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 = 3.5226425 3.5226425 3.5226425 Created orthogonal box = (0.0000000 -57.236166 0.0000000) to (20.236040 57.236166 4.9817688) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5189201 4.3360732 4.9817688 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.236166 0.0000000) to (20.236040 57.236166 4.9817688) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5189201 4.3360732 4.9817688 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.236166 0.0000000) to (20.236040 57.236166 4.9817688) create_atoms CPU = 0.001 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 20 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 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_381861218831_004#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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 7.144 | 7.144 | 7.144 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4234.2809 0 -4234.2809 43816.314 199 0 -4462.1865 0 -4462.1865 4546.7106 Loop time of 11.8396 on 1 procs for 199 steps with 1056 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4234.28094680118 -4462.18275434801 -4462.18648440296 Force two-norm initial, final = 348.24504 0.27888225 Force max component initial, final = 93.588297 0.036227769 Final line search alpha, max atom move = 0.80968849 0.029333207 Iterations, force evaluations = 199 362 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.607 | 11.607 | 11.607 | 0.0 | 98.04 Neigh | 0.13398 | 0.13398 | 0.13398 | 0.0 | 1.13 Comm | 0.067658 | 0.067658 | 0.067658 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03087 | | | 0.26 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14752.0 ave 14752 max 14752 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: 658112.0 ave 658112 max 658112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 658112 Ave neighs/atom = 623.21212 Neighbor list builds = 4 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 199 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.146 | 7.146 | 7.146 Mbytes Step Temp E_pair E_mol TotEng Press Volume 199 0 -4462.1865 0 -4462.1865 4546.7106 11540.102 201 0 -4462.2357 0 -4462.2357 -117.32173 11568.982 Loop time of 0.129312 on 1 procs for 2 steps with 1056 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 = -4462.18648440292 -4462.23174424665 -4462.23566703366 Force two-norm initial, final = 59.154885 6.0005516 Force max component initial, final = 40.805425 5.5537246 Final line search alpha, max atom move = 0.00014152469 0.00078598915 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12699 | 0.12699 | 0.12699 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049394 | 0.00049394 | 0.00049394 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001828 | | | 1.41 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14792.0 ave 14792 max 14792 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: 657900.0 ave 657900 max 657900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657900 Ave neighs/atom = 623.01136 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 7.284 | 7.284 | 7.284 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4462.2357 0 -4462.2357 -117.32173 Loop time of 2.44e-06 on 1 procs for 0 steps with 1056 atoms 204.9% 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 | | 2.44e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14792.0 ave 14792 max 14792 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: 657332.0 ave 657332 max 657332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657332 Ave neighs/atom = 622.47348 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 7.284 | 7.284 | 7.284 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 -4462.2357 -4462.2357 20.234391 114.64914 4.9869405 -117.32173 -117.32173 137.07998 280.88297 -769.92813 2.3248351 682.21793 Loop time of 2.826e-06 on 1 procs for 0 steps with 1056 atoms 247.7% 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 | | 2.826e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14792.0 ave 14792 max 14792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 328666.0 ave 328666 max 328666 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 657332.0 ave 657332 max 657332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657332 Ave neighs/atom = 622.47348 Neighbor list builds = 0 Dangerous builds = 0 1056 -4462.23566703366 eV 2.32483513232899 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12