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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -46.716541 0.0000000) to (28.607922 46.716541 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2014403 5.3086978 5.7504086 Created 1049 atoms using lattice units in orthogonal box = (0.0000000 -46.716541 0.0000000) to (28.607922 46.716541 8.6256130) create_atoms CPU = 0.002 seconds 1049 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2014403 5.3086978 5.7504086 Created 1073 atoms using lattice units in orthogonal box = (0.0000000 -46.716541 0.0000000) to (28.607922 46.716541 8.6256130) create_atoms CPU = 0.001 seconds 1073 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 27 3 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 2112 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_663355627503_001#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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9370.4493 0 -9370.4493 5278.7195 13 0 -9382.16 0 -9382.16 4206.7283 Loop time of 3.37192 on 1 procs for 13 steps with 2112 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9370.44930450527 -9382.15782901254 -9382.16000591045 Force two-norm initial, final = 22.985258 0.11220908 Force max component initial, final = 2.3833536 0.0078857569 Final line search alpha, max atom move = 1.0000000 0.0078857569 Iterations, force evaluations = 13 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3664 | 3.3664 | 3.3664 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023065 | 0.0023065 | 0.0023065 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003199 | | | 0.09 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7494.00 ave 7494 max 7494 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: 282528.0 ave 282528 max 282528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 282528 Ave neighs/atom = 133.77273 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -9382.16 0 -9382.16 4206.7283 23055.628 18 0 -9382.4463 0 -9382.4463 -96.52804 23108.556 Loop time of 0.935185 on 1 procs for 5 steps with 2112 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9382.16000591049 -9382.44577565457 -9382.44634376583 Force two-norm initial, final = 147.56517 3.8572105 Force max component initial, final = 144.65768 3.2635256 Final line search alpha, max atom move = 0.00013287744 0.00043364894 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93205 | 0.93205 | 0.93205 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046232 | 0.00046232 | 0.00046232 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002673 | | | 0.29 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7494.00 ave 7494 max 7494 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: 282034.0 ave 282034 max 282034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 282034 Ave neighs/atom = 133.53883 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.711 | 5.711 | 5.711 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9382.4463 0 -9382.4463 -96.52804 Loop time of 2.238e-06 on 1 procs for 0 steps with 2112 atoms 178.7% 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 | | 2.238e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7494.00 ave 7494 max 7494 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: 281664.0 ave 281664 max 281664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281664 Ave neighs/atom = 133.36364 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.711 | 5.711 | 5.711 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 -9382.4463 -9382.4463 28.587737 93.818969 8.6159343 -96.52804 -96.52804 -226.1091 63.409383 -126.8844 2.3692885 655.78936 Loop time of 2.466e-06 on 1 procs for 0 steps with 2112 atoms 243.3% 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 | | 2.466e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7494.00 ave 7494 max 7494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140832.0 ave 140832 max 140832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 281664.0 ave 281664 max 281664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281664 Ave neighs/atom = 133.36364 Neighbor list builds = 0 Dangerous builds = 0 2112 -9382.44634376583 eV 2.36928845682409 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05