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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -37.966881 0.0000000) to (46.499742 37.966881 8.8671529) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9181490 5.5224553 5.9114353 Created 1320 atoms using lattice units in orthogonal box = (0.0000000 -37.966881 0.0000000) to (46.499742 37.966881 8.8671529) create_atoms CPU = 0.002 seconds 1320 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9181490 5.5224553 5.9114353 Created 1326 atoms using lattice units in orthogonal box = (0.0000000 -37.966881 0.0000000) to (46.499742 37.966881 8.8671529) create_atoms CPU = 0.002 seconds 1326 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 22 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2628 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.993 | 5.993 | 5.993 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6188.247 0 -6188.247 246999.02 74 0 -9259.2487 0 -9259.2487 1101.8515 Loop time of 17.6156 on 1 procs for 74 steps with 2628 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 = -6188.24696831579 -9259.24269264481 -9259.24872620422 Force two-norm initial, final = 3928.3749 0.23084206 Force max component initial, final = 512.07830 0.030891621 Final line search alpha, max atom move = 1.0000000 0.030891621 Iterations, force evaluations = 74 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.542 | 17.542 | 17.542 | 0.0 | 99.58 Neigh | 0.043462 | 0.043462 | 0.043462 | 0.0 | 0.25 Comm | 0.012262 | 0.012262 | 0.012262 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01799 | | | 0.10 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7834.00 ave 7834 max 7834 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: 345540.0 ave 345540 max 345540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 345540 Ave neighs/atom = 131.48402 Neighbor list builds = 2 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.991 | 5.991 | 5.991 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -9259.2487 0 -9259.2487 1101.8515 31309.033 78 0 -9259.4444 0 -9259.4444 111.53106 31331.688 Loop time of 0.835382 on 1 procs for 4 steps with 2628 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9259.24872620421 -9259.44383894755 -9259.4443680997 Force two-norm initial, final = 100.46645 4.2477660 Force max component initial, final = 75.768338 3.7453247 Final line search alpha, max atom move = 0.00024873722 0.00093160165 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8326 | 0.8326 | 0.8326 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037994 | 0.00037994 | 0.00037994 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002397 | | | 0.29 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7617.00 ave 7617 max 7617 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: 346428.0 ave 346428 max 346428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346428 Ave neighs/atom = 131.82192 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.131 | 6.131 | 6.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9259.4444 0 -9259.4444 111.53106 Loop time of 2.098e-06 on 1 procs for 0 steps with 2628 atoms 143.0% 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 | | 2.098e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7847.00 ave 7847 max 7847 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: 346404.0 ave 346404 max 346404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346404 Ave neighs/atom = 131.81279 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.131 | 6.131 | 6.131 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 -9259.4444 -9259.4444 46.537324 76.140798 8.8422943 111.53106 111.53106 78.510642 192.04303 64.039503 2.3095192 1431.9143 Loop time of 2.322e-06 on 1 procs for 0 steps with 2628 atoms 258.4% 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 | | 2.322e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7847.00 ave 7847 max 7847 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173202.0 ave 173202 max 173202 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346404.0 ave 346404 max 346404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346404 Ave neighs/atom = 131.81279 Neighbor list builds = 0 Dangerous builds = 0 2628 -9259.4443680997 eV 2.30951924024102 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19