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 -68.547623 0.0000000) to (34.273812 68.547623 3.6330168) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0062871 5.0062871 3.6330168 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -68.547623 0.0000000) to (34.273812 68.547623 3.6330168) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0062871 5.0062871 3.6330168 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -68.547623 0.0000000) to (34.273812 68.547623 3.6330168) create_atoms CPU = 0.002 seconds 714 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 = 9 36 1 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 2 atoms, new total = 1424 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 = 9 36 1 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) = 5.532 | 5.532 | 5.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5426.9317 0 -5426.9317 81435.122 87 0 -6070.9166 0 -6070.9166 4710.3513 Loop time of 3.87374 on 1 procs for 87 steps with 1424 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5426.93171643807 -6070.91115786489 -6070.91656948288 Force two-norm initial, final = 1035.7918 0.32418158 Force max component initial, final = 295.24876 0.044523879 Final line search alpha, max atom move = 1.0000000 0.044523879 Iterations, force evaluations = 87 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7773 | 3.7773 | 3.7773 | 0.0 | 97.51 Neigh | 0.031763 | 0.031763 | 0.031763 | 0.0 | 0.82 Comm | 0.036898 | 0.036898 | 0.036898 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02778 | | | 0.72 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10081.0 ave 10081 max 10081 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: 238280.0 ave 238280 max 238280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238280 Ave neighs/atom = 167.33146 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 = 9 36 1 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 : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -6070.9166 0 -6070.9166 4710.3513 17070.734 91 0 -6071.1 0 -6071.1 -520.76054 17128.456 Loop time of 0.146513 on 1 procs for 4 steps with 1424 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 = -6070.91656948288 -6071.09540510126 -6071.09999361156 Force two-norm initial, final = 109.68316 10.388740 Force max component initial, final = 86.105012 8.0585491 Final line search alpha, max atom move = 9.5156290e-05 0.00076682163 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14088 | 0.14088 | 0.14088 | 0.0 | 96.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013953 | 0.0013953 | 0.0013953 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004237 | | | 2.89 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10051.0 ave 10051 max 10051 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: 238640.0 ave 238640 max 238640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238640 Ave neighs/atom = 167.58427 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 = 9 36 1 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) = 5.670 | 5.670 | 5.670 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6071.1 0 -6071.1 -520.76054 Loop time of 6.966e-06 on 1 procs for 0 steps with 1424 atoms 172.3% 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 | | 6.966e-06 | | |100.00 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10061.0 ave 10061 max 10061 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: 225152.0 ave 225152 max 225152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225152 Ave neighs/atom = 158.11236 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 = 9 36 1 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) = 5.670 | 5.670 | 5.670 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 -6071.1 -6071.1 34.221637 137.37028 3.6435493 -520.76054 -520.76054 -752.64013 -560.58802 -249.05347 2.2963468 363.613 Loop time of 7.217e-06 on 1 procs for 0 steps with 1424 atoms 235.6% 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 | | 7.217e-06 | | |100.00 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10061.0 ave 10061 max 10061 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112576.0 ave 112576 max 112576 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225152.0 ave 225152 max 225152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225152 Ave neighs/atom = 158.11236 Neighbor list builds = 0 Dangerous builds = 0 1424 -6071.09999361156 eV 2.29634678424718 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04