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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -41.102893 0.0000000) to (17.798075 41.102893 6.2925696) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9326915 5.1378616 6.2925696 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -41.102893 0.0000000) to (17.798075 41.102893 6.2925696) create_atoms CPU = 0.002 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9326915 5.1378616 6.2925696 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -41.102893 0.0000000) to (17.798075 41.102893 6.2925696) create_atoms CPU = 0.002 seconds 396 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 22 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 776 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2773.3701 0 -2773.3701 167837.28 137 0 -3299.9604 0 -3299.9604 19851.501 Loop time of 3.83968 on 1 procs for 137 steps with 776 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 = -2773.37013401892 -3299.95735571979 -3299.96037322122 Force two-norm initial, final = 595.65480 0.22014397 Force max component initial, final = 156.28596 0.020529666 Final line search alpha, max atom move = 1.0000000 0.020529666 Iterations, force evaluations = 137 264 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7555 | 3.7555 | 3.7555 | 0.0 | 97.81 Neigh | 0.019098 | 0.019098 | 0.019098 | 0.0 | 0.50 Comm | 0.035252 | 0.035252 | 0.035252 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02984 | | | 0.78 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4949.00 ave 4949 max 4949 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: 130080.0 ave 130080 max 130080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130080 Ave neighs/atom = 167.62887 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -3299.9604 0 -3299.9604 19851.501 9206.6882 149 0 -3301.1932 0 -3301.1932 52.347479 9320.1589 Loop time of 0.181501 on 1 procs for 12 steps with 776 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 = -3299.96037322124 -3301.19208614799 -3301.1932474329 Force two-norm initial, final = 228.48768 0.94373649 Force max component initial, final = 200.20476 0.36867297 Final line search alpha, max atom move = 0.00027576229 0.00010166610 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17418 | 0.17418 | 0.17418 | 0.0 | 95.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015922 | 0.0015922 | 0.0015922 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005733 | | | 3.16 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5439.00 ave 5439 max 5439 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: 129928.0 ave 129928 max 129928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129928 Ave neighs/atom = 167.43299 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.122 | 5.122 | 5.122 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3301.1932 0 -3301.1932 52.347479 Loop time of 6.084e-06 on 1 procs for 0 steps with 776 atoms 180.8% 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 | | 6.084e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5301.00 ave 5301 max 5301 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: 122528.0 ave 122528 max 122528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122528 Ave neighs/atom = 157.89691 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.122 | 5.122 | 5.122 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 -3301.1932 -3301.1932 17.759677 83.136425 6.3124349 52.347479 52.347479 63.239784 39.993177 53.809477 2.398663 560.44719 Loop time of 7.146e-06 on 1 procs for 0 steps with 776 atoms 279.9% 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 | | 7.146e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5301.00 ave 5301 max 5301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61264.0 ave 61264 max 61264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122528.0 ave 122528 max 122528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122528 Ave neighs/atom = 157.89691 Neighbor list builds = 0 Dangerous builds = 0 776 -3301.1932474329 eV 2.39866303230215 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04