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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -62.700241 0.0000000) to (25.597266 62.700241 8.8671532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1433439 5.4340209 5.9114354 Created 1197 atoms using lattice units in orthogonal box = (0.0000000 -62.700241 0.0000000) to (25.597266 62.700241 8.8671532) create_atoms CPU = 0.002 seconds 1197 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1433439 5.4340209 5.9114354 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -62.700241 0.0000000) to (25.597266 62.700241 8.8671532) create_atoms CPU = 0.002 seconds 1205 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 33 3 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2400 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_657255834688_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.475 | 6.475 | 6.475 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7896.7644 0 -7896.7644 51289.861 53 0 -8477.8755 0 -8477.8755 4021.1266 Loop time of 2.01019 on 1 procs for 53 steps with 2400 atoms 95.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7896.76442479461 -8477.86864709826 -8477.87546975816 Force two-norm initial, final = 793.60540 0.28835853 Force max component initial, final = 103.75121 0.046374582 Final line search alpha, max atom move = 1.0000000 0.046374582 Iterations, force evaluations = 53 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9636 | 1.9636 | 1.9636 | 0.0 | 97.68 Neigh | 0.025163 | 0.025163 | 0.025163 | 0.0 | 1.25 Comm | 0.009252 | 0.009252 | 0.009252 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01219 | | | 0.61 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9554.00 ave 9554 max 9554 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: 418162.0 ave 418162 max 418162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 418162 Ave neighs/atom = 174.23417 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.475 | 6.475 | 6.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -8477.8755 0 -8477.8755 4021.1266 28462.76 59 0 -8478.2194 0 -8478.2194 4.114284 28547.284 Loop time of 0.195914 on 1 procs for 6 steps with 2400 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 = -8477.87546975819 -8478.21926343367 -8478.21937130481 Force two-norm initial, final = 159.36507 0.58760181 Force max component initial, final = 151.91083 0.41707152 Final line search alpha, max atom move = 0.00032034499 0.00013360677 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1904 | 0.1904 | 0.1904 | 0.0 | 97.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079293 | 0.00079293 | 0.00079293 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004725 | | | 2.41 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9538.00 ave 9538 max 9538 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: 418308.0 ave 418308 max 418308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 418308 Ave neighs/atom = 174.29500 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.613 | 6.613 | 6.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8478.2194 0 -8478.2194 4.114284 Loop time of 1.786e-06 on 1 procs for 0 steps with 2400 atoms 168.0% 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 | | 1.786e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9538.00 ave 9538 max 9538 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: 417998.0 ave 417998 max 417998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 417998 Ave neighs/atom = 174.16583 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.613 | 6.613 | 6.613 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 -8478.2194 -8478.2194 25.594541 125.99861 8.85221 4.114284 4.114284 23.405065 -3.0700736 -7.9921395 2.3914192 647.93551 Loop time of 2.523e-06 on 1 procs for 0 steps with 2400 atoms 237.8% 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 | | 2.523e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9538.00 ave 9538 max 9538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 208999.0 ave 208999 max 208999 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 417998.0 ave 417998 max 417998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 417998 Ave neighs/atom = 174.16583 Neighbor list builds = 0 Dangerous builds = 0 2400 -8478.21937130481 eV 2.39141923268697 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02