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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -61.308722 0.0000000) to (30.654361 61.308722 4.2107003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2054575 5.2054575 4.2107003 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -61.308722 0.0000000) to (30.654361 61.308722 4.2107003) create_atoms CPU = 0.002 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2054575 5.2054575 4.2107003 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -61.308722 0.0000000) to (30.654361 61.308722 4.2107003) create_atoms CPU = 0.001 seconds 426 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 28 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 850 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_878712978062_003#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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.993 | 4.993 | 4.993 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3023.3031 0 -3023.3031 40685.073 41 0 -3164.0171 0 -3164.0171 3136.2362 Loop time of 1.7411 on 1 procs for 41 steps with 850 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 = -3023.30308209884 -3164.01405012442 -3164.01712778042 Force two-norm initial, final = 551.98442 0.10315431 Force max component initial, final = 229.41256 0.032731490 Final line search alpha, max atom move = 1.0000000 0.032731490 Iterations, force evaluations = 41 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7025 | 1.7025 | 1.7025 | 0.0 | 97.78 Neigh | 0.019155 | 0.019155 | 0.019155 | 0.0 | 1.10 Comm | 0.010835 | 0.010835 | 0.010835 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008645 | | | 0.50 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6855.00 ave 6855 max 6855 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: 147540.0 ave 147540 max 147540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147540 Ave neighs/atom = 173.57647 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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.993 | 4.993 | 4.993 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3164.0171 0 -3164.0171 3136.2362 15827.009 53 0 -3164.278 0 -3164.278 -9.4944163 15951.103 Loop time of 0.380714 on 1 procs for 12 steps with 850 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 = -3164.01712778042 -3164.27770612782 -3164.27803784187 Force two-norm initial, final = 59.854917 0.26164911 Force max component initial, final = 52.569052 0.11945912 Final line search alpha, max atom move = 0.00098584741 0.00011776846 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35207 | 0.35207 | 0.35207 | 0.0 | 92.48 Neigh | 0.019149 | 0.019149 | 0.019149 | 0.0 | 5.03 Comm | 0.0023758 | 0.0023758 | 0.0023758 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007116 | | | 1.87 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6860.00 ave 6860 max 6860 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: 146668.0 ave 146668 max 146668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146668 Ave neighs/atom = 172.55059 Neighbor list builds = 1 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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.131 | 5.131 | 5.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3164.278 0 -3164.278 -9.4944163 Loop time of 6.374e-06 on 1 procs for 0 steps with 850 atoms 188.3% 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 | | 6.374e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6865.00 ave 6865 max 6865 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: 146560.0 ave 146560 max 146560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146560 Ave neighs/atom = 172.42353 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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.131 | 5.131 | 5.131 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 -3164.278 -3164.278 30.607246 124.02043 4.2021665 -9.4944163 -9.4944163 -11.019789 -12.136121 -5.3273386 2.712054 575.26118 Loop time of 7.378e-06 on 1 procs for 0 steps with 850 atoms 216.9% 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 | | 7.378e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6865.00 ave 6865 max 6865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73280.0 ave 73280 max 73280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146560.0 ave 146560 max 146560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146560 Ave neighs/atom = 172.42353 Neighbor list builds = 0 Dangerous builds = 0 850 -3164.27803784187 eV 2.71205404778537 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03