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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -49.555135 0.0000000) to (13.486218 49.555135 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7798079 5.5057256 5.8858683 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.555135 0.0000000) to (13.486218 49.555135 8.8288024) create_atoms CPU = 0.001 seconds 507 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7798079 5.5057256 5.8858683 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.555135 0.0000000) to (13.486218 49.555135 8.8288024) create_atoms CPU = 0.001 seconds 507 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 33 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 999 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4201.2506 0 -4201.2506 1467.1346 62 0 -4229.0808 0 -4229.0808 -10962.23 Loop time of 3.58032 on 1 procs for 62 steps with 999 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 = -4201.25062502508 -4229.07693041539 -4229.08084635633 Force two-norm initial, final = 30.313027 0.19072779 Force max component initial, final = 7.0002664 0.047378027 Final line search alpha, max atom move = 1.0000000 0.047378027 Iterations, force evaluations = 62 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5651 | 3.5651 | 3.5651 | 0.0 | 99.57 Neigh | 0.0058309 | 0.0058309 | 0.0058309 | 0.0 | 0.16 Comm | 0.0041341 | 0.0041341 | 0.0041341 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005262 | | | 0.15 Nlocal: 999.000 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4048.00 ave 4048 max 4048 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: 77958.0 ave 77958 max 77958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77958 Ave neighs/atom = 78.036036 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.567 | 4.567 | 4.567 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -4229.0808 0 -4229.0808 -10962.23 11800.778 66 0 -4229.2105 0 -4229.2105 -4120.1887 11749.898 Loop time of 0.22831 on 1 procs for 4 steps with 999 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 = -4229.08084635633 -4229.20942298422 -4229.21050185597 Force two-norm initial, final = 80.673086 0.20361411 Force max component initial, final = 65.133330 0.051084079 Final line search alpha, max atom move = 0.00023360429 1.1933460e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22698 | 0.22698 | 0.22698 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021748 | 0.00021748 | 0.00021748 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001117 | | | 0.49 Nlocal: 999.000 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3937.00 ave 3937 max 3937 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: 77918.0 ave 77918 max 77918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77918 Ave neighs/atom = 77.995996 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.705 | 4.705 | 4.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4229.2105 0 -4229.2105 -4120.1887 Loop time of 1.695e-06 on 1 procs for 0 steps with 999 atoms 177.0% 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 | | 1.695e-06 | | |100.00 Nlocal: 999.000 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3939.00 ave 3939 max 3939 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: 77952.0 ave 77952 max 77952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77952 Ave neighs/atom = 78.030030 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.705 | 4.705 | 4.705 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 -4229.2105 -4229.2105 13.468821 99.11027 8.802091 -4120.1887 -4120.1887 -1.9755581 -12358.779 0.18813736 2.296543 465.51281 Loop time of 1.62e-06 on 1 procs for 0 steps with 999 atoms 123.5% 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 | | 1.62e-06 | | |100.00 Nlocal: 999.000 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3939.00 ave 3939 max 3939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38976.0 ave 38976 max 38976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77952.0 ave 77952 max 77952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77952 Ave neighs/atom = 78.030030 Neighbor list builds = 0 Dangerous builds = 0 999 -4229.21050185597 eV 2.29654297748158 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04