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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -58.811065 0.0000000) to (29.405532 58.811065 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0715352 4.0715352 3.6473074 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.811065 0.0000000) to (29.405532 58.811065 3.6473074) create_atoms CPU = 0.003 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0715352 4.0715352 3.6473074 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.811065 0.0000000) to (29.405532 58.811065 3.6473074) create_atoms CPU = 0.002 seconds 522 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 1042 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_608695023236_000#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.352 | 5.352 | 5.352 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3670.6298 0 -3670.6298 127764.16 70 0 -4310.4947 0 -4310.4947 7813.0694 Loop time of 17.7614 on 1 procs for 70 steps with 1042 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 = -3670.62983605692 -4310.49048064949 -4310.49472058546 Force two-norm initial, final = 1368.1652 0.29266299 Force max component initial, final = 510.39607 0.074953558 Final line search alpha, max atom move = 1.0000000 0.074953558 Iterations, force evaluations = 70 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.681 | 17.681 | 17.681 | 0.0 | 99.55 Neigh | 0.048162 | 0.048162 | 0.048162 | 0.0 | 0.27 Comm | 0.01601 | 0.01601 | 0.01601 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01641 | | | 0.09 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5097.00 ave 5097 max 5097 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: 56000.0 ave 56000 max 56000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56000 Ave neighs/atom = 53.742802 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.346 | 5.346 | 5.346 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -4310.4947 0 -4310.4947 7813.0694 12615.093 75 0 -4310.6712 0 -4310.6712 133.8908 12673.813 Loop time of 1.12451 on 1 procs for 5 steps with 1042 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 = -4310.49472058546 -4310.6682140315 -4310.67118028768 Force two-norm initial, final = 108.16524 1.9221703 Force max component initial, final = 76.683233 1.2951443 Final line search alpha, max atom move = 6.5200770e-05 8.4444408e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1207 | 1.1207 | 1.1207 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076647 | 0.00076647 | 0.00076647 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003062 | | | 0.27 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4376.00 ave 4376 max 4376 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: 56068.0 ave 56068 max 56068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56068 Ave neighs/atom = 53.808061 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.484 | 5.484 | 5.484 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4310.6712 0 -4310.6712 133.8908 Loop time of 5.893e-06 on 1 procs for 0 steps with 1042 atoms 203.6% 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 | | 5.893e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4376.00 ave 4376 max 4376 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: 56056.0 ave 56056 max 56056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56056 Ave neighs/atom = 53.796545 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.484 | 5.484 | 5.484 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 -4310.6712 -4310.6712 29.408846 117.64615 3.6631239 133.8908 133.8908 163.7458 147.35704 90.569563 2.3068661 142.35456 Loop time of 6.906e-06 on 1 procs for 0 steps with 1042 atoms 275.1% 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 | | 6.906e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4376.00 ave 4376 max 4376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28028.0 ave 28028 max 28028 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56056.0 ave 56056 max 56056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56056 Ave neighs/atom = 53.796545 Neighbor list builds = 0 Dangerous builds = 0 1042 -4310.67118028768 eV 2.30686606217417 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19