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 = 3.3024436 3.3024436 3.3024436 Created orthogonal box = (0.0000000 -35.260448 0.0000000) to (20.357629 35.260448 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3572709 4.9488348 5.7200000 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -35.260448 0.0000000) to (20.357629 35.260448 5.7200000) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3572709 4.9488348 5.7200000 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -35.260448 0.0000000) to (20.357629 35.260448 5.7200000) create_atoms CPU = 0.000 seconds 229 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 22 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 456 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_072689718616_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.451 | 4.451 | 4.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3271.7836 0 -3271.7836 39078.891 88 0 -3386.7285 0 -3386.7285 8707.1227 Loop time of 2.06246 on 1 procs for 88 steps with 456 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 = -3271.78356531068 -3386.72524674157 -3386.72851673587 Force two-norm initial, final = 177.39562 0.20375450 Force max component initial, final = 74.919720 0.037495680 Final line search alpha, max atom move = 0.84100965 0.031534229 Iterations, force evaluations = 88 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.047 | 2.047 | 2.047 | 0.0 | 99.25 Neigh | 0.0067205 | 0.0067205 | 0.0067205 | 0.0 | 0.33 Comm | 0.0043951 | 0.0043951 | 0.0043951 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004299 | | | 0.21 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2509.00 ave 2509 max 2509 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: 27854.0 ave 27854 max 27854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27854 Ave neighs/atom = 61.083333 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.451 | 4.451 | 4.451 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -3386.7285 0 -3386.7285 8707.1227 8211.8509 91 0 -3386.8343 0 -3386.8343 -2.2083468 8248.4303 Loop time of 0.0757547 on 1 procs for 3 steps with 456 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 = -3386.72851673587 -3386.83271166528 -3386.83425520816 Force two-norm initial, final = 78.283022 0.53495499 Force max component initial, final = 49.782628 0.37560794 Final line search alpha, max atom move = 0.00018673728 7.0140003e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075114 | 0.075114 | 0.075114 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011509 | 0.00011509 | 0.00011509 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005258 | | | 0.69 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2465.00 ave 2465 max 2465 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: 27868.0 ave 27868 max 27868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27868 Ave neighs/atom = 61.114035 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.589 | 4.589 | 4.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3386.8343 0 -3386.8343 -2.2083468 Loop time of 1.762e-06 on 1 procs for 0 steps with 456 atoms 170.3% 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 | | 1.762e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2456.00 ave 2456 max 2456 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: 27680.0 ave 27680 max 27680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27680 Ave neighs/atom = 60.701754 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.589 | 4.589 | 4.589 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 -3386.8343 -3386.8343 20.36952 70.659672 5.730848 -2.2083468 -2.2083468 4.8417014 61.629772 -73.096514 2.6662651 434.95315 Loop time of 1.593e-06 on 1 procs for 0 steps with 456 atoms 188.3% 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 | | 1.593e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2456.00 ave 2456 max 2456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13840.0 ave 13840 max 13840 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27680.0 ave 27680 max 27680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27680 Ave neighs/atom = 60.701754 Neighbor list builds = 0 Dangerous builds = 0 456 -3386.83425520816 eV 2.6662650566753 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02