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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -40.845628 0.0000000) to (20.010189 40.845628 8.9488288) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3360505 4.9014754 5.9658858 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -40.845628 0.0000000) to (20.010189 40.845628 8.9488288) create_atoms CPU = 0.001 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3360505 4.9014754 5.9658858 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -40.845628 0.0000000) to (20.010189 40.845628 8.9488288) create_atoms CPU = 0.001 seconds 612 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 5 19 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1200 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_673777079812_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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 5 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.520 | 5.520 | 5.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3802.8819 0 -3802.8819 21353.101 44 0 -3894.983 0 -3894.983 5273.5738 Loop time of 0.729256 on 1 procs for 44 steps with 1200 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 = -3802.88194435764 -3894.98035991959 -3894.98303084157 Force two-norm initial, final = 91.596605 0.17959229 Force max component initial, final = 12.294663 0.015231271 Final line search alpha, max atom move = 1.0000000 0.015231271 Iterations, force evaluations = 44 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71861 | 0.71861 | 0.71861 | 0.0 | 98.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0054112 | 0.0054112 | 0.0054112 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005239 | | | 0.72 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7002.00 ave 7002 max 7002 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: 270192.0 ave 270192 max 270192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270192 Ave neighs/atom = 225.16000 Neighbor list builds = 0 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 5 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.520 | 5.520 | 5.520 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3894.983 0 -3894.983 5273.5738 14628.27 48 0 -3895.1304 0 -3895.1304 49.078687 14686.195 Loop time of 0.050613 on 1 procs for 4 steps with 1200 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 = -3894.98303084156 -3895.12870087665 -3895.13043071854 Force two-norm initial, final = 93.058773 1.8965559 Force max component initial, final = 75.485444 1.1793424 Final line search alpha, max atom move = 0.00011525013 0.00013591937 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.048826 | 0.048826 | 0.048826 | 0.0 | 96.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030906 | 0.00030906 | 0.00030906 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001478 | | | 2.92 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 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: 268728.0 ave 268728 max 268728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268728 Ave neighs/atom = 223.94000 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 5 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.658 | 5.658 | 5.658 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3895.1304 0 -3895.1304 49.078687 Loop time of 8.064e-06 on 1 procs for 0 steps with 1200 atoms 124.0% 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 | | 8.064e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 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: 268536.0 ave 268536 max 268536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268536 Ave neighs/atom = 223.78000 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 5 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.658 | 5.658 | 5.658 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 -3895.1304 -3895.1304 20.037624 81.944167 8.9442725 49.078687 49.078687 -103.61622 129.05756 121.79471 2.3212808 670.36379 Loop time of 2.492e-06 on 1 procs for 0 steps with 1200 atoms 200.6% 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 | | 2.492e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134268.0 ave 134268 max 134268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 268536.0 ave 268536 max 268536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268536 Ave neighs/atom = 223.78000 Neighbor list builds = 0 Dangerous builds = 0 1200 -3895.13043071854 eV 2.32128083293392 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01