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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -69.398046 0.0000000) to (34.699023 69.398046 4.0612135) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2286199 5.2286199 4.0612135 Created 584 atoms using lattice units in orthogonal box = (0.0000000 -69.398046 0.0000000) to (34.699023 69.398046 4.0612135) create_atoms CPU = 0.001 seconds 584 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2286199 5.2286199 4.0612135 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.398046 0.0000000) to (34.699023 69.398046 4.0612135) create_atoms CPU = 0.001 seconds 586 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 29 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1170 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_411898953661_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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.481 | 5.481 | 5.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3058.3004 0 -3058.3004 12771.255 62 0 -3141.5717 0 -3141.5717 4794.6768 Loop time of 1.35328 on 1 procs for 62 steps with 1170 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3058.30037652707 -3141.56894037249 -3141.57174013969 Force two-norm initial, final = 108.30191 0.16651336 Force max component initial, final = 43.760877 0.030049664 Final line search alpha, max atom move = 1.0000000 0.030049664 Iterations, force evaluations = 62 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3213 | 1.3213 | 1.3213 | 0.0 | 97.64 Neigh | 0.014854 | 0.014854 | 0.014854 | 0.0 | 1.10 Comm | 0.0099225 | 0.0099225 | 0.0099225 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007188 | | | 0.53 Nlocal: 1170.00 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10292.0 ave 10292 max 10292 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: 262400.0 ave 262400 max 262400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262400 Ave neighs/atom = 224.27350 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -3141.5717 0 -3141.5717 4794.6768 19559.165 69 0 -3141.9043 0 -3141.9043 -113.06795 19686.107 Loop time of 0.11185 on 1 procs for 7 steps with 1170 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 = -3141.57174013971 -3141.903486361 -3141.90433013714 Force two-norm initial, final = 113.92139 2.6949881 Force max component initial, final = 96.521178 2.0873599 Final line search alpha, max atom move = 0.00023762295 0.00049600461 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10816 | 0.10816 | 0.10816 | 0.0 | 96.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068419 | 0.00068419 | 0.00068419 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003005 | | | 2.69 Nlocal: 1170.00 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10296.0 ave 10296 max 10296 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: 261992.0 ave 261992 max 261992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261992 Ave neighs/atom = 223.92479 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.619 | 5.619 | 5.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3141.9043 0 -3141.9043 -113.06795 Loop time of 1.715e-06 on 1 procs for 0 steps with 1170 atoms 233.2% 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 | | 1.715e-06 | | |100.00 Nlocal: 1170.00 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10296.0 ave 10296 max 10296 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: 261628.0 ave 261628 max 261628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261628 Ave neighs/atom = 223.61368 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.619 | 5.619 | 5.619 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 -3141.9043 -3141.9043 34.64451 139.68052 4.0680809 -113.06795 -113.06795 -131.10278 -37.931609 -170.16946 2.5673623 596.09748 Loop time of 2.546e-06 on 1 procs for 0 steps with 1170 atoms 235.7% 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 | | 2.546e-06 | | |100.00 Nlocal: 1170.00 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10296.0 ave 10296 max 10296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130814.0 ave 130814 max 130814 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261628.0 ave 261628 max 261628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261628 Ave neighs/atom = 223.61368 Neighbor list builds = 0 Dangerous builds = 0 1170 -3141.90433013714 eV 2.56736225963803 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01