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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -51.628669 0.0000000) to (36.506982 51.628669 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7265854 4.5554708 5.1120000 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -51.628669 0.0000000) to (36.506982 51.628669 5.1120000) create_atoms CPU = 0.004 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7265854 4.5554708 5.1120000 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -51.628669 0.0000000) to (36.506982 51.628669 5.1120000) create_atoms CPU = 0.004 seconds 821 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1634 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_887933271505_003#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.714 | 4.714 | 4.714 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5161.0551 0 -5161.0551 71613.21 29 0 -5786.8556 0 -5786.8556 4509.0248 Loop time of 1.62724 on 1 procs for 29 steps with 1634 atoms 62.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5161.05514345139 -5786.85561302423 -5786.85561302423 Force two-norm initial, final = 754.80933 0.78040731 Force max component initial, final = 118.46917 0.065408152 Final line search alpha, max atom move = 1.0820615e-08 7.0775644e-10 Iterations, force evaluations = 29 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5806 | 1.5806 | 1.5806 | 0.0 | 97.14 Neigh | 0.015661 | 0.015661 | 0.015661 | 0.0 | 0.96 Comm | 0.016049 | 0.016049 | 0.016049 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01488 | | | 0.91 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5567.00 ave 5567 max 5567 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: 89554.0 ave 89554 max 89554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89554 Ave neighs/atom = 54.806610 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.716 | 4.716 | 4.716 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -5786.8556 0 -5786.8556 4509.0248 19270.266 34 0 -5786.99 0 -5786.99 43.372306 19332.19 Loop time of 0.172829 on 1 procs for 5 steps with 1634 atoms 57.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5786.85561302423 -5786.98756894846 -5786.9899710061 Force two-norm initial, final = 98.519183 1.7387389 Force max component initial, final = 77.694413 1.5149497 Final line search alpha, max atom move = 6.0772282e-05 9.2066953e-05 Iterations, force evaluations = 5 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16582 | 0.16582 | 0.16582 | 0.0 | 95.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013565 | 0.0013565 | 0.0013565 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005651 | | | 3.27 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5598.00 ave 5598 max 5598 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: 89558.0 ave 89558 max 89558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89558 Ave neighs/atom = 54.809058 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.854 | 4.854 | 4.854 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5786.99 0 -5786.99 43.372306 Loop time of 6.444e-06 on 1 procs for 0 steps with 1634 atoms 186.2% 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 | | 6.444e-06 | | |100.00 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5607.00 ave 5607 max 5607 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: 89428.0 ave 89428 max 89428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89428 Ave neighs/atom = 54.729498 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.854 | 4.854 | 4.854 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 -5786.99 -5786.99 36.513491 103.63422 5.1088659 43.372306 43.372306 -17.984152 22.624922 125.47615 2.3253917 873.54436 Loop time of 6.555e-06 on 1 procs for 0 steps with 1634 atoms 198.3% 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 | | 6.555e-06 | | |100.00 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5607.00 ave 5607 max 5607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44714.0 ave 44714 max 44714 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 89428.0 ave 89428 max 89428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89428 Ave neighs/atom = 54.729498 Neighbor list builds = 0 Dangerous builds = 0 1634 -5786.9899710061 eV 2.32539174411876 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02