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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -73.268508 0.0000000) to (25.902899 73.268508 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9495584 6.2542834 5.7209934 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -73.268508 0.0000000) to (25.902899 73.268508 5.7209934) create_atoms CPU = 0.002 seconds 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9495584 6.2542834 5.7209934 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -73.268508 0.0000000) to (25.902899 73.268508 5.7209934) create_atoms CPU = 0.001 seconds 658 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 9 47 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 9 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.664 | 4.664 | 4.664 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4360.3479 0 -4360.3479 564.42533 19 0 -4373.6703 0 -4373.6703 -2169.4743 Loop time of 1.12993 on 1 procs for 19 steps with 1304 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4360.34792094123 -4373.6671944066 -4373.6702511131 Force two-norm initial, final = 15.767065 0.58439890 Force max component initial, final = 4.2942430 0.22408493 Final line search alpha, max atom move = 0.82227714 0.18425991 Iterations, force evaluations = 19 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.126 | 1.126 | 1.126 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013788 | 0.0013788 | 0.0013788 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00254 | | | 0.22 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4948.00 ave 4948 max 4948 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: 70384.0 ave 70384 max 70384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70384 Ave neighs/atom = 53.975460 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 9 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -4373.6703 0 -4373.6703 -2169.4743 21715.367 22 0 -4373.7117 0 -4373.7117 -206.30833 21656.938 Loop time of 0.247335 on 1 procs for 3 steps with 1304 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 = -4373.6702511131 -4373.71140320692 -4373.71171321057 Force two-norm initial, final = 42.427486 0.59390532 Force max component initial, final = 32.654544 0.21650974 Final line search alpha, max atom move = 0.00061595339 0.00013335991 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24555 | 0.24555 | 0.24555 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025493 | 0.00025493 | 0.00025493 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001535 | | | 0.62 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4954.00 ave 4954 max 4954 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: 70548.0 ave 70548 max 70548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70548 Ave neighs/atom = 54.101227 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 9 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.802 | 4.802 | 4.802 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4373.7117 0 -4373.7117 -206.30833 Loop time of 2.183e-06 on 1 procs for 0 steps with 1304 atoms 183.2% 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 | | 2.183e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4954.00 ave 4954 max 4954 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: 70564.0 ave 70564 max 70564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70564 Ave neighs/atom = 54.113497 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 9 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.802 | 4.802 | 4.802 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 -4373.7117 -4373.7117 25.877957 146.53702 5.7110995 -206.30833 -206.30833 -10.122514 -614.65151 5.8490418 2.6185628 454.48904 Loop time of 2.322e-06 on 1 procs for 0 steps with 1304 atoms 215.3% 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 | | 2.322e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4954.00 ave 4954 max 4954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35282.0 ave 35282 max 35282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70564.0 ave 70564 max 70564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70564 Ave neighs/atom = 54.113497 Neighbor list builds = 0 Dangerous builds = 0 1304 -4373.71171321057 eV 2.61856277832032 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01