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 -34.560211 0.0000000) to (28.215967 34.560211 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0308524 3.9964295 4.6544275 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -34.560211 0.0000000) to (28.215967 34.560211 6.9816412) create_atoms CPU = 0.001 seconds 590 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0308524 3.9964295 4.6544275 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -34.560211 0.0000000) to (28.215967 34.560211 6.9816412) create_atoms CPU = 0.001 seconds 590 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 = 10 23 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1160 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 = 10 23 3 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4891.5329 0 -4891.5329 5818.5081 69 0 -4945.9531 0 -4945.9531 -12697.591 Loop time of 8.31717 on 1 procs for 69 steps with 1160 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 = -4891.53285573884 -4945.9489997519 -4945.95309353362 Force two-norm initial, final = 97.249290 0.19523217 Force max component initial, final = 31.522630 0.051229026 Final line search alpha, max atom move = 1.0000000 0.051229026 Iterations, force evaluations = 69 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2982 | 8.2982 | 8.2982 | 0.0 | 99.77 Neigh | 0.0067912 | 0.0067912 | 0.0067912 | 0.0 | 0.08 Comm | 0.0049758 | 0.0049758 | 0.0049758 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007215 | | | 0.09 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4042.00 ave 4042 max 4042 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: 75892.0 ave 75892 max 75892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75892 Ave neighs/atom = 65.424138 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 = 10 23 3 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4945.9531 0 -4945.9531 -12697.591 13616.292 74 0 -4946.4184 0 -4946.4184 -128.21058 13511.025 Loop time of 0.456125 on 1 procs for 5 steps with 1160 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 = -4945.95309353364 -4946.41612166021 -4946.4183811983 Force two-norm initial, final = 170.03242 3.8871311 Force max component initial, final = 125.68839 3.8644188 Final line search alpha, max atom move = 9.7580929e-05 0.00037709357 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45457 | 0.45457 | 0.45457 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023406 | 0.00023406 | 0.00023406 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001323 | | | 0.29 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4374.00 ave 4374 max 4374 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: 75520.0 ave 75520 max 75520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75520 Ave neighs/atom = 65.103448 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 = 10 23 3 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) = 4.720 | 4.720 | 4.720 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4946.4184 0 -4946.4184 -128.21058 Loop time of 1.99e-06 on 1 procs for 0 steps with 1160 atoms 150.8% 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 | | 1.99e-06 | | |100.00 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4374.00 ave 4374 max 4374 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: 75648.0 ave 75648 max 75648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75648 Ave neighs/atom = 65.213793 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 = 10 23 3 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) = 4.720 | 4.720 | 4.720 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 -4946.4184 -4946.4184 28.090758 69.120422 6.9585454 -128.21058 -128.21058 -31.882808 -809.48698 456.73804 2.2092016 866.85961 Loop time of 2.1e-06 on 1 procs for 0 steps with 1160 atoms 190.5% 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 | | 2.1e-06 | | |100.00 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4374.00 ave 4374 max 4374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37824.0 ave 37824 max 37824 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75648.0 ave 75648 max 75648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75648 Ave neighs/atom = 65.213793 Neighbor list builds = 0 Dangerous builds = 0 1160 -4946.4183811983 eV 2.20920163523494 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09