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 = 3.6336621 3.6336621 3.6336621 Created orthogonal box = (0.0000000 -51.899075 0.0000000) to (36.698188 51.899075 5.1387742) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7565785 4.5793302 5.1387742 Created 814 atoms using lattice units in orthogonal box = (0.0000000 -51.899075 0.0000000) to (36.698188 51.899075 5.1387742) create_atoms CPU = 0.001 seconds 814 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7565785 4.5793302 5.1387742 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -51.899075 0.0000000) to (36.698188 51.899075 5.1387742) create_atoms CPU = 0.001 seconds 822 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 37 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1632 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_529419924683_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.723 | 4.723 | 4.723 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6560.622 0 -6560.622 8793.3784 46 0 -6677.666 0 -6677.666 6537.5333 Loop time of 33.5136 on 1 procs for 46 steps with 1632 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 = -6560.62203526325 -6677.65948916329 -6677.66598635979 Force two-norm initial, final = 46.157850 0.21580127 Force max component initial, final = 9.0526630 0.020090821 Final line search alpha, max atom move = 1.0000000 0.020090821 Iterations, force evaluations = 46 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.496 | 33.496 | 33.496 | 0.0 | 99.95 Neigh | 0.0071397 | 0.0071397 | 0.0071397 | 0.0 | 0.02 Comm | 0.0046081 | 0.0046081 | 0.0046081 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005987 | | | 0.02 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5874.00 ave 5874 max 5874 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: 93158.0 ave 93158 max 93158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93158 Ave neighs/atom = 57.082108 Neighbor list builds = 1 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.719 | 4.719 | 4.719 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -6677.666 0 -6677.666 6537.5333 19574.639 50 0 -6677.87 0 -6677.87 271.9571 19658.651 Loop time of 2.36188 on 1 procs for 4 steps with 1632 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 = -6677.6659863598 -6677.86755711211 -6677.8700159702 Force two-norm initial, final = 139.75785 6.0749728 Force max component initial, final = 95.853213 4.3904146 Final line search alpha, max atom move = 0.00022084217 0.00096958867 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3603 | 2.3603 | 2.3603 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024053 | 0.00024053 | 0.00024053 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00135 | | | 0.06 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5573.00 ave 5573 max 5573 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: 91624.0 ave 91624 max 91624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91624 Ave neighs/atom = 56.142157 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.857 | 4.857 | 4.857 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6677.87 0 -6677.87 271.9571 Loop time of 1.826e-06 on 1 procs for 0 steps with 1632 atoms 164.3% 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 | | 1.826e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5569.00 ave 5569 max 5569 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: 91208.0 ave 91208 max 91208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91208 Ave neighs/atom = 55.887255 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.857 | 4.857 | 4.857 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 -6677.87 -6677.87 36.710791 104.16289 5.1409924 271.9571 271.9571 149.80947 359.07533 306.98649 2.4262082 882.83528 Loop time of 1.721e-06 on 1 procs for 0 steps with 1632 atoms 174.3% 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 | | 1.721e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5569.00 ave 5569 max 5569 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45604.0 ave 45604 max 45604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91208.0 ave 91208 max 91208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91208 Ave neighs/atom = 55.887255 Neighbor list builds = 0 Dangerous builds = 0 1632 -4172.36646393701 eV 2.42620819705815 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:37