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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -49.103044 0.0000000) to (24.551522 49.103044 3.1435003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4273237 4.4273237 3.1435003 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -49.103044 0.0000000) to (24.551522 49.103044 3.1435003) create_atoms CPU = 0.001 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4273237 4.4273237 3.1435003 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -49.103044 0.0000000) to (24.551522 49.103044 3.1435003) create_atoms CPU = 0.000 seconds 245 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 20 1 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 486 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1835.6187 0 -1835.6187 289962.74 117 0 -3243.4434 0 -3243.4434 -4354.9239 Loop time of 1.34345 on 1 procs for 117 steps with 486 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1835.61869538962 -3243.44044437963 -3243.44336366814 Force two-norm initial, final = 3384.0557 0.29022276 Force max component initial, final = 1622.1647 0.030199961 Final line search alpha, max atom move = 0.85014477 0.025674338 Iterations, force evaluations = 117 208 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3066 | 1.3066 | 1.3066 | 0.0 | 97.25 Neigh | 0.015661 | 0.015661 | 0.015661 | 0.0 | 1.17 Comm | 0.013883 | 0.013883 | 0.013883 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007358 | | | 0.55 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7452.00 ave 7452 max 7452 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: 133600.0 ave 133600 max 133600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133600 Ave neighs/atom = 274.89712 Neighbor list builds = 2 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -3243.4434 0 -3243.4434 -4354.9239 7579.3216 171 0 -3251.5968 0 -3251.5968 -1111.8689 7560.7564 Loop time of 0.475551 on 1 procs for 54 steps with 486 atoms 92.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3243.44336366815 -3251.59517005747 -3251.59681481895 Force two-norm initial, final = 200.71400 10.038334 Force max component initial, final = 176.54289 5.9391680 Final line search alpha, max atom move = 0.00053371541 0.0031698255 Iterations, force evaluations = 54 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4369 | 0.4369 | 0.4369 | 0.0 | 91.87 Neigh | 0.016321 | 0.016321 | 0.016321 | 0.0 | 3.43 Comm | 0.0040887 | 0.0040887 | 0.0040887 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01824 | | | 3.84 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7302.00 ave 7302 max 7302 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: 131954.0 ave 131954 max 131954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131954 Ave neighs/atom = 271.51029 Neighbor list builds = 2 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3251.5968 0 -3251.5968 -1111.8689 Loop time of 1.918e-06 on 1 procs for 0 steps with 486 atoms 156.4% 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 | | 1.918e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7302.00 ave 7302 max 7302 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: 131978.0 ave 131978 max 131978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131978 Ave neighs/atom = 271.55967 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.065 | 5.065 | 5.065 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 -3251.5968 -3251.5968 25.228736 100.67296 2.9768496 -1111.8689 -1111.8689 -1152.9085 -990.86881 -1191.8295 2.6398441 155.90373 Loop time of 2.291e-06 on 1 procs for 0 steps with 486 atoms 218.2% 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 | | 2.291e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7302.00 ave 7302 max 7302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65989.0 ave 65989 max 65989 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 131978.0 ave 131978 max 131978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131978 Ave neighs/atom = 271.55967 Neighbor list builds = 0 Dangerous builds = 0 486 -3251.59681481895 eV 2.63984408395621 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02