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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -57.415919 0.0000000) to (33.149096 57.415919 4.9599800) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4528637 4.5704214 4.9599800 Created 804 atoms using lattice units in orthogonal box = (0.0000000 -57.415919 0.0000000) to (33.149096 57.415919 4.9599800) create_atoms CPU = 0.002 seconds 804 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4528637 4.5704214 4.9599800 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -57.415919 0.0000000) to (33.149096 57.415919 4.9599800) create_atoms CPU = 0.002 seconds 806 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 36 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1608 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.120 | 5.120 | 5.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6203.2266 0 -6203.2266 72948.661 80 0 -6876.0675 0 -6876.0675 4719.5147 Loop time of 18.2191 on 1 procs for 80 steps with 1608 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6203.22662902329 -6876.06179039101 -6876.06754387422 Force two-norm initial, final = 895.61636 0.24406543 Force max component initial, final = 310.17300 0.044103399 Final line search alpha, max atom move = 1.0000000 0.044103399 Iterations, force evaluations = 80 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.163 | 18.163 | 18.163 | 0.0 | 99.69 Neigh | 0.022192 | 0.022192 | 0.022192 | 0.0 | 0.12 Comm | 0.017564 | 0.017564 | 0.017564 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01602 | | | 0.09 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7179.00 ave 7179 max 7179 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: 159620.0 ave 159620 max 159620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159620 Ave neighs/atom = 99.266169 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.121 | 5.121 | 5.121 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -6876.0675 0 -6876.0675 4719.5147 18880.519 82 0 -6876.1524 0 -6876.1524 -347.75715 18935.907 Loop time of 0.578155 on 1 procs for 2 steps with 1608 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 = -6876.06754387422 -6876.14743366336 -6876.15239466377 Force two-norm initial, final = 98.765350 9.5267524 Force max component initial, final = 70.980676 8.5581103 Final line search alpha, max atom move = 5.5199652e-05 0.00047240471 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57641 | 0.57641 | 0.57641 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027316 | 0.00027316 | 0.00027316 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001471 | | | 0.25 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7154.00 ave 7154 max 7154 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: 159208.0 ave 159208 max 159208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159208 Ave neighs/atom = 99.009950 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.259 | 5.259 | 5.259 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6876.1524 0 -6876.1524 -347.75715 Loop time of 2.431e-06 on 1 procs for 0 steps with 1608 atoms 164.5% 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 | | 2.431e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7135.00 ave 7135 max 7135 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: 151220.0 ave 151220 max 151220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151220 Ave neighs/atom = 94.042289 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.259 | 5.259 | 5.259 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 -6876.1524 -6876.1524 33.165539 114.99921 4.9648277 -347.75715 -347.75715 -724.46516 33.474493 -352.28079 2.3065813 754.67456 Loop time of 2.398e-06 on 1 procs for 0 steps with 1608 atoms 208.5% 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 | | 2.398e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7135.00 ave 7135 max 7135 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75610.0 ave 75610 max 75610 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 151220.0 ave 151220 max 151220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151220 Ave neighs/atom = 94.042289 Neighbor list builds = 0 Dangerous builds = 0 1608 -6876.15239466377 eV 2.30658132774318 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19