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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -80.604751 0.0000000) to (49.357635 80.604751 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7080258 5.7571914 6.6478321 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -80.604751 0.0000000) to (49.357635 80.604751 9.9717481) create_atoms CPU = 0.003 seconds 2357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7080258 5.7571914 6.6478321 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -80.604751 0.0000000) to (49.357635 80.604751 9.9717481) create_atoms CPU = 0.003 seconds 2357 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 53 4 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 47 atoms, new total = 4667 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 53 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.781 | 5.781 | 5.781 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15664.535 0 -15664.535 -773.47752 20 0 -15684.771 0 -15684.771 -4013.4359 Loop time of 3.76821 on 1 procs for 20 steps with 4667 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 = -15664.5354857601 -15684.7671762726 -15684.7710980907 Force two-norm initial, final = 21.731827 0.89887742 Force max component initial, final = 4.2642286 0.13349878 Final line search alpha, max atom move = 0.54133609 0.072267708 Iterations, force evaluations = 20 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7578 | 3.7578 | 3.7578 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032306 | 0.0032306 | 0.0032306 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007196 | | | 0.19 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9428.00 ave 9428 max 9428 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: 250326.0 ave 250326 max 250326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250326 Ave neighs/atom = 53.637454 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 53 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.781 | 5.781 | 5.781 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -15684.771 0 -15684.771 -4013.4359 79344.4 23 0 -15685.042 0 -15685.042 -1047.3409 79107.896 Loop time of 0.689748 on 1 procs for 3 steps with 4667 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 = -15684.7710980906 -15685.0358295985 -15685.0419373421 Force two-norm initial, final = 244.86534 0.86845654 Force max component initial, final = 197.37426 0.15412554 Final line search alpha, max atom move = 5.0034910e-05 7.7116577e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68625 | 0.68625 | 0.68625 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043577 | 0.00043577 | 0.00043577 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003063 | | | 0.44 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9446.00 ave 9446 max 9446 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: 250952.0 ave 250952 max 250952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250952 Ave neighs/atom = 53.771588 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 53 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.919 | 5.919 | 5.919 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15685.042 0 -15685.042 -1047.3409 Loop time of 2.064e-06 on 1 procs for 0 steps with 4667 atoms 193.8% 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 | | 2.064e-06 | | |100.00 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9446.00 ave 9446 max 9446 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: 251004.0 ave 251004 max 251004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251004 Ave neighs/atom = 53.782730 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 53 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.919 | 5.919 | 5.919 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 -15685.042 -15685.042 49.319525 161.2095 9.9497074 -1047.3409 -1047.3409 3.1191028 -3146.3052 1.1634515 2.4937784 2200.8831 Loop time of 2.197e-06 on 1 procs for 0 steps with 4667 atoms 227.6% 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 | | 2.197e-06 | | |100.00 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9446.00 ave 9446 max 9446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125502.0 ave 125502 max 125502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 251004.0 ave 251004 max 251004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251004 Ave neighs/atom = 53.782730 Neighbor list builds = 0 Dangerous builds = 0 4667 -15685.0419373421 eV 2.49377838927474 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05