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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -36.115137 0.0000000) to (18.055763 36.115137 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0556137 5.0556137 3.6111526 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.115137 0.0000000) to (18.055763 36.115137 3.6111526) create_atoms CPU = 0.001 seconds 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0556137 5.0556137 3.6111526 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.115137 0.0000000) to (18.055763 36.115137 3.6111526) create_atoms CPU = 0.000 seconds 201 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 398 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1655.7479 0 -1655.7479 19787.471 67 0 -1683.4136 0 -1683.4136 -2015.8731 Loop time of 2.64401 on 1 procs for 67 steps with 398 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1655.74785126492 -1683.41209730164 -1683.41363209022 Force two-norm initial, final = 34.767301 0.15478415 Force max component initial, final = 12.594641 0.036219058 Final line search alpha, max atom move = 1.0000000 0.036219058 Iterations, force evaluations = 67 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6384 | 2.6384 | 2.6384 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026932 | 0.0026932 | 0.0026932 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002911 | | | 0.11 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2486.00 ave 2486 max 2486 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: 21332.0 ave 21332 max 21332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21332 Ave neighs/atom = 53.597990 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -1683.4136 0 -1683.4136 -2015.8731 4709.5668 73 0 -1683.4798 0 -1683.4798 -1350.8816 4707.8651 Loop time of 0.174203 on 1 procs for 6 steps with 398 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 = -1683.41363209022 -1683.47925250135 -1683.4797913664 Force two-norm initial, final = 21.672369 0.75074997 Force max component initial, final = 20.591587 0.60562946 Final line search alpha, max atom move = 0.00065160874 0.00039463345 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17318 | 0.17318 | 0.17318 | 0.0 | 99.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016838 | 0.00016838 | 0.00016838 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000859 | | | 0.49 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2506.00 ave 2506 max 2506 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: 21410.0 ave 21410 max 21410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21410 Ave neighs/atom = 53.793970 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1683.4798 0 -1683.4798 -1350.8816 Loop time of 1.93e-06 on 1 procs for 0 steps with 398 atoms 155.4% 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 | | 1.93e-06 | | |100.00 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2518.00 ave 2518 max 2518 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: 21424.0 ave 21424 max 21424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21424 Ave neighs/atom = 53.829146 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.951 | 4.951 | 4.951 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 -1683.4798 -1683.4798 17.968657 72.230275 3.6273472 -1350.8816 -1350.8816 -205.11296 -3717.6971 -129.8346 2.3141284 101.77384 Loop time of 3.629e-06 on 1 procs for 0 steps with 398 atoms 165.3% 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 | | 3.629e-06 | | |100.00 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2518.00 ave 2518 max 2518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10712.0 ave 10712 max 10712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21424.0 ave 21424 max 21424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21424 Ave neighs/atom = 53.829146 Neighbor list builds = 0 Dangerous builds = 0 398 -1683.4797913664 eV 2.31412842240212 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03