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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -48.904129 0.0000000) to (59.890124 48.904129 9.9130839) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7428886 6.0287772 6.6087226 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.904129 0.0000000) to (59.890124 48.904129 9.9130839) create_atoms CPU = 0.002 seconds 1755 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7428886 6.0287772 6.6087226 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.904129 0.0000000) to (59.890124 48.904129 9.9130839) create_atoms CPU = 0.002 seconds 1755 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 17 28 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 42 atoms, new total = 3468 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 17 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 6.074 | 6.074 | 6.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11523.971 0 -11523.971 4061.2635 109 0 -11625.995 0 -11625.995 -5184.4267 Loop time of 27.2135 on 1 procs for 109 steps with 3468 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 = -11523.9710575118 -11625.9862549195 -11625.995350525 Force two-norm initial, final = 54.046515 0.28426656 Force max component initial, final = 6.5537361 0.077829318 Final line search alpha, max atom move = 0.97005816 0.075498965 Iterations, force evaluations = 109 204 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.124 | 27.124 | 27.124 | 0.0 | 99.67 Neigh | 0.042312 | 0.042312 | 0.042312 | 0.0 | 0.16 Comm | 0.017501 | 0.017501 | 0.017501 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02983 | | | 0.11 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8486.00 ave 8486 max 8486 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: 295470.0 ave 295470 max 295470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295470 Ave neighs/atom = 85.198962 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 17 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.083 | 6.083 | 6.083 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -11625.995 0 -11625.995 -5184.4267 58068.354 113 0 -11626.481 0 -11626.481 -834.07789 57741.802 Loop time of 0.796947 on 1 procs for 4 steps with 3468 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 = -11625.995350525 -11626.4763323831 -11626.4812279462 Force two-norm initial, final = 244.51090 10.816214 Force max component initial, final = 190.26847 10.773191 Final line search alpha, max atom move = 5.1870771e-05 0.00055881372 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79389 | 0.79389 | 0.79389 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004056 | 0.0004056 | 0.0004056 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002648 | | | 0.33 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8768.00 ave 8768 max 8768 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: 295780.0 ave 295780 max 295780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295780 Ave neighs/atom = 85.288351 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 17 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 6.221 | 6.221 | 6.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11626.481 0 -11626.481 -834.07789 Loop time of 1.906e-06 on 1 procs for 0 steps with 3468 atoms 262.3% 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 | | 1.906e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8818.00 ave 8818 max 8818 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: 296180.0 ave 296180 max 296180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296180 Ave neighs/atom = 85.403691 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 17 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 6.221 | 6.221 | 6.221 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 -11626.481 -11626.481 59.762646 97.808257 9.8783633 -834.07789 -834.07789 298.2902 -2825.5218 24.997912 2.4492376 2176.3422 Loop time of 2.075e-06 on 1 procs for 0 steps with 3468 atoms 192.8% 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 | | 2.075e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8818.00 ave 8818 max 8818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148090.0 ave 148090 max 148090 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 296180.0 ave 296180 max 296180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296180 Ave neighs/atom = 85.403691 Neighbor list builds = 0 Dangerous builds = 0 3468 -11626.4812279462 eV 2.44923760787437 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:28