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 -43.758881 0.0000000) to (30.942202 43.758881 5.9548295) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8760448 5.6724476 5.9548295 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -43.758881 0.0000000) to (30.942202 43.758881 5.9548295) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8760448 5.6724476 5.9548295 Created 440 atoms using lattice units in orthogonal box = (0.0000000 -43.758881 0.0000000) to (30.942202 43.758881 5.9548295) create_atoms CPU = 0.001 seconds 440 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 20 2 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 = 872 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 20 2 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) = 4.978 | 4.978 | 4.978 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2413.4313 0 -2413.4313 220421.46 60 0 -3246.5114 0 -3246.5114 5876.134 Loop time of 1.36077 on 1 procs for 60 steps with 872 atoms 92.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2413.43128357514 -3246.50852102481 -3246.51141441842 Force two-norm initial, final = 2128.5851 0.096737249 Force max component initial, final = 335.83681 0.0075525248 Final line search alpha, max atom move = 1.0000000 0.0075525248 Iterations, force evaluations = 60 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3406 | 1.3406 | 1.3406 | 0.0 | 98.52 Neigh | 0.0083142 | 0.0083142 | 0.0083142 | 0.0 | 0.61 Comm | 0.006151 | 0.006151 | 0.006151 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005703 | | | 0.42 Nlocal: 872.000 ave 872 max 872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5773.00 ave 5773 max 5773 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: 150896.0 ave 150896 max 150896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150896 Ave neighs/atom = 173.04587 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 20 2 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.981 | 4.981 | 4.981 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -3246.5114 0 -3246.5114 5876.134 16125.632 73 0 -3247.0477 0 -3247.0477 25.797796 16346.958 Loop time of 0.176636 on 1 procs for 13 steps with 872 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 = -3246.51141441843 -3247.04667220072 -3247.04772888013 Force two-norm initial, final = 106.10779 0.57404106 Force max component initial, final = 81.675516 0.41174941 Final line search alpha, max atom move = 0.00056094333 0.00023096808 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16355 | 0.16355 | 0.16355 | 0.0 | 92.59 Neigh | 0.0087461 | 0.0087461 | 0.0087461 | 0.0 | 4.95 Comm | 0.00087871 | 0.00087871 | 0.00087871 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003463 | | | 1.96 Nlocal: 872.000 ave 872 max 872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6120.00 ave 6120 max 6120 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: 149152.0 ave 149152 max 149152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149152 Ave neighs/atom = 171.04587 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 20 2 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) = 5.118 | 5.118 | 5.118 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3247.0477 0 -3247.0477 25.797796 Loop time of 1.73e-06 on 1 procs for 0 steps with 872 atoms 173.4% 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 | | 1.73e-06 | | |100.00 Nlocal: 872.000 ave 872 max 872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6087.00 ave 6087 max 6087 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: 149168.0 ave 149168 max 149168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149168 Ave neighs/atom = 171.06422 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 20 2 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) = 5.118 | 5.118 | 5.118 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 -3247.0477 -3247.0477 30.942374 88.630636 5.9607299 25.797796 25.797796 40.356065 24.22518 12.812143 2.806599 1805.5321 Loop time of 1.473e-06 on 1 procs for 0 steps with 872 atoms 203.7% 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 | | 1.473e-06 | | |100.00 Nlocal: 872.000 ave 872 max 872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6087.00 ave 6087 max 6087 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74584.0 ave 74584 max 74584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149168.0 ave 149168 max 149168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149168 Ave neighs/atom = 171.06422 Neighbor list builds = 0 Dangerous builds = 0 872 -3247.04772888013 eV 2.80659895501048 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02