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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -35.957799 0.0000000) to (25.423486 35.957799 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4864975 5.6398806 5.0346005 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -35.957799 0.0000000) to (25.423486 35.957799 5.0346005) create_atoms CPU = 0.001 seconds 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4864975 5.6398806 5.0346005 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -35.957799 0.0000000) to (25.423486 35.957799 5.0346005) create_atoms CPU = 0.001 seconds 410 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 = 7 19 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 = 804 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_657255834688_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 = 7 19 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) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3486.435 0 -3486.435 -2289.2871 53 0 -3517.0985 0 -3517.0985 -5982.0484 Loop time of 0.711996 on 1 procs for 53 steps with 804 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3486.43500277261 -3517.09520750867 -3517.09847260132 Force two-norm initial, final = 35.721201 0.25273018 Force max component initial, final = 10.157877 0.062693562 Final line search alpha, max atom move = 1.0000000 0.062693562 Iterations, force evaluations = 53 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6955 | 0.6955 | 0.6955 | 0.0 | 97.68 Neigh | 0.0084142 | 0.0084142 | 0.0084142 | 0.0 | 1.18 Comm | 0.0045806 | 0.0045806 | 0.0045806 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003505 | | | 0.49 Nlocal: 804.000 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5913.00 ave 5913 max 5913 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: 139848.0 ave 139848 max 139848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139848 Ave neighs/atom = 173.94030 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 = 7 19 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.976 | 4.976 | 4.976 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -3517.0985 0 -3517.0985 -5982.0484 9204.9875 55 0 -3517.1396 0 -3517.1396 -1041.8499 9181.2342 Loop time of 0.0284505 on 1 procs for 2 steps with 804 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 = -3517.09847260131 -3517.13654894318 -3517.13958018271 Force two-norm initial, final = 44.804889 2.7669964 Force max component initial, final = 33.359510 2.3318368 Final line search alpha, max atom move = 9.6678519e-05 0.00022543853 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.027639 | 0.027639 | 0.027639 | 0.0 | 97.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016935 | 0.00016935 | 0.00016935 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006425 | | | 2.26 Nlocal: 804.000 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5931.00 ave 5931 max 5931 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: 139808.0 ave 139808 max 139808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139808 Ave neighs/atom = 173.89055 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 = 7 19 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3517.1396 0 -3517.1396 -1041.8499 Loop time of 1.581e-06 on 1 procs for 0 steps with 804 atoms 126.5% 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 | | 1.581e-06 | | |100.00 Nlocal: 804.000 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5931.00 ave 5931 max 5931 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: 139904.0 ave 139904 max 139904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139904 Ave neighs/atom = 174.00995 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 = 7 19 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) = 5.114 | 5.114 | 5.114 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 -3517.1396 -3517.1396 25.39429 71.915598 5.0273822 -1041.8499 -1041.8499 406.4512 -3278.3663 -253.63477 2.3633757 733.93936 Loop time of 7.801e-06 on 1 procs for 0 steps with 804 atoms 128.2% 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 | | 7.801e-06 | | |100.00 Nlocal: 804.000 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5931.00 ave 5931 max 5931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69952.0 ave 69952 max 69952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139904.0 ave 139904 max 139904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139904 Ave neighs/atom = 174.00995 Neighbor list builds = 0 Dangerous builds = 0 804 -3517.13958018271 eV 2.36337572058417 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01