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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -64.278083 0.0000000) to (37.110969 64.278083 6.3029846) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7093798 5.7685459 6.3029846 Created 1248 atoms using lattice units in orthogonal box = (0.0000000 -64.278083 0.0000000) to (37.110969 64.278083 6.3029846) create_atoms CPU = 0.008 seconds 1248 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7093798 5.7685459 6.3029846 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -64.278083 0.0000000) to (37.110969 64.278083 6.3029846) create_atoms CPU = 0.008 seconds 1252 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 ghost atom cutoff = 8 binsize = 4, bins = 10 33 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2496 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_748636486270_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 ghost atom cutoff = 8 binsize = 4, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.521 | 6.521 | 6.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7723.8025 0 -7723.8025 84720.507 127 0 -8515.0328 0 -8515.0328 4377.4324 Loop time of 11.5379 on 1 procs for 127 steps with 2496 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 = -7723.80252564625 -8515.02641795171 -8515.0328358021 Force two-norm initial, final = 1352.4004 0.20264240 Force max component initial, final = 335.95769 0.020638547 Final line search alpha, max atom move = 1.0000000 0.020638547 Iterations, force evaluations = 127 231 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.186 | 11.186 | 11.186 | 0.0 | 96.95 Neigh | 0.22808 | 0.22808 | 0.22808 | 0.0 | 1.98 Comm | 0.063169 | 0.063169 | 0.063169 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06018 | | | 0.52 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10909.0 ave 10909 max 10909 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: 438584.0 ave 438584 max 438584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438584 Ave neighs/atom = 175.71474 Neighbor list builds = 4 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 ghost atom cutoff = 8 binsize = 4, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 127 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.524 | 6.524 | 6.524 Mbytes Step Temp E_pair E_mol TotEng Press Volume 127 0 -8515.0328 0 -8515.0328 4377.4324 30070.556 132 0 -8515.3111 0 -8515.3111 -10.543685 30162.749 Loop time of 0.393407 on 1 procs for 5 steps with 2496 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 = -8515.03283580195 -8515.30969375957 -8515.31110219951 Force two-norm initial, final = 167.21564 1.6732934 Force max component initial, final = 153.84185 1.1706549 Final line search alpha, max atom move = 7.0081447e-05 8.2041192e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3842 | 0.3842 | 0.3842 | 0.0 | 97.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00199 | 0.00199 | 0.00199 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007217 | | | 1.83 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11214.0 ave 11214 max 11214 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: 438512.0 ave 438512 max 438512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438512 Ave neighs/atom = 175.68590 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 ghost atom cutoff = 8 binsize = 4, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.662 | 6.662 | 6.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8515.3111 0 -8515.3111 -10.543685 Loop time of 6.185e-06 on 1 procs for 0 steps with 2496 atoms 194.0% 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 | | 6.185e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11226.0 ave 11226 max 11226 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: 438336.0 ave 438336 max 438336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438336 Ave neighs/atom = 175.61538 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 ghost atom cutoff = 8 binsize = 4, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.662 | 6.662 | 6.662 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 -8515.3111 -8515.3111 37.085704 129.05588 6.302119 -10.543685 -10.543685 -62.140189 -25.387774 55.896907 2.2749239 1005.7166 Loop time of 6.676e-06 on 1 procs for 0 steps with 2496 atoms 254.6% 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 | | 6.676e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11226.0 ave 11226 max 11226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 219168.0 ave 219168 max 219168 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 438336.0 ave 438336 max 438336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438336 Ave neighs/atom = 175.61538 Neighbor list builds = 0 Dangerous builds = 0 2496 -8515.31110219951 eV 2.27492386038196 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13