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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -43.745299 0.0000000) to (53.576830 43.745299 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1375043 5.3932560 5.9120667 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -43.745299 0.0000000) to (53.576830 43.745299 8.8681001) create_atoms CPU = 0.003 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1375043 5.3932560 5.9120667 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -43.745299 0.0000000) to (53.576830 43.745299 8.8681001) create_atoms CPU = 0.002 seconds 1757 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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 3503 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_390178379548_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.686 | 5.686 | 5.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11834.992 0 -11834.992 36323.23 22 0 -12364.663 0 -12364.663 5077.5234 Loop time of 2.00077 on 1 procs for 22 steps with 3503 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 = -11834.9922242508 -12364.6516492541 -12364.6628646681 Force two-norm initial, final = 364.69222 0.33472875 Force max component initial, final = 58.045748 0.089935242 Final line search alpha, max atom move = 1.0000000 0.089935242 Iterations, force evaluations = 22 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9906 | 1.9906 | 1.9906 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035952 | 0.0035952 | 0.0035952 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00655 | | | 0.33 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8294.00 ave 8294 max 8294 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: 272744.0 ave 272744 max 272744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272744 Ave neighs/atom = 77.860120 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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.686 | 5.686 | 5.686 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -12364.663 0 -12364.663 5077.5234 41568.944 29 0 -12365.351 0 -12365.351 6.9797844 41714.968 Loop time of 0.591749 on 1 procs for 7 steps with 3503 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 = -12364.6628646681 -12365.3505616572 -12365.3511898479 Force two-norm initial, final = 280.04048 1.7965714 Force max component initial, final = 260.19939 1.4569884 Final line search alpha, max atom move = 9.5649903e-05 0.00013936080 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58553 | 0.58553 | 0.58553 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071752 | 0.00071752 | 0.00071752 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005502 | | | 0.93 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8256.00 ave 8256 max 8256 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: 271150.0 ave 271150 max 271150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271150 Ave neighs/atom = 77.405081 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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.823 | 5.823 | 5.823 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12365.351 0 -12365.351 6.9797844 Loop time of 2.32e-06 on 1 procs for 0 steps with 3503 atoms 129.3% 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 | | 2.32e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8240.00 ave 8240 max 8240 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: 270850.0 ave 270850 max 270850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270850 Ave neighs/atom = 77.319440 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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.823 | 5.823 | 5.823 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 -12365.351 -12365.351 53.53823 88.002546 8.8538603 6.9797844 6.9797844 -33.131529 -1.7988538 55.869736 2.2613951 1599.2538 Loop time of 3.943e-06 on 1 procs for 0 steps with 3503 atoms 228.3% 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 | | 3.943e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8240.00 ave 8240 max 8240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135425.0 ave 135425 max 135425 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270850.0 ave 270850 max 270850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270850 Ave neighs/atom = 77.319440 Neighbor list builds = 0 Dangerous builds = 0 3503 -12365.3511898479 eV 2.26139511995828 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03