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 = 4.0515263 4.0515263 4.0515263 Created orthogonal box = (0.0000000 -46.548493 0.0000000) to (32.914755 46.548493 5.7297234) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9819178 6.3475218 5.7297234 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -46.548493 0.0000000) to (32.914755 46.548493 5.7297234) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9819178 6.3475218 5.7297234 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -46.548493 0.0000000) to (32.914755 46.548493 5.7297234) create_atoms CPU = 0.001 seconds 532 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 9 24 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1815.4309 0 -1815.4309 243343.97 75 0 -3537.9654 0 -3537.9654 6686.4156 Loop time of 1.84892 on 1 procs for 75 steps with 1056 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 = -1815.43086920675 -3537.96213852002 -3537.96544472598 Force two-norm initial, final = 3029.2770 0.17384359 Force max component initial, final = 682.98973 0.023710663 Final line search alpha, max atom move = 1.0000000 0.023710663 Iterations, force evaluations = 75 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7846 | 1.7846 | 1.7846 | 0.0 | 96.52 Neigh | 0.035689 | 0.035689 | 0.035689 | 0.0 | 1.93 Comm | 0.015174 | 0.015174 | 0.015174 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0135 | | | 0.73 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5802.00 ave 5802 max 5802 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: 140192.0 ave 140192 max 140192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140192 Ave neighs/atom = 132.75758 Neighbor list builds = 2 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.009 | 5.009 | 5.009 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -3537.9654 0 -3537.9654 6686.4156 17557.388 80 0 -3538.2665 0 -3538.2665 13.439784 17679.144 Loop time of 0.116509 on 1 procs for 5 steps with 1056 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 = -3537.96544472598 -3538.26575435515 -3538.26650924595 Force two-norm initial, final = 132.16703 1.0401876 Force max component initial, final = 91.171722 0.65261241 Final line search alpha, max atom move = 0.00017979900 0.00011733906 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1122 | 0.1122 | 0.1122 | 0.0 | 96.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076437 | 0.00076437 | 0.00076437 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003547 | | | 3.04 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6256.00 ave 6256 max 6256 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: 140416.0 ave 140416 max 140416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140416 Ave neighs/atom = 132.96970 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.147 | 5.147 | 5.147 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3538.2665 0 -3538.2665 13.439784 Loop time of 3.317e-06 on 1 procs for 0 steps with 1056 atoms 150.7% 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 | | 3.317e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6256.00 ave 6256 max 6256 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: 140280.0 ave 140280 max 140280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140280 Ave neighs/atom = 132.84091 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.147 | 5.147 | 5.147 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 -3538.2665 -3538.2665 33.009222 93.456018 5.730845 13.439784 13.439784 -59.312894 54.321117 45.311129 2.6857916 733.89655 Loop time of 3.415e-06 on 1 procs for 0 steps with 1056 atoms 205.0% 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 | | 3.415e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6256.00 ave 6256 max 6256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70140.0 ave 70140 max 70140 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 140280.0 ave 140280 max 140280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140280 Ave neighs/atom = 132.84091 Neighbor list builds = 0 Dangerous builds = 0 1056 -3538.2665092362 eV 2.68579156156006 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02