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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -37.383438 0.0000000) to (26.432067 37.383438 4.0308524) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9175938 4.7812379 4.0308524 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -37.383438 0.0000000) to (26.432067 37.383438 4.0308524) create_atoms CPU = 0.001 seconds 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9175938 4.7812379 4.0308524 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -37.383438 0.0000000) to (26.432067 37.383438 4.0308524) create_atoms CPU = 0.001 seconds 345 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 25 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 684 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2892.2666 0 -2892.2666 11417.187 24 0 -2922.9222 0 -2922.9222 -4389.8285 Loop time of 1.66602 on 1 procs for 24 steps with 684 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 = -2892.26659159101 -2922.91969654745 -2922.92221815635 Force two-norm initial, final = 55.478798 0.14661110 Force max component initial, final = 16.116200 0.032671018 Final line search alpha, max atom move = 0.88703568 0.028980359 Iterations, force evaluations = 24 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6583 | 1.6583 | 1.6583 | 0.0 | 99.53 Neigh | 0.0043601 | 0.0043601 | 0.0043601 | 0.0 | 0.26 Comm | 0.0016293 | 0.0016293 | 0.0016293 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001778 | | | 0.11 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4508.00 ave 4508 max 4508 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: 44712.0 ave 44712 max 44712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44712 Ave neighs/atom = 65.368421 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -2922.9222 0 -2922.9222 -4389.8285 7965.9441 27 0 -2922.9527 0 -2922.9527 -2129.6365 7955.014 Loop time of 0.22001 on 1 procs for 3 steps with 684 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 = -2922.92221815635 -2922.95201474521 -2922.9527021823 Force two-norm initial, final = 27.903953 1.4928736 Force max component initial, final = 27.899900 1.4435560 Final line search alpha, max atom move = 0.00024008478 0.00034657582 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21915 | 0.21915 | 0.21915 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016538 | 0.00016538 | 0.00016538 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006909 | | | 0.31 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4508.00 ave 4508 max 4508 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: 44802.0 ave 44802 max 44802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44802 Ave neighs/atom = 65.500000 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.654 | 4.654 | 4.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2922.9527 0 -2922.9527 -2129.6365 Loop time of 1.785e-06 on 1 procs for 0 steps with 684 atoms 112.0% 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 | | 1.785e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4508.00 ave 4508 max 4508 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: 44804.0 ave 44804 max 44804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44804 Ave neighs/atom = 65.502924 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.654 | 4.654 | 4.654 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 -2922.9527 -2922.9527 26.450597 74.766876 4.0225017 -2129.6365 -2129.6365 -70.079239 -6028.6939 -290.1365 2.2850718 400.6217 Loop time of 1.737e-06 on 1 procs for 0 steps with 684 atoms 172.7% 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 | | 1.737e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4508.00 ave 4508 max 4508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22402.0 ave 22402 max 22402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44804.0 ave 44804 max 44804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44804 Ave neighs/atom = 65.502924 Neighbor list builds = 0 Dangerous builds = 0 684 -2922.9527021823 eV 2.28507180526556 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02