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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -62.609227 0.0000000) to (31.304614 62.609227 3.6390874) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0764238 5.0764238 3.6390874 Created 591 atoms using lattice units in orthogonal box = (0.0000000 -62.609227 0.0000000) to (31.304614 62.609227 3.6390874) create_atoms CPU = 0.001 seconds 591 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0764238 5.0764238 3.6390874 Created 593 atoms using lattice units in orthogonal box = (0.0000000 -62.609227 0.0000000) to (31.304614 62.609227 3.6390874) create_atoms CPU = 0.001 seconds 593 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 27 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1184 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_609260676108_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.905 | 5.905 | 5.905 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3745.2474 0 -3745.2474 48729.58 55 0 -3876.3058 0 -3876.3058 4410.9378 Loop time of 2.0366 on 1 procs for 55 steps with 1184 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 = -3745.24743802266 -3876.3021062857 -3876.30575017891 Force two-norm initial, final = 293.41175 0.16246768 Force max component initial, final = 69.731804 0.013923014 Final line search alpha, max atom move = 1.0000000 0.013923014 Iterations, force evaluations = 55 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9981 | 1.9981 | 1.9981 | 0.0 | 98.11 Neigh | 0.019179 | 0.019179 | 0.019179 | 0.0 | 0.94 Comm | 0.011759 | 0.011759 | 0.011759 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007541 | | | 0.37 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12408.0 ave 12408 max 12408 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: 376788.0 ave 376788 max 376788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376788 Ave neighs/atom = 318.23311 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.897 | 5.897 | 5.897 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3876.3058 0 -3876.3058 4410.9378 14264.914 60 0 -3876.454 0 -3876.454 -269.7698 14311.43 Loop time of 0.175512 on 1 procs for 5 steps with 1184 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 = -3876.30575017891 -3876.45195286278 -3876.45400748375 Force two-norm initial, final = 82.853439 6.6793351 Force max component initial, final = 76.638490 5.5792518 Final line search alpha, max atom move = 0.00011748141 0.00065545838 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17133 | 0.17133 | 0.17133 | 0.0 | 97.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077116 | 0.00077116 | 0.00077116 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003412 | | | 1.94 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12028.0 ave 12028 max 12028 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: 376930.0 ave 376930 max 376930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376930 Ave neighs/atom = 318.35304 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.034 | 6.034 | 6.034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3876.454 0 -3876.454 -269.7698 Loop time of 1.789e-06 on 1 procs for 0 steps with 1184 atoms 167.7% 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 | | 1.789e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12010.0 ave 12010 max 12010 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: 376714.0 ave 376714 max 376714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376714 Ave neighs/atom = 318.17061 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.034 | 6.034 | 6.034 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 -3876.454 -3876.454 31.285453 125.76175 3.6374082 -269.7698 -269.7698 183.61903 -368.61478 -624.31366 2.281117 307.97878 Loop time of 2.471e-06 on 1 procs for 0 steps with 1184 atoms 202.3% 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 | | 2.471e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12010.0 ave 12010 max 12010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 188357.0 ave 188357 max 188357 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 376714.0 ave 376714 max 376714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376714 Ave neighs/atom = 318.17061 Neighbor list builds = 0 Dangerous builds = 0 1184 -3876.45400748375 eV 2.28111702075756 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02