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 = 4.0816549 4.0816549 4.0816549 Created orthogonal box = (0.0000000 -47.599867 0.0000000) to (23.799934 47.599867 4.0816549) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5999844 5.5999844 4.0816549 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -47.599867 0.0000000) to (23.799934 47.599867 4.0816549) create_atoms CPU = 0.002 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5999844 5.5999844 4.0816549 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -47.599867 0.0000000) to (23.799934 47.599867 4.0816549) create_atoms CPU = 0.001 seconds 274 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 16 1 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 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_049243498555_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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.351 | 5.351 | 5.351 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1889.2381 0 -1889.2381 14367.179 53 0 -1942.8639 0 -1942.8639 5120.9589 Loop time of 3.47921 on 1 procs for 53 steps with 544 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 = -1889.23809853484 -1942.86259882495 -1942.86391401336 Force two-norm initial, final = 85.160705 0.074611922 Force max component initial, final = 23.859002 0.010921631 Final line search alpha, max atom move = 1.0000000 0.010921631 Iterations, force evaluations = 53 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3907 | 3.3907 | 3.3907 | 0.0 | 97.46 Neigh | 0.058358 | 0.058358 | 0.058358 | 0.0 | 1.68 Comm | 0.020347 | 0.020347 | 0.020347 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009809 | | | 0.28 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9102.00 ave 9102 max 9102 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: 232324.0 ave 232324 max 232324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232324 Ave neighs/atom = 427.06618 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.351 | 5.351 | 5.351 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1942.8639 0 -1942.8639 5120.9589 9247.9988 62 0 -1943.0422 0 -1943.0422 -80.172115 9300.2082 Loop time of 0.413862 on 1 procs for 9 steps with 544 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 = -1942.86391401336 -1943.04213910589 -1943.04222946156 Force two-norm initial, final = 57.330996 1.0288796 Force max component initial, final = 50.450970 0.97045314 Final line search alpha, max atom move = 0.0012052352 0.0011696243 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40589 | 0.40589 | 0.40589 | 0.0 | 98.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002185 | 0.002185 | 0.002185 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005786 | | | 1.40 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9081.00 ave 9081 max 9081 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: 232200.0 ave 232200 max 232200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232200 Ave neighs/atom = 426.83824 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.489 | 5.489 | 5.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1943.0422 0 -1943.0422 -80.172115 Loop time of 7.076e-06 on 1 procs for 0 steps with 544 atoms 226.1% 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 | | 7.076e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9081.00 ave 9081 max 9081 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: 231712.0 ave 231712 max 231712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231712 Ave neighs/atom = 425.94118 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.489 | 5.489 | 5.489 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 -1943.0422 -1943.0422 23.772221 95.97076 4.0764674 -80.172115 -80.172115 -37.313858 -36.231913 -166.97058 2.5643417 349.08206 Loop time of 7.036e-06 on 1 procs for 0 steps with 544 atoms 241.6% 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 | | 7.036e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9081.00 ave 9081 max 9081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115856.0 ave 115856 max 115856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 231712.0 ave 231712 max 231712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231712 Ave neighs/atom = 425.94118 Neighbor list builds = 0 Dangerous builds = 0 544 -1943.04222946156 eV 2.56434172427072 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04