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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2303163 6.0575610 5.1068645 Created 687 atoms using lattice units in orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) create_atoms CPU = 0.002 seconds 687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2303163 6.0575610 5.1068645 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -47.359113 0.0000000) to (33.487950 47.359113 5.1068645) create_atoms CPU = 0.002 seconds 695 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1382 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_179420363944_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5492.2535 0 -5492.2535 67134.673 582 0 -5882.6274 0 -5882.6274 12560.633 Loop time of 100.578 on 1 procs for 582 steps with 1382 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 = -5492.25352425673 -5882.62169482968 -5882.62735327229 Force two-norm initial, final = 373.30558 0.26047151 Force max component initial, final = 53.842572 0.061450147 Final line search alpha, max atom move = 1.0000000 0.061450147 Iterations, force evaluations = 582 1084 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 100.21 | 100.21 | 100.21 | 0.0 | 99.63 Neigh | 0.18363 | 0.18363 | 0.18363 | 0.0 | 0.18 Comm | 0.098561 | 0.098561 | 0.098561 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08989 | | | 0.09 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6339.00 ave 6339 max 6339 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: 142802.0 ave 142802 max 142802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142802 Ave neighs/atom = 103.32996 Neighbor list builds = 19 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 582 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press Volume 582 0 -5882.6274 0 -5882.6274 12560.633 16198.562 607 0 -5893.8994 0 -5893.8994 1.6359312 16292.374 Loop time of 3.21793 on 1 procs for 25 steps with 1382 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 = -5882.62735327229 -5893.89907919779 -5893.8994022469 Force two-norm initial, final = 703.67322 2.2489133 Force max component initial, final = 517.94350 1.1825793 Final line search alpha, max atom move = 0.00059000010 0.00069772190 Iterations, force evaluations = 25 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1859 | 3.1859 | 3.1859 | 0.0 | 99.00 Neigh | 0.020246 | 0.020246 | 0.020246 | 0.0 | 0.63 Comm | 0.0019645 | 0.0019645 | 0.0019645 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009845 | | | 0.31 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6434.00 ave 6434 max 6434 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: 145692.0 ave 145692 max 145692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 145692 Ave neighs/atom = 105.42113 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.201 | 5.201 | 5.201 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5893.8994 0 -5893.8994 1.6359312 Loop time of 2.322e-06 on 1 procs for 0 steps with 1382 atoms 172.3% 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 | | 2.322e-06 | | |100.00 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6432.00 ave 6432 max 6432 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: 145650.0 ave 145650 max 145650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 145650 Ave neighs/atom = 105.39074 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.201 | 5.201 | 5.201 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 -5893.8994 -5893.8994 33.748407 96.752245 4.9896495 1.6359312 1.6359312 117.19821 -69.967345 -42.323069 2.351624 2552.8407 Loop time of 2.389e-06 on 1 procs for 0 steps with 1382 atoms 209.3% 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 | | 2.389e-06 | | |100.00 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6432.00 ave 6432 max 6432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72825.0 ave 72825 max 72825 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 145650.0 ave 145650 max 145650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 145650 Ave neighs/atom = 105.39074 Neighbor list builds = 0 Dangerous builds = 0 1382 -5893.8994022469 eV 2.35162403779762 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:44