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 = 3.9946083 3.9946083 3.9946083 Created orthogonal box = (0.0000000 -49.410576 0.0000000) to (23.292369 49.410576 5.6492293) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8506968 6.7818438 5.6492293 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -49.410576 0.0000000) to (23.292369 49.410576 5.6492293) create_atoms CPU = 0.004 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8506968 6.7818438 5.6492293 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -49.410576 0.0000000) to (23.292369 49.410576 5.6492293) create_atoms CPU = 0.003 seconds 412 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 7 27 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 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 820 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_623376124862_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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 4.958 | 4.958 | 4.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2621.922 0 -2621.922 12257.691 102 0 -2689.008 0 -2689.008 -240.29059 Loop time of 4.28575 on 1 procs for 102 steps with 820 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 = -2621.92199739198 -2689.00575503495 -2689.00800724897 Force two-norm initial, final = 83.027706 0.097039636 Force max component initial, final = 19.228160 0.013060511 Final line search alpha, max atom move = 1.0000000 0.013060511 Iterations, force evaluations = 102 196 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2271 | 4.2271 | 4.2271 | 0.0 | 98.63 Neigh | 0.014057 | 0.014057 | 0.014057 | 0.0 | 0.33 Comm | 0.022712 | 0.022712 | 0.022712 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02189 | | | 0.51 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4974.00 ave 4974 max 4974 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: 107360.0 ave 107360 max 107360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107360 Ave neighs/atom = 130.92683 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.958 | 4.958 | 4.958 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -2689.008 0 -2689.008 -240.29059 13003.276 105 0 -2689.0242 0 -2689.0242 -15.306552 12994.376 Loop time of 0.110295 on 1 procs for 3 steps with 820 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 = -2689.00800724897 -2689.02402607879 -2689.02421138726 Force two-norm initial, final = 13.541295 0.26268448 Force max component initial, final = 12.653750 0.20791022 Final line search alpha, max atom move = 0.00089416443 0.00018590593 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10797 | 0.10797 | 0.10797 | 0.0 | 97.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052719 | 0.00052719 | 0.00052719 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001796 | | | 1.63 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014.00 ave 5014 max 5014 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: 107184.0 ave 107184 max 107184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107184 Ave neighs/atom = 130.71220 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 5.095 | 5.095 | 5.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2689.0242 0 -2689.0242 -15.306552 Loop time of 5.734e-06 on 1 procs for 0 steps with 820 atoms 191.8% 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 | | 5.734e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014.00 ave 5014 max 5014 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: 107296.0 ave 107296 max 107296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107296 Ave neighs/atom = 130.84878 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 5.095 | 5.095 | 5.095 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 -2689.0242 -2689.0242 23.306358 98.608121 5.6541631 -15.306552 -15.306552 -25.650245 -10.85565 -9.4137601 2.644525 1137.8314 Loop time of 6.936e-06 on 1 procs for 0 steps with 820 atoms 259.5% 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 | | 6.936e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014.00 ave 5014 max 5014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53648.0 ave 53648 max 53648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107296.0 ave 107296 max 107296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107296 Ave neighs/atom = 130.84878 Neighbor list builds = 0 Dangerous builds = 0 820 -2689.02421138726 eV 2.64452499504056 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04