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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -41.594254 0.0000000) to (29.409019 41.594254 5.1194532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2382769 5.6714501 5.1194532 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.594254 0.0000000) to (29.409019 41.594254 5.1194532) create_atoms CPU = 0.003 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2382769 5.6714501 5.1194532 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.594254 0.0000000) to (29.409019 41.594254 5.1194532) create_atoms CPU = 0.002 seconds 532 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3662.9136 0 -3662.9136 5387.7433 79 0 -3700.6354 0 -3700.6354 -7963.147 Loop time of 2.83746 on 1 procs for 79 steps with 1048 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 = -3662.91358414564 -3700.63250740609 -3700.63542057341 Force two-norm initial, final = 33.203890 0.14471862 Force max component initial, final = 6.7335873 0.020089645 Final line search alpha, max atom move = 1.0000000 0.020089645 Iterations, force evaluations = 79 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.785 | 2.785 | 2.785 | 0.0 | 98.15 Neigh | 0.02199 | 0.02199 | 0.02199 | 0.0 | 0.78 Comm | 0.016975 | 0.016975 | 0.016975 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01351 | | | 0.48 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7040.00 ave 7040 max 7040 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: 180704.0 ave 180704 max 180704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180704 Ave neighs/atom = 172.42748 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.031 | 5.031 | 5.031 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3700.6354 0 -3700.6354 -7963.147 12524.704 85 0 -3700.8485 0 -3700.8485 -2049.6735 12468.617 Loop time of 0.150507 on 1 procs for 6 steps with 1048 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 = -3700.63542057343 -3700.84781200532 -3700.84852593341 Force two-norm initial, final = 86.775855 1.6623751 Force max component initial, final = 84.425440 1.5840200 Final line search alpha, max atom move = 0.00022722857 0.00035993460 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14602 | 0.14602 | 0.14602 | 0.0 | 97.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082833 | 0.00082833 | 0.00082833 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003664 | | | 2.43 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7016.00 ave 7016 max 7016 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: 180312.0 ave 180312 max 180312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180312 Ave neighs/atom = 172.05344 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.169 | 5.169 | 5.169 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3700.8485 0 -3700.8485 -2049.6735 Loop time of 3e-06 on 1 procs for 0 steps with 1048 atoms 166.7% 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 | | 3e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7016.00 ave 7016 max 7016 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: 180440.0 ave 180440 max 180440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180440 Ave neighs/atom = 172.17557 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.169 | 5.169 | 5.169 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 -3700.8485 -3700.8485 29.427006 83.188508 5.0934127 -2049.6735 -2049.6735 -60.250715 -5886.2636 -202.50606 2.3971607 648.20181 Loop time of 3.151e-06 on 1 procs for 0 steps with 1048 atoms 158.7% 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 | | 3.151e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7016.00 ave 7016 max 7016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90220.0 ave 90220 max 90220 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180440.0 ave 180440 max 180440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180440 Ave neighs/atom = 172.17557 Neighbor list builds = 0 Dangerous builds = 0 1048 -3700.84852593341 eV 2.39716071998835 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03