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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -52.432559 0.0000000) to (30.271952 52.432559 7.0065955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4868469 6.2419714 7.0065955 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -52.432559 0.0000000) to (30.271952 52.432559 7.0065955) create_atoms CPU = 0.004 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4868469 6.2419714 7.0065955 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.432559 0.0000000) to (30.271952 52.432559 7.0065955) create_atoms CPU = 0.004 seconds 676 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 25 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_106969701023_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.110 | 5.110 | 5.110 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4438.4637 0 -4438.4637 18821.273 53 0 -4569.5196 0 -4569.5196 5444.5557 Loop time of 2.48699 on 1 procs for 53 steps with 1344 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 = -4438.46369845608 -4569.51546092938 -4569.51963570522 Force two-norm initial, final = 171.65854 0.13278352 Force max component initial, final = 31.300412 0.012719312 Final line search alpha, max atom move = 1.0000000 0.012719312 Iterations, force evaluations = 53 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4257 | 2.4257 | 2.4257 | 0.0 | 97.53 Neigh | 0.028599 | 0.028599 | 0.028599 | 0.0 | 1.15 Comm | 0.017184 | 0.017184 | 0.017184 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01554 | | | 0.62 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6775.00 ave 6775 max 6775 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: 191760.0 ave 191760 max 191760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191760 Ave neighs/atom = 142.67857 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.109 | 5.109 | 5.109 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -4569.5196 0 -4569.5196 5444.5557 22242.24 62 0 -4569.9895 0 -4569.9895 2.9297681 22388.912 Loop time of 0.302413 on 1 procs for 9 steps with 1344 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4569.51963570539 -4569.98939183111 -4569.98948125781 Force two-norm initial, final = 146.45467 0.42242789 Force max component initial, final = 128.88630 0.27899860 Final line search alpha, max atom move = 0.00052012831 0.00014511507 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29408 | 0.29408 | 0.29408 | 0.0 | 97.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018059 | 0.0018059 | 0.0018059 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006522 | | | 2.16 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6712.00 ave 6712 max 6712 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: 189944.0 ave 189944 max 189944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189944 Ave neighs/atom = 141.32738 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.247 | 5.247 | 5.247 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4569.9895 0 -4569.9895 2.9297681 Loop time of 6.816e-06 on 1 procs for 0 steps with 1344 atoms 176.1% 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 | | 6.816e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6712.00 ave 6712 max 6712 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: 189344.0 ave 189344 max 189344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189344 Ave neighs/atom = 140.88095 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.247 | 5.247 | 5.247 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 -4569.9895 -4569.9895 30.263037 105.69671 6.9993706 2.9297681 2.9297681 -12.992213 1.8366413 19.944876 2.6314519 968.01763 Loop time of 7.086e-06 on 1 procs for 0 steps with 1344 atoms 239.9% 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 | | 7.086e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6712.00 ave 6712 max 6712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94672.0 ave 94672 max 94672 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 189344.0 ave 189344 max 189344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189344 Ave neighs/atom = 140.88095 Neighbor list builds = 0 Dangerous builds = 0 1344 -4569.98948125781 eV 2.6314518504176 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03