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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -44.499063 0.0000000) to (22.249532 44.499063 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5599251 3.5599251 3.1465590 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -44.499063 0.0000000) to (22.249532 44.499063 3.1465590) create_atoms CPU = 0.001 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5599251 3.5599251 3.1465590 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -44.499063 0.0000000) to (22.249532 44.499063 3.1465590) create_atoms CPU = 0.000 seconds 202 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 31 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 402 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2688.0856 0 -2688.0856 39232.748 21 0 -4531.9414 0 -4531.9414 31725.061 Loop time of 2.16453 on 1 procs for 21 steps with 402 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2688.08563427942 -4531.93790561488 -4531.94144453949 Force two-norm initial, final = 24.353657 10624.193 Force max component initial, final = 6.6204919 5381.2986 Final line search alpha, max atom move = 1.8061158e-08 9.7192486e-05 Iterations, force evaluations = 21 232 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.155 | 2.155 | 2.155 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057738 | 0.0057738 | 0.0057738 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003795 | | | 0.18 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3063.00 ave 3063 max 3063 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: 23260.0 ave 23260 max 23260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23260 Ave neighs/atom = 57.860697 Neighbor list builds = 0 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -4531.9414 0 -4531.9414 31725.061 6230.7111 25 0 -4533.0506 0 -4533.0506 30861.148 6230.7967 Loop time of 0.427448 on 1 procs for 4 steps with 402 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 = -4531.94144453946 -4533.05012052744 -4533.05064131394 Force two-norm initial, final = 10626.489 241.70014 Force max component initial, final = 5381.2986 170.02046 Final line search alpha, max atom move = 4.5875449e-08 7.7997648e-06 Iterations, force evaluations = 4 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42193 | 0.42193 | 0.42193 | 0.0 | 98.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001016 | 0.001016 | 0.001016 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004502 | | | 1.05 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3063.00 ave 3063 max 3063 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: 23320.0 ave 23320 max 23320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23320 Ave neighs/atom = 58.009950 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.570 | 4.570 | 4.570 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4533.0506 0 -4533.0506 30861.148 Loop time of 1.716e-06 on 1 procs for 0 steps with 402 atoms 116.6% 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 | | 1.716e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3063.00 ave 3063 max 3063 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: 23320.0 ave 23320 max 23320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23320 Ave neighs/atom = 58.009950 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.570 | 4.570 | 4.570 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 -4533.0506 -4533.0506 22.249624 88.998683 3.1465695 30861.148 30861.148 29146.72 43719.045 19717.678 0.0056881119 437.0904 Loop time of 2.158e-06 on 1 procs for 0 steps with 402 atoms 185.4% 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 | | 2.158e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3063.00 ave 3063 max 3063 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11660.0 ave 11660 max 11660 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23320.0 ave 23320 max 23320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23320 Ave neighs/atom = 58.009950 Neighbor list builds = 0 Dangerous builds = 0 402 -4533.05064131394 eV 0.00568811188801374 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02