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 = 2.8553126 2.8553126 2.8553126 Created orthogonal box = (0.0000000 -50.434876 0.0000000) to (29.118589 50.434876 4.9455465) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4797830 4.5262068 4.9455465 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -50.434876 0.0000000) to (29.118589 50.434876 4.9455465) create_atoms CPU = 0.004 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4797830 4.5262068 4.9455465 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -50.434876 0.0000000) to (29.118589 50.434876 4.9455465) create_atoms CPU = 0.004 seconds 628 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 24 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1252 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.495 | 5.495 | 5.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4441.0692 0 -4441.0692 104742.6 49 0 -5003.2135 0 -5003.2135 8129.7813 Loop time of 3.19863 on 1 procs for 49 steps with 1252 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 = -4441.06918398012 -5003.20867925764 -5003.21352032594 Force two-norm initial, final = 1521.7382 0.27090061 Force max component initial, final = 535.24431 0.062438953 Final line search alpha, max atom move = 1.0000000 0.062438953 Iterations, force evaluations = 49 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1658 | 3.1658 | 3.1658 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01878 | 0.01878 | 0.01878 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01401 | | | 0.44 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9134.00 ave 9134 max 9134 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: 285416.0 ave 285416 max 285416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 285416 Ave neighs/atom = 227.96805 Neighbor list builds = 0 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.495 | 5.495 | 5.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -5003.2135 0 -5003.2135 8129.7813 14525.984 55 0 -5003.5929 0 -5003.5929 66.230628 14592.573 Loop time of 0.293395 on 1 procs for 6 steps with 1252 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 = -5003.21352032593 -5003.58938929694 -5003.59288798701 Force two-norm initial, final = 153.62471 1.1756991 Force max component initial, final = 142.69495 0.92320049 Final line search alpha, max atom move = 0.00012386946 0.00011435635 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28679 | 0.28679 | 0.28679 | 0.0 | 97.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016056 | 0.0016056 | 0.0016056 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005001 | | | 1.70 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9110.00 ave 9110 max 9110 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: 283592.0 ave 283592 max 283592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283592 Ave neighs/atom = 226.51118 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.633 | 5.633 | 5.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5003.5929 0 -5003.5929 66.230628 Loop time of 7.046e-06 on 1 procs for 0 steps with 1252 atoms 170.3% 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 | | 7.046e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9110.00 ave 9110 max 9110 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: 282072.0 ave 282072 max 282072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 282072 Ave neighs/atom = 225.29712 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.633 | 5.633 | 5.633 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 -5003.5929 -5003.5929 29.084831 101.42203 4.9468992 66.230628 66.230628 40.254677 57.047638 101.38957 2.2466611 605.56361 Loop time of 6.726e-06 on 1 procs for 0 steps with 1252 atoms 282.5% 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 | | 6.726e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9110.00 ave 9110 max 9110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141036.0 ave 141036 max 141036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 282072.0 ave 282072 max 282072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 282072 Ave neighs/atom = 225.29712 Neighbor list builds = 0 Dangerous builds = 0 1252 -5003.59288798701 eV 2.24666107903043 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04