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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -38.896333 0.0000000) to (19.446361 38.896333 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6939492 4.6939492 3.6110985 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -38.896333 0.0000000) to (19.446361 38.896333 3.6110985) create_atoms CPU = 0.002 seconds 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6939492 4.6939492 3.6110985 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -38.896333 0.0000000) to (19.446361 38.896333 3.6110985) create_atoms CPU = 0.001 seconds 233 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 23 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 460 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_110119204723_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1917.1941 0 -1917.1941 15012.943 57 0 -1941.5978 0 -1941.5978 -4986.7664 Loop time of 7.636 on 1 procs for 57 steps with 460 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1917.19411218729 -1941.59592742193 -1941.59776248493 Force two-norm initial, final = 40.216466 0.12224404 Force max component initial, final = 13.304028 0.031326683 Final line search alpha, max atom move = 1.0000000 0.031326683 Iterations, force evaluations = 57 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6112 | 7.6112 | 7.6112 | 0.0 | 99.68 Neigh | 0.0073819 | 0.0073819 | 0.0073819 | 0.0 | 0.10 Comm | 0.0092793 | 0.0092793 | 0.0092793 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008148 | | | 0.11 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3671.00 ave 3671 max 3671 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: 57332.0 ave 57332 max 57332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57332 Ave neighs/atom = 124.63478 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -1941.5978 0 -1941.5978 -4986.7664 5462.813 65 0 -1941.6803 0 -1941.6803 -3065.4672 5456.543 Loop time of 0.733522 on 1 procs for 8 steps with 460 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 = -1941.59776248492 -1941.67990442806 -1941.6803103731 Force two-norm initial, final = 22.362141 2.0073473 Force max component initial, final = 22.360895 1.9717520 Final line search alpha, max atom move = 0.00047889450 0.00094426119 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72997 | 0.72997 | 0.72997 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076823 | 0.00076823 | 0.00076823 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002783 | | | 0.38 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3663.00 ave 3663 max 3663 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: 58348.0 ave 58348 max 58348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58348 Ave neighs/atom = 126.84348 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1941.6803 0 -1941.6803 -3065.4672 Loop time of 6.205e-06 on 1 procs for 0 steps with 460 atoms 193.4% 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 | | 6.205e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3680.00 ave 3680 max 3680 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: 58120.0 ave 58120 max 58120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58120 Ave neighs/atom = 126.34783 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.603 | 4.603 | 4.603 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 -1941.6803 -1941.6803 19.316344 77.792665 3.6312319 -3065.4672 -3065.4672 -575.08451 -8555.0921 -66.225101 2.3141633 280.17264 Loop time of 7.096e-06 on 1 procs for 0 steps with 460 atoms 267.8% 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 | | 7.096e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3680.00 ave 3680 max 3680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29060.0 ave 29060 max 29060 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58120.0 ave 58120 max 58120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58120 Ave neighs/atom = 126.34783 Neighbor list builds = 0 Dangerous builds = 0 460 -1941.6803103731 eV 2.31416332002362 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09