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 = 3.6406460 3.6406460 3.6406460 Created orthogonal box = (0.0000000 -56.868709 0.0000000) to (28.434354 56.868709 3.6406460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1275065 5.1275065 3.6406460 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.868709 0.0000000) to (28.434354 56.868709 3.6406460) create_atoms CPU = 0.003 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1275065 5.1275065 3.6406460 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.868709 0.0000000) to (28.434354 56.868709 3.6406460) create_atoms CPU = 0.002 seconds 490 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_945018740343_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 = 6 24 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) = 5.844 | 5.844 | 5.844 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2964.521 0 -2964.521 81524.575 64 0 -3197.0097 0 -3197.0097 7232.881 Loop time of 9.71036 on 1 procs for 64 steps with 978 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 = -2964.52104422108 -3197.00669657143 -3197.00973618297 Force two-norm initial, final = 502.06864 0.14223620 Force max component initial, final = 109.05125 0.010390938 Final line search alpha, max atom move = 1.0000000 0.010390938 Iterations, force evaluations = 64 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.628 | 9.628 | 9.628 | 0.0 | 99.15 Neigh | 0.038363 | 0.038363 | 0.038363 | 0.0 | 0.40 Comm | 0.028122 | 0.028122 | 0.028122 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01585 | | | 0.16 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11432.0 ave 11432 max 11432 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: 311544.0 ave 311544 max 311544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311544 Ave neighs/atom = 318.55215 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 = 6 24 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.847 | 5.847 | 5.847 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -3197.0097 0 -3197.0097 7232.881 11774.031 71 0 -3197.2656 0 -3197.2656 352.41541 11830.175 Loop time of 0.804703 on 1 procs for 7 steps with 978 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 = -3197.00973618299 -3197.26386231382 -3197.26563042234 Force two-norm initial, final = 104.28240 5.6183964 Force max component initial, final = 92.706737 4.4721588 Final line search alpha, max atom move = 0.00012426760 0.00055574446 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79592 | 0.79592 | 0.79592 | 0.0 | 98.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021456 | 0.0021456 | 0.0021456 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006642 | | | 0.83 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11446.0 ave 11446 max 11446 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: 311840.0 ave 311840 max 311840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311840 Ave neighs/atom = 318.85481 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 = 6 24 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) = 5.985 | 5.985 | 5.985 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3197.2656 0 -3197.2656 352.41541 Loop time of 6.385e-06 on 1 procs for 0 steps with 978 atoms 187.9% 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 | | 6.385e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11446.0 ave 11446 max 11446 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: 311500.0 ave 311500 max 311500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311500 Ave neighs/atom = 318.50716 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 = 6 24 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) = 5.985 | 5.985 | 5.985 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 -3197.2656 -3197.2656 28.450019 114.40116 3.6347803 352.41541 352.41541 606.00415 462.24733 -11.005253 2.2829482 155.04805 Loop time of 6.515e-06 on 1 procs for 0 steps with 978 atoms 307.0% 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 | | 6.515e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11446.0 ave 11446 max 11446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155750.0 ave 155750 max 155750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 311500.0 ave 311500 max 311500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311500 Ave neighs/atom = 318.50716 Neighbor list builds = 0 Dangerous builds = 0 978 -3197.26563042234 eV 2.28294823174636 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11