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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -51.251973 0.0000000) to (25.625987 51.251973 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3515826 4.3515826 3.5200000 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -51.251973 0.0000000) to (25.625987 51.251973 3.5200000) create_atoms CPU = 0.002 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3515826 4.3515826 3.5200000 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.251973 0.0000000) to (25.625987 51.251973 3.5200000) create_atoms CPU = 0.001 seconds 426 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 24 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 8.72488399972482 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.407 | 5.407 | 5.407 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3725.6417 0 -3725.6417 11656.6 42 0 -3766.104 0 -3766.104 13243.515 Loop time of 2.2692 on 1 procs for 42 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 = -3725.64169660307 -3766.10073397492 -3766.10399364992 Force two-norm initial, final = 27.417891 0.17746891 Force max component initial, final = 4.5846987 0.021981888 Final line search alpha, max atom move = 1.0000000 0.021981888 Iterations, force evaluations = 42 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2151 | 2.2151 | 2.2151 | 0.0 | 97.62 Neigh | 0.028057 | 0.028057 | 0.028057 | 0.0 | 1.24 Comm | 0.016173 | 0.016173 | 0.016173 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009882 | | | 0.44 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9158.00 ave 9158 max 9158 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: 210084.0 ave 210084 max 210084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210084 Ave neighs/atom = 247.15765 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.407 | 5.407 | 5.407 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -3766.104 0 -3766.104 13243.515 9246.2119 49 0 -3766.4511 0 -3766.4511 142.81258 9313.8893 Loop time of 0.269355 on 1 procs for 7 steps with 850 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 = -3766.10399364992 -3766.45097788974 -3766.45110929683 Force two-norm initial, final = 135.87122 1.6607664 Force max component initial, final = 101.00198 1.2655922 Final line search alpha, max atom move = 0.00060358855 0.00076389693 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26262 | 0.26262 | 0.26262 | 0.0 | 97.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016864 | 0.0016864 | 0.0016864 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005046 | | | 1.87 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9164.00 ave 9164 max 9164 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: 210368.0 ave 210368 max 210368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210368 Ave neighs/atom = 247.49176 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.545 | 5.545 | 5.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3766.4511 0 -3766.4511 142.81258 Loop time of 6.225e-06 on 1 procs for 0 steps with 850 atoms 176.7% 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 | | 6.225e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9152.00 ave 9152 max 9152 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: 210040.0 ave 210040 max 210040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210040 Ave neighs/atom = 247.10588 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.545 | 5.545 | 5.545 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 -3766.4511 -3766.4511 25.639105 103.11671 3.5228907 142.81258 142.81258 217.81878 174.80381 35.815139 2.2203484 329.26715 Loop time of 7.137e-06 on 1 procs for 0 steps with 850 atoms 238.2% 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 | | 7.137e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9152.00 ave 9152 max 9152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105020.0 ave 105020 max 105020 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210040.0 ave 210040 max 210040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210040 Ave neighs/atom = 247.10588 Neighbor list builds = 0 Dangerous builds = 0 850 -3766.45110929683 eV 2.22034844164299 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03