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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -67.305620 0.0000000) to (38.858918 67.305620 6.0935645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7332830 5.1490638 6.0935645 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.305620 0.0000000) to (38.858918 67.305620 6.0935645) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7332830 5.1490638 6.0935645 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.305620 0.0000000) to (38.858918 67.305620 6.0935645) create_atoms CPU = 0.008 seconds 1466 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 29 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_149104665840_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 29 2 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) = 12.50 | 12.50 | 12.50 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11422.86 0 -11422.86 106529.57 119 0 -12792.019 0 -12792.019 4358.9784 Loop time of 27.1122 on 1 procs for 119 steps with 2926 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 = -11422.8603773892 -12792.0069469308 -12792.0190761588 Force two-norm initial, final = 2454.0694 0.37428129 Force max component initial, final = 753.18217 0.070355723 Final line search alpha, max atom move = 0.79541793 0.055962204 Iterations, force evaluations = 119 213 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.623 | 26.623 | 26.623 | 0.0 | 98.20 Neigh | 0.33454 | 0.33454 | 0.33454 | 0.0 | 1.23 Comm | 0.088092 | 0.088092 | 0.088092 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06672 | | | 0.25 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17010.0 ave 17010 max 17010 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: 963996.0 ave 963996 max 963996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 963996 Ave neighs/atom = 329.45865 Neighbor list builds = 3 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 = 9 29 2 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 : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.51 | 12.51 | 12.51 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -12792.019 0 -12792.019 4358.9784 31874.505 122 0 -12792.165 0 -12792.165 -1.9925896 31954.523 Loop time of 0.91669 on 1 procs for 3 steps with 2926 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 = -12792.0190761588 -12792.1607327011 -12792.1647726825 Force two-norm initial, final = 159.36020 0.45595342 Force max component initial, final = 125.33109 0.13011991 Final line search alpha, max atom move = 4.3411100e-05 5.6486486e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90561 | 0.90561 | 0.90561 | 0.0 | 98.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026649 | 0.0026649 | 0.0026649 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008416 | | | 0.92 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17014.0 ave 17014 max 17014 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: 952444.0 ave 952444 max 952444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 952444 Ave neighs/atom = 325.51059 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 = 9 29 2 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) = 12.02 | 12.02 | 12.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12792.165 0 -12792.165 -1.9925896 Loop time of 8.249e-06 on 1 procs for 0 steps with 2926 atoms 194.0% 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 | | 8.249e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16994.0 ave 16994 max 16994 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: 947244.0 ave 947244 max 947244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 947244 Ave neighs/atom = 323.73342 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 = 9 29 2 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) = 12.02 | 12.02 | 12.02 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 -12792.165 -12792.165 38.854154 134.86069 6.0983102 -1.9925896 -1.9925896 -6.4376355 -6.069332 6.5291986 2.1776075 780.86949 Loop time of 3.7075e-05 on 1 procs for 0 steps with 2926 atoms 67.4% 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 | | 3.708e-05 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16994.0 ave 16994 max 16994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 473622.0 ave 473622 max 473622 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 947244.0 ave 947244 max 947244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 947244 Ave neighs/atom = 323.73342 Neighbor list builds = 0 Dangerous builds = 0 2926 -12792.1647726825 eV 2.17760745820109 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30