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 = 3.6336621 3.6336621 3.6336621 Created orthogonal box = (0.0000000 -59.040020 0.0000000) to (20.873799 59.040020 5.1387742) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6928544 4.4727288 5.1387742 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -59.040020 0.0000000) to (20.873799 59.040020 5.1387742) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6928544 4.4727288 5.1387742 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.040020 0.0000000) to (20.873799 59.040020 5.1387742) create_atoms CPU = 0.001 seconds 530 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1050 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_529419924683_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4251.3752 0 -4251.3752 707.7903 77 0 -4297.8897 0 -4297.8897 -2532.2551 Loop time of 76.8669 on 1 procs for 77 steps with 1050 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 = -4251.37519187202 -4297.88655327213 -4297.88967550577 Force two-norm initial, final = 31.809695 0.15792120 Force max component initial, final = 8.3020333 0.036985937 Final line search alpha, max atom move = 1.0000000 0.036985937 Iterations, force evaluations = 77 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 76.823 | 76.823 | 76.823 | 0.0 | 99.94 Neigh | 0.018572 | 0.018572 | 0.018572 | 0.0 | 0.02 Comm | 0.012407 | 0.012407 | 0.012407 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01311 | | | 0.02 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4704.00 ave 4704 max 4704 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: 58796.0 ave 58796 max 58796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58796 Ave neighs/atom = 55.996190 Neighbor list builds = 2 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -4297.8897 0 -4297.8897 -2532.2551 12665.943 79 0 -4297.9085 0 -4297.9085 -8.0372518 12643.369 Loop time of 2.64689 on 1 procs for 2 steps with 1050 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 = -4297.88967550577 -4297.90816342064 -4297.90850504701 Force two-norm initial, final = 34.994199 0.54732123 Force max component initial, final = 23.663406 0.35805139 Final line search alpha, max atom move = 0.00044242643 0.00015841140 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6449 | 2.6449 | 2.6449 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035667 | 0.00035667 | 0.00035667 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001587 | | | 0.06 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4712.00 ave 4712 max 4712 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: 58912.0 ave 58912 max 58912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58912 Ave neighs/atom = 56.106667 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.753 | 4.753 | 4.753 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4297.9085 0 -4297.9085 -8.0372518 Loop time of 3.031e-06 on 1 procs for 0 steps with 1050 atoms 165.0% 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 | | 3.031e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4718.00 ave 4718 max 4718 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: 59012.0 ave 59012 max 59012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59012 Ave neighs/atom = 56.201905 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.753 | 4.753 | 4.753 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 -4297.9085 -4297.9085 20.85534 118.0181 5.1368501 -8.0372518 -8.0372518 -21.914633 43.158411 -45.355533 2.4120916 487.46831 Loop time of 3.136e-06 on 1 procs for 0 steps with 1050 atoms 159.4% 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 | | 3.136e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4718.00 ave 4718 max 4718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29506.0 ave 29506 max 29506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59012.0 ave 59012 max 59012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59012 Ave neighs/atom = 56.201905 Neighbor list builds = 0 Dangerous builds = 0 1050 -2685.91173443742 eV 2.41209158689681 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:21