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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -81.094997 0.0000000) to (46.820218 81.094997 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2892830 6.4553231 7.0055407 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -81.094997 0.0000000) to (46.820218 81.094997 7.0055407) create_atoms CPU = 0.011 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2892830 6.4553231 7.0055407 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.094997 0.0000000) to (46.820218 81.094997 7.0055407) create_atoms CPU = 0.011 seconds 1610 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 49 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3218 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.835 | 5.835 | 5.835 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10551.792 0 -10551.792 14659.372 128 0 -10787.416 0 -10787.416 3482.7463 Loop time of 55.4715 on 1 procs for 128 steps with 3218 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 = -10551.7924931324 -10787.4055545302 -10787.4162381316 Force two-norm initial, final = 202.69900 0.27902569 Force max component initial, final = 35.080001 0.053086469 Final line search alpha, max atom move = 1.0000000 0.053086469 Iterations, force evaluations = 128 215 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 55.098 | 55.098 | 55.098 | 0.0 | 99.33 Neigh | 0.24511 | 0.24511 | 0.24511 | 0.0 | 0.44 Comm | 0.054403 | 0.054403 | 0.054403 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0744 | | | 0.13 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9111.00 ave 9111 max 9111 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: 249468.0 ave 249468 max 249468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249468 Ave neighs/atom = 77.522685 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 128 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.824 | 5.824 | 5.824 Mbytes Step Temp E_pair E_mol TotEng Press Volume 128 0 -10787.416 0 -10787.416 3482.7463 53198.471 134 0 -10787.961 0 -10787.961 -185.46329 53443.609 Loop time of 1.99517 on 1 procs for 6 steps with 3218 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 = -10787.4162381316 -10787.9522595068 -10787.9610184592 Force two-norm initial, final = 228.67360 10.997720 Force max component initial, final = 204.65348 7.3799251 Final line search alpha, max atom move = 5.4257286e-05 0.00040041471 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.986 | 1.986 | 1.986 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015439 | 0.0015439 | 0.0015439 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007617 | | | 0.38 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8726.00 ave 8726 max 8726 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: 249528.0 ave 249528 max 249528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249528 Ave neighs/atom = 77.541330 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.962 | 5.962 | 5.962 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10787.961 0 -10787.961 -185.46329 Loop time of 6.976e-06 on 1 procs for 0 steps with 3218 atoms 215.0% 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 | | 6.976e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8726.00 ave 8726 max 8726 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: 249432.0 ave 249432 max 249432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249432 Ave neighs/atom = 77.511498 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.962 | 5.962 | 5.962 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 -10787.961 -10787.961 46.814737 163.13244 6.9979824 -185.46329 -185.46329 -221.21557 -125.45153 -209.72275 2.5291447 1156.0405 Loop time of 6.636e-06 on 1 procs for 0 steps with 3218 atoms 286.3% 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 | | 6.636e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8726.00 ave 8726 max 8726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124716.0 ave 124716 max 124716 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 249432.0 ave 249432 max 249432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249432 Ave neighs/atom = 77.511498 Neighbor list builds = 0 Dangerous builds = 0 3218 -10787.9610184592 eV 2.52914467973545 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:59