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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -62.179130 0.0000000) to (35.897105 62.179130 6.0968202) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226316 5.5798624 6.0968202 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.179130 0.0000000) to (35.897105 62.179130 6.0968202) create_atoms CPU = 0.003 seconds 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226316 5.5798624 6.0968202 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.179130 0.0000000) to (35.897105 62.179130 6.0968202) create_atoms CPU = 0.003 seconds 1250 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 = 10 32 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 22 atoms, new total = 2478 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 = 10 32 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) = 6.527 | 6.527 | 6.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10942.919 0 -10942.919 -375.74119 27 0 -10984.034 0 -10984.034 -5096.2125 Loop time of 1.0586 on 1 procs for 27 steps with 2478 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10942.9190557607 -10984.0243451146 -10984.0335160915 Force two-norm initial, final = 37.184829 0.36944650 Force max component initial, final = 5.8630375 0.088953598 Final line search alpha, max atom move = 0.83419997 0.074205089 Iterations, force evaluations = 27 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0463 | 1.0463 | 1.0463 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0059096 | 0.0059096 | 0.0059096 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006433 | | | 0.61 Nlocal: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10836.0 ave 10836 max 10836 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: 433840.0 ave 433840 max 433840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 433840 Ave neighs/atom = 175.07667 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 32 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.527 | 6.527 | 6.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -10984.034 0 -10984.034 -5096.2125 27216.824 29 0 -10984.117 0 -10984.117 -1266.6373 27160.796 Loop time of 0.0827768 on 1 procs for 2 steps with 2478 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 = -10984.0335160913 -10984.1135748961 -10984.1167911027 Force two-norm initial, final = 111.65982 3.5174980 Force max component initial, final = 92.450780 3.2615971 Final line search alpha, max atom move = 4.9579807e-05 0.00016170936 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.081043 | 0.081043 | 0.081043 | 0.0 | 97.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031876 | 0.00031876 | 0.00031876 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001415 | | | 1.71 Nlocal: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10836.0 ave 10836 max 10836 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: 435628.0 ave 435628 max 435628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 435628 Ave neighs/atom = 175.79822 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 = 10 32 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) = 6.665 | 6.665 | 6.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10984.117 0 -10984.117 -1266.6373 Loop time of 1.702e-06 on 1 procs for 0 steps with 2478 atoms 117.5% 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 | | 1.702e-06 | | |100.00 Nlocal: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10836.0 ave 10836 max 10836 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: 435798.0 ave 435798 max 435798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 435798 Ave neighs/atom = 175.86683 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 = 10 32 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) = 6.665 | 6.665 | 6.665 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 -10984.117 -10984.117 35.869148 124.35826 6.0890117 -1266.6373 -1266.6373 192.2471 -3917.9836 -74.175566 2.2518967 1002.2 Loop time of 1.754e-06 on 1 procs for 0 steps with 2478 atoms 228.1% 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 | | 1.754e-06 | | |100.00 Nlocal: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10836.0 ave 10836 max 10836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217899.0 ave 217899 max 217899 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 435798.0 ave 435798 max 435798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 435798 Ave neighs/atom = 175.86683 Neighbor list builds = 0 Dangerous builds = 0 2478 -10984.1167911027 eV 2.25189672971998 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01