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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -43.626830 0.0000000) to (14.542277 43.626830 4.0333018) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5931833 5.5931833 4.0333018 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -43.626830 0.0000000) to (14.542277 43.626830 4.0333018) create_atoms CPU = 0.001 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5931833 5.5931833 4.0333018 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -43.626830 0.0000000) to (14.542277 43.626830 4.0333018) create_atoms CPU = 0.000 seconds 158 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -983.9246 0 -983.9246 33462.952 90 0 -1047.8017 0 -1047.8017 6274.0538 Loop time of 0.669527 on 1 procs for 90 steps with 312 atoms 76.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -983.924597539745 -1047.80079911588 -1047.80170374739 Force two-norm initial, final = 136.59436 0.064108204 Force max component initial, final = 41.028174 0.0086501762 Final line search alpha, max atom move = 1.0000000 0.0086501762 Iterations, force evaluations = 90 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65513 | 0.65513 | 0.65513 | 0.0 | 97.85 Neigh | 0.0059723 | 0.0059723 | 0.0059723 | 0.0 | 0.89 Comm | 0.0050608 | 0.0050608 | 0.0050608 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00336 | | | 0.50 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3733.00 ave 3733 max 3733 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: 45972.0 ave 45972 max 45972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45972 Ave neighs/atom = 147.34615 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -1047.8017 0 -1047.8017 6274.0538 5117.723 101 0 -1047.9659 0 -1047.9659 62.130803 5155.943 Loop time of 0.0471379 on 1 procs for 11 steps with 312 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1047.80170374739 -1047.96590030261 -1047.96593595096 Force two-norm initial, final = 40.051250 0.39293022 Force max component initial, final = 36.340560 0.20973234 Final line search alpha, max atom move = 0.0032224907 0.00067586051 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044853 | 0.044853 | 0.044853 | 0.0 | 95.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043651 | 0.00043651 | 0.00043651 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001848 | | | 3.92 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3743.00 ave 3743 max 3743 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: 45408.0 ave 45408 max 45408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45408 Ave neighs/atom = 145.53846 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1047.9659 0 -1047.9659 62.130803 Loop time of 1.675e-06 on 1 procs for 0 steps with 312 atoms 179.1% 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 | | 1.675e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3743.00 ave 3743 max 3743 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: 44168.0 ave 44168 max 44168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44168 Ave neighs/atom = 141.56410 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.595 | 4.595 | 4.595 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 -1047.9659 -1047.9659 14.534835 88.130243 4.0250663 62.130803 62.130803 65.139639 65.246654 56.006116 2.5979359 201.05659 Loop time of 1.512e-06 on 1 procs for 0 steps with 312 atoms 132.3% 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 | | 1.512e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3743.00 ave 3743 max 3743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22084.0 ave 22084 max 22084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44168.0 ave 44168 max 44168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44168 Ave neighs/atom = 141.56410 Neighbor list builds = 0 Dangerous builds = 0 312 -1047.96593595096 eV 2.59793587996802 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01