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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -58.674285 0.0000000) to (20.744492 58.674285 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6575889 6.2230303 5.1069410 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.674285 0.0000000) to (20.744492 58.674285 5.1069410) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6575889 6.2230303 5.1069410 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.674285 0.0000000) to (20.744492 58.674285 5.1069410) 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 44 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4402.8381 0 -4402.8381 24200.779 37 0 -4485.9705 0 -4485.9705 6106.013 Loop time of 3.85232 on 1 procs for 37 steps with 1058 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4402.83811822963 -4485.96677227757 -4485.97049217626 Force two-norm initial, final = 121.96347 0.26836578 Force max component initial, final = 37.578671 0.053911538 Final line search alpha, max atom move = 1.0000000 0.053911538 Iterations, force evaluations = 37 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8442 | 3.8442 | 3.8442 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033662 | 0.0033662 | 0.0033662 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004739 | | | 0.12 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4198.00 ave 4198 max 4198 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: 57268.0 ave 57268 max 57268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57268 Ave neighs/atom = 54.128544 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -4485.9705 0 -4485.9705 6106.013 12432.013 42 0 -4486.1653 0 -4486.1653 149.48842 12476.436 Loop time of 0.393379 on 1 procs for 5 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 = -4485.97049217626 -4486.16432253028 -4486.16532721212 Force two-norm initial, final = 100.63022 2.1690536 Force max component initial, final = 94.736967 1.5690430 Final line search alpha, max atom move = 0.00027559323 0.00043241762 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39165 | 0.39165 | 0.39165 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024132 | 0.00024132 | 0.00024132 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001483 | | | 0.38 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4181.00 ave 4181 max 4181 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: 57084.0 ave 57084 max 57084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57084 Ave neighs/atom = 53.954631 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.507 | 5.507 | 5.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4486.1653 0 -4486.1653 149.48842 Loop time of 2.196e-06 on 1 procs for 0 steps with 1058 atoms 182.1% 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 | | 2.196e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4181.00 ave 4181 max 4181 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: 57064.0 ave 57064 max 57064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57064 Ave neighs/atom = 53.935728 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.507 | 5.507 | 5.507 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 -4486.1653 -4486.1653 20.740678 117.84336 5.104609 149.48842 149.48842 73.13174 202.3401 172.99342 2.3008424 320.82337 Loop time of 2.301e-06 on 1 procs for 0 steps with 1058 atoms 217.3% 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 | | 2.301e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4181.00 ave 4181 max 4181 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28532.0 ave 28532 max 28532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57064.0 ave 57064 max 57064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57064 Ave neighs/atom = 53.935728 Neighbor list builds = 0 Dangerous builds = 0 1058 -4486.16532721212 eV 2.30084236524181 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04