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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -42.663951 0.0000000) to (15.083984 42.663951 5.1737640) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2110524 6.2741104 5.1737640 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.663951 0.0000000) to (15.083984 42.663951 5.1737640) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2110524 6.2741104 5.1737640 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.663951 0.0000000) to (15.083984 42.663951 5.1737640) create_atoms CPU = 0.001 seconds 274 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 24 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 7.3 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.519 | 4.519 | 4.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2078.3434 0 -2078.3434 30880.571 378 0 -2141.9709 0 -2141.9709 -53673.6 Loop time of 3.25591 on 1 procs for 378 steps with 546 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 = -2078.34344779362 -2141.96936775134 -2141.9709274256 Force two-norm initial, final = 83.217242 0.12753457 Force max component initial, final = 21.816205 0.016430190 Final line search alpha, max atom move = 1.0000000 0.016430190 Iterations, force evaluations = 378 744 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1633 | 3.1633 | 3.1633 | 0.0 | 97.16 Neigh | 0.036944 | 0.036944 | 0.036944 | 0.0 | 1.13 Comm | 0.031607 | 0.031607 | 0.031607 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02404 | | | 0.74 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4164.00 ave 4164 max 4164 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: 75220.0 ave 75220 max 75220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75220 Ave neighs/atom = 137.76557 Neighbor list builds = 7 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 378 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.519 | 4.519 | 4.519 Mbytes Step Temp E_pair E_mol TotEng Press Volume 378 0 -2141.9709 0 -2141.9709 -53673.6 6659.0727 514 0 -2161.0548 0 -2161.0548 515.09585 6492.8658 Loop time of 0.668261 on 1 procs for 136 steps with 546 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 = -2141.97092742561 -2161.05301623797 -2161.0547973577 Force two-norm initial, final = 489.04433 4.6009805 Force max component initial, final = 375.15006 2.7728116 Final line search alpha, max atom move = 0.00021947856 0.00060857270 Iterations, force evaluations = 136 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61501 | 0.61501 | 0.61501 | 0.0 | 92.03 Neigh | 0.021073 | 0.021073 | 0.021073 | 0.0 | 3.15 Comm | 0.0057639 | 0.0057639 | 0.0057639 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02642 | | | 3.95 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4310.00 ave 4310 max 4310 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: 77528.0 ave 77528 max 77528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77528 Ave neighs/atom = 141.99267 Neighbor list builds = 4 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.658 | 4.658 | 4.658 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2161.0548 0 -2161.0548 515.09585 Loop time of 2.09e-06 on 1 procs for 0 steps with 546 atoms 143.5% 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 | | 2.09e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4350.00 ave 4350 max 4350 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: 76776.0 ave 76776 max 76776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76776 Ave neighs/atom = 140.61538 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.658 | 4.658 | 4.658 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 -2161.0548 -2161.0548 14.367628 80.705579 5.599481 515.09585 515.09585 394.16324 410.60659 740.51773 2.3426651 1603.2219 Loop time of 1.767e-06 on 1 procs for 0 steps with 546 atoms 169.8% 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 | | 1.767e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4350.00 ave 4350 max 4350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38388.0 ave 38388 max 38388 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76776.0 ave 76776 max 76776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76776 Ave neighs/atom = 140.61538 Neighbor list builds = 0 Dangerous builds = 0 546 -2161.0547973577 eV 2.34266505892934 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04