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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -58.673407 0.0000000) to (20.744182 58.673407 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6575042 6.2229371 5.1068646 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.673407 0.0000000) to (20.744182 58.673407 5.1068646) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6575042 6.2229371 5.1068646 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.673407 0.0000000) to (20.744182 58.673407 5.1068646) create_atoms CPU = 0.002 seconds 530 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_179158257180_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.620 | 4.620 | 4.620 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4282.6825 0 -4282.6825 49911.689 876 0 -4513.4346 0 -4513.4346 5922.684 Loop time of 68.0645 on 1 procs for 876 steps with 1058 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 = -4282.68245500875 -4513.43021682452 -4513.43459627223 Force two-norm initial, final = 190.94480 0.20353800 Force max component initial, final = 48.603000 0.046913055 Final line search alpha, max atom move = 1.0000000 0.046913055 Iterations, force evaluations = 876 1636 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 67.656 | 67.656 | 67.656 | 0.0 | 99.40 Neigh | 0.19254 | 0.19254 | 0.19254 | 0.0 | 0.28 Comm | 0.11284 | 0.11284 | 0.11284 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.103 | | | 0.15 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5054.00 ave 5054 max 5054 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: 68330.0 ave 68330 max 68330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68330 Ave neighs/atom = 64.584121 Neighbor list builds = 31 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 876 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.621 | 4.621 | 4.621 Mbytes Step Temp E_pair E_mol TotEng Press Volume 876 0 -4513.4346 0 -4513.4346 5922.684 12431.455 905 0 -4524.9002 0 -4524.9002 -12.815526 12452.391 Loop time of 1.05822 on 1 procs for 29 steps with 1058 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 = -4513.43459627222 -4524.89805967987 -4524.90024869526 Force two-norm initial, final = 626.13422 0.71440847 Force max component initial, final = 461.06114 0.23621739 Final line search alpha, max atom move = 0.00014301473 3.3782566e-05 Iterations, force evaluations = 29 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0427 | 1.0427 | 1.0427 | 0.0 | 98.54 Neigh | 0.0058683 | 0.0058683 | 0.0058683 | 0.0 | 0.55 Comm | 0.0015828 | 0.0015828 | 0.0015828 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00805 | | | 0.76 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5100.00 ave 5100 max 5100 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: 68280.0 ave 68280 max 68280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68280 Ave neighs/atom = 64.536862 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.761 | 4.761 | 4.761 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4524.9002 0 -4524.9002 -12.815526 Loop time of 2.463e-06 on 1 procs for 0 steps with 1058 atoms 203.0% 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 | | 2.463e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5151.00 ave 5151 max 5151 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: 68264.0 ave 68264 max 68264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68264 Ave neighs/atom = 64.521739 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.761 | 4.761 | 4.761 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 -4524.9002 -4524.9002 21.065658 119.13031 4.9619849 -12.815526 -12.815526 -30.863714 1.847757 -9.4306211 2.3595436 1615.6221 Loop time of 2.665e-06 on 1 procs for 0 steps with 1058 atoms 187.6% 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 | | 2.665e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5151.00 ave 5151 max 5151 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34132.0 ave 34132 max 34132 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68264.0 ave 68264 max 68264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68264 Ave neighs/atom = 64.521739 Neighbor list builds = 0 Dangerous builds = 0 1058 -4524.90024869526 eV 2.35954358036698 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:09