alpha, max atom move = 1.0000000 0.018422484 Iterations, force evaluations = 259 502 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1719 | 3.1719 | 3.1719 | 0.0 | 96.90 Neigh | 0.04947 | 0.04947 | 0.04947 | 0.0 | 1.51 Comm | 0.028784 | 0.028784 | 0.028784 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02318 | | | 0.71 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5191.00 ave 5191 max 5191 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: 112816.0 ave 112816 max 112816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112816 Ave neighs/atom = 137.58049 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 259 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.965 | 4.965 | 4.965 Mbytes Step Temp E_pair E_mol TotEng Press Volume 259 0 -3214.2163 0 -3214.2163 -40140.739 9988.6191 362 0 -3238.1806 0 -3238.1806 -412.69391 9824.4449 Loop time of 0.761973 on 1 procs for 103 steps with 820 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 = -3214.21634100261 -3238.17836742121 -3238.1805748095 Force two-norm initial, final = 627.61064 6.8494200 Force max component initial, final = 571.66041 4.0731846 Final line search alpha, max atom move = 0.00015716838 0.00064017581 Iterations, force evaluations = 103 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68741 | 0.68741 | 0.68741 | 0.0 | 90.21 Neigh | 0.041395 | 0.041395 | 0.041395 | 0.0 | 5.43 Comm | 0.0058745 | 0.0058745 | 0.0058745 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0273 | | | 3.58 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5314.00 ave 5314 max 5314 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: 115144.0 ave 115144 max 115144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115144 Ave neighs/atom = 140.41951 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.104 | 5.104 | 5.104 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3238.1806 0 -3238.1806 -412.69391 Loop time of 1.799e-06 on 1 procs for 0 steps with 820 atoms 111.2% 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 | | 1.799e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5314.00 ave 5314 max 5314 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: 115032.0 ave 115032 max 115032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115032 Ave neighs/atom = 140.28293 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.104 | 5.104 | 5.104 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 -3238.1806 -3238.1806 20.676899 85.348443 5.5670742 -412.69391 -412.69391 -643.85877 -603.48506 9.2621116 2.3131458 2057.7922 Loop time of 2.069e-06 on 1 procs for 0 steps with 820 atoms 241.7% 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 | | 2.069e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5314.00 ave 5314 max 5314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57516.0 ave 57516 max 57516 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 115032.0 ave 115032 max 115032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115032 Ave neighs/atom = 140.28293 Neighbor list builds = 0 Dangerous builds = 0 820 -3238.18057480951 eV 2.31314579590488 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04