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 = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -41.950267 0.0000000) to (29.663318 41.950267 5.1250408) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7555692 6.2612338 5.1250408 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.950267 0.0000000) to (29.663318 41.950267 5.1250408) create_atoms CPU = 0.001 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7555692 6.2612338 5.1250408 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.950267 0.0000000) to (29.663318 41.950267 5.1250408) create_atoms CPU = 0.001 seconds 538 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 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1068 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_427873955970_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 24 2 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) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3509.8284 0 -3509.8284 187326.5 323 0 -4528.682 0 -4528.682 -12170.873 Loop time of 42.2678 on 1 procs for 323 steps with 1068 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 = -3509.82838856834 -4528.67801508128 -4528.68197069984 Force two-norm initial, final = 2045.9539 0.19771258 Force max component initial, final = 470.45004 0.046141129 Final line search alpha, max atom move = 1.0000000 0.046141129 Iterations, force evaluations = 323 555 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 42.114 | 42.114 | 42.114 | 0.0 | 99.64 Neigh | 0.091741 | 0.091741 | 0.091741 | 0.0 | 0.22 Comm | 0.033672 | 0.033672 | 0.033672 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02868 | | | 0.07 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5896.00 ave 5896 max 5896 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: 130484.0 ave 130484 max 130484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130484 Ave neighs/atom = 122.17603 Neighbor list builds = 11 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 24 2 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 : 323 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press Volume 323 0 -4528.682 0 -4528.682 -12170.873 12755.039 354 0 -4540.4227 0 -4540.4227 -6.3594569 12637.712 Loop time of 2.80849 on 1 procs for 31 steps with 1068 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 = -4528.68197069984 -4540.42134414603 -4540.42268774669 Force two-norm initial, final = 627.20025 1.2355752 Force max component initial, final = 549.76639 0.35372663 Final line search alpha, max atom move = 0.00020853935 7.3765921e-05 Iterations, force evaluations = 31 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7995 | 2.7995 | 2.7995 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014736 | 0.0014736 | 0.0014736 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007538 | | | 0.27 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5909.00 ave 5909 max 5909 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: 130612.0 ave 130612 max 130612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130612 Ave neighs/atom = 122.29588 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 24 2 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) = 5.145 | 5.145 | 5.145 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4540.4227 0 -4540.4227 -6.3594569 Loop time of 1.555e-06 on 1 procs for 0 steps with 1068 atoms 128.6% 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 | | 1.555e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5930.00 ave 5930 max 5930 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: 129314.0 ave 129314 max 129314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129314 Ave neighs/atom = 121.08052 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 24 2 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) = 5.145 | 5.145 | 5.145 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 -4540.4227 -4540.4227 30.328109 83.777625 4.9738774 -6.3594569 -6.3594569 -39.425729 -23.174499 43.521857 2.2969308 4057.9391 Loop time of 1.645e-06 on 1 procs for 0 steps with 1068 atoms 243.2% 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 | | 1.645e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5930.00 ave 5930 max 5930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64657.0 ave 64657 max 64657 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129314.0 ave 129314 max 129314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129314 Ave neighs/atom = 121.08052 Neighbor list builds = 0 Dangerous builds = 0 1068 -4540.42268774669 eV 2.29693084284555 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:45