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 -40.855121 0.0000000) to (28.888933 40.855121 5.7208612) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0980470 6.4086465 5.7208612 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.855121 0.0000000) to (28.888933 40.855121 5.7208612) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0980470 6.4086465 5.7208612 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.855121 0.0000000) to (28.888933 40.855121 5.7208612) create_atoms CPU = 0.001 seconds 410 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 = 7 20 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 10 atoms, new total = 808 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 = 7 20 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) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2655.7995 0 -2655.7995 16266.28 58 0 -2746.3254 0 -2746.3254 -1217.1014 Loop time of 0.659331 on 1 procs for 58 steps with 808 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2655.79949049879 -2746.32327519964 -2746.32538030587 Force two-norm initial, final = 161.36565 0.10158239 Force max component initial, final = 48.308728 0.014906316 Final line search alpha, max atom move = 1.0000000 0.014906316 Iterations, force evaluations = 58 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62991 | 0.62991 | 0.62991 | 0.0 | 95.54 Neigh | 0.021891 | 0.021891 | 0.021891 | 0.0 | 3.32 Comm | 0.00408 | 0.00408 | 0.00408 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003447 | | | 0.52 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4984.00 ave 4984 max 4984 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: 114072.0 ave 114072 max 114072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114072 Ave neighs/atom = 141.17822 Neighbor list builds = 3 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 = 7 20 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -2746.3254 0 -2746.3254 -1217.1014 13504.217 61 0 -2746.3562 0 -2746.3562 -99.366058 13485.647 Loop time of 0.0340167 on 1 procs for 3 steps with 808 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 = -2746.32538030587 -2746.35398359655 -2746.35616458132 Force two-norm initial, final = 23.176604 1.5264069 Force max component initial, final = 20.428399 1.0940673 Final line search alpha, max atom move = 0.00030938959 0.00033849304 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033073 | 0.033073 | 0.033073 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018461 | 0.00018461 | 0.00018461 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007596 | | | 2.23 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4984.00 ave 4984 max 4984 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: 114068.0 ave 114068 max 114068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114068 Ave neighs/atom = 141.17327 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 = 7 20 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2746.3562 0 -2746.3562 -99.366058 Loop time of 1.581e-06 on 1 procs for 0 steps with 808 atoms 189.8% 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 | | 1.581e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4984.00 ave 4984 max 4984 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: 114156.0 ave 114156 max 114156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114156 Ave neighs/atom = 141.28218 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 = 7 20 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) = 5.097 | 5.097 | 5.097 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 -2746.3562 -2746.3562 28.812395 81.847551 5.7185606 -99.366058 -99.366058 -129.63745 -112.72326 -55.737465 2.5770165 689.81364 Loop time of 1.886e-06 on 1 procs for 0 steps with 808 atoms 212.1% 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 | | 1.886e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4984.00 ave 4984 max 4984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57078.0 ave 57078 max 57078 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114156.0 ave 114156 max 114156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114156 Ave neighs/atom = 141.28218 Neighbor list builds = 0 Dangerous builds = 0 808 -2746.35616458132 eV 2.57701649945608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01