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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -42.154632 0.0000000) to (14.903913 42.154632 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1369054 6.1992106 5.1120000 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.154632 0.0000000) to (14.903913 42.154632 5.1120000) create_atoms CPU = 0.003 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1369054 6.1992106 5.1120000 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.154632 0.0000000) to (14.903913 42.154632 5.1120000) create_atoms CPU = 0.003 seconds 274 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 6 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_887933271505_003#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1709.2892 0 -1709.2892 89601.803 98 0 -1941.4551 0 -1941.4551 7480.7159 Loop time of 2.707 on 1 procs for 98 steps with 546 atoms 41.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -1709.28919290495 -1941.45507320592 -1941.45507320592 Force two-norm initial, final = 301.97131 0.38212531 Force max component initial, final = 110.98025 0.064943220 Final line search alpha, max atom move = 5.4435862e-08 3.5352401e-09 Iterations, force evaluations = 98 225 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6569 | 2.6569 | 2.6569 | 0.0 | 98.15 Neigh | 0.011856 | 0.011856 | 0.011856 | 0.0 | 0.44 Comm | 0.020083 | 0.020083 | 0.020083 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01814 | | | 0.67 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2702.00 ave 2702 max 2702 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: 30800.0 ave 30800 max 30800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30800 Ave neighs/atom = 56.410256 Neighbor list builds = 2 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -1941.4551 0 -1941.4551 7480.7159 6423.4219 100 0 -1941.4868 0 -1941.4868 6235.5454 6429.07 Loop time of 0.118419 on 1 procs for 2 steps with 546 atoms 40.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1941.45507320592 -1941.48592397226 -1941.48679511193 Force two-norm initial, final = 59.053805 50.893037 Force max component initial, final = 52.686756 46.598872 Final line search alpha, max atom move = 3.3403130e-07 1.5565482e-05 Iterations, force evaluations = 2 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11505 | 0.11505 | 0.11505 | 0.0 | 97.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077669 | 0.00077669 | 0.00077669 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002594 | | | 2.19 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2708.00 ave 2708 max 2708 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: 30936.0 ave 30936 max 30936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30936 Ave neighs/atom = 56.659341 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1941.4868 0 -1941.4868 6235.5454 Loop time of 6.194e-06 on 1 procs for 0 steps with 546 atoms 0.0% 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 | | 6.194e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2708.00 ave 2708 max 2708 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: 30920.0 ave 30920 max 30920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30920 Ave neighs/atom = 56.630037 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.622 | 4.622 | 4.622 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 -1941.4868 -1941.4868 14.906207 84.326931 5.1146359 6235.5454 6235.5454 2879.7662 4208.0646 11618.805 2.4009476 467.61859 Loop time of 6.715e-06 on 1 procs for 0 steps with 546 atoms 253.2% 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 | | 6.715e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2708.00 ave 2708 max 2708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15460.0 ave 15460 max 15460 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30920.0 ave 30920 max 30920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30920 Ave neighs/atom = 56.630037 Neighbor list builds = 0 Dangerous builds = 0 546 -1941.48679511193 eV 2.400947635978 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03