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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -30.034170 0.0000000) to (36.784196 30.034170 7.0144709) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6816249 4.3686066 4.6763139 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -30.034170 0.0000000) to (36.784196 30.034170 7.0144709) create_atoms CPU = 0.001 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6816249 4.3686066 4.6763139 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -30.034170 0.0000000) to (36.784196 30.034170 7.0144709) create_atoms CPU = 0.001 seconds 662 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 = 11 18 3 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 8 atoms, new total = 1310 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_260546967793_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 = 11 18 3 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4747.2138 0 -4747.2138 104614.97 83 0 -5585.7494 0 -5585.7494 -1469.7804 Loop time of 16.6588 on 1 procs for 83 steps with 1310 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 = -4747.21384273243 -5585.74433117039 -5585.74935038027 Force two-norm initial, final = 964.13297 0.23223178 Force max component initial, final = 163.90487 0.044952837 Final line search alpha, max atom move = 0.87192768 0.039195623 Iterations, force evaluations = 83 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.598 | 16.598 | 16.598 | 0.0 | 99.64 Neigh | 0.041867 | 0.041867 | 0.041867 | 0.0 | 0.25 Comm | 0.0079817 | 0.0079817 | 0.0079817 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01061 | | | 0.06 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4936.00 ave 4936 max 4936 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: 146236.0 ave 146236 max 146236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146236 Ave neighs/atom = 111.63053 Neighbor list builds = 4 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 = 11 18 3 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.044 | 5.044 | 5.044 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -5585.7494 0 -5585.7494 -1469.7804 15498.934 87 0 -5585.8665 0 -5585.8665 13.267089 15485.268 Loop time of 0.901501 on 1 procs for 4 steps with 1310 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5585.74935038024 -5585.86634087968 -5585.86648580244 Force two-norm initial, final = 67.027617 0.76561583 Force max component initial, final = 58.249763 0.46094796 Final line search alpha, max atom move = 0.00034286126 0.00015804120 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89938 | 0.89938 | 0.89938 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031999 | 0.00031999 | 0.00031999 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001802 | | | 0.20 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4937.00 ave 4937 max 4937 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: 146120.0 ave 146120 max 146120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146120 Ave neighs/atom = 111.54198 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 = 11 18 3 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) = 5.182 | 5.182 | 5.182 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5585.8665 0 -5585.8665 13.267089 Loop time of 2.228e-06 on 1 procs for 0 steps with 1310 atoms 134.6% 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 | | 2.228e-06 | | |100.00 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4923.00 ave 4923 max 4923 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: 146120.0 ave 146120 max 146120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146120 Ave neighs/atom = 111.54198 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 = 11 18 3 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) = 5.182 | 5.182 | 5.182 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 -5585.8665 -5585.8665 36.768157 60.206057 6.9953055 13.267089 13.267089 -41.588686 33.82848 47.561472 2.2998151 1902.3847 Loop time of 2.083e-06 on 1 procs for 0 steps with 1310 atoms 192.0% 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 | | 2.083e-06 | | |100.00 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4923.00 ave 4923 max 4923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73060.0 ave 73060 max 73060 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146120.0 ave 146120 max 146120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146120 Ave neighs/atom = 111.54198 Neighbor list builds = 0 Dangerous builds = 0 1310 -5585.86648580244 eV 2.29981513588913 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18