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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -62.613639 0.0000000) to (25.561911 62.613639 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1348587 5.4265154 5.9032705 Created 1194 atoms using lattice units in orthogonal box = (0.0000000 -62.613639 0.0000000) to (25.561911 62.613639 8.8549058) create_atoms CPU = 0.008 seconds 1194 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1348587 5.4265154 5.9032705 Created 1202 atoms using lattice units in orthogonal box = (0.0000000 -62.613639 0.0000000) to (25.561911 62.613639 8.8549058) create_atoms CPU = 0.007 seconds 1202 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 33 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2396 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.470 | 6.470 | 6.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8355.4612 0 -8355.4612 11623.933 87 0 -8463.5753 0 -8463.5753 527.74686 Loop time of 5.56505 on 1 procs for 87 steps with 2396 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 = -8355.46121688672 -8463.56739058483 -8463.57526707195 Force two-norm initial, final = 70.498913 0.27537395 Force max component initial, final = 9.1912157 0.039480853 Final line search alpha, max atom move = 1.0000000 0.039480853 Iterations, force evaluations = 87 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3225 | 5.3225 | 5.3225 | 0.0 | 95.64 Neigh | 0.16961 | 0.16961 | 0.16961 | 0.0 | 3.05 Comm | 0.033387 | 0.033387 | 0.033387 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03958 | | | 0.71 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9383.00 ave 9383 max 9383 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: 400218.0 ave 400218 max 400218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400218 Ave neighs/atom = 167.03589 Neighbor list builds = 3 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.469 | 6.469 | 6.469 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -8463.5753 0 -8463.5753 527.74686 28344.984 91 0 -8463.6939 0 -8463.6939 18.654103 28355.187 Loop time of 0.251392 on 1 procs for 4 steps with 2396 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 = -8463.5752670719 -8463.69374939414 -8463.69393970498 Force two-norm initial, final = 73.907165 1.4384927 Force max component initial, final = 66.275892 1.2689222 Final line search alpha, max atom move = 0.00021809768 0.00027674900 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2444 | 0.2444 | 0.2444 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014228 | 0.0014228 | 0.0014228 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005571 | | | 2.22 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9324.00 ave 9324 max 9324 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: 403028.0 ave 403028 max 403028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403028 Ave neighs/atom = 168.20868 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.607 | 6.607 | 6.607 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8463.6939 0 -8463.6939 18.654103 Loop time of 6.284e-06 on 1 procs for 0 steps with 2396 atoms 191.0% 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 | | 6.284e-06 | | |100.00 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9341.00 ave 9341 max 9341 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: 401666.0 ave 401666 max 401666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401666 Ave neighs/atom = 167.64023 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.607 | 6.607 | 6.607 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 -8463.6939 -8463.6939 25.521984 125.57488 8.8473932 18.654103 18.654103 71.586966 15.019284 -30.643942 2.3673764 1143.3785 Loop time of 7.317e-06 on 1 procs for 0 steps with 2396 atoms 246.0% 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 | | 7.317e-06 | | |100.00 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9341.00 ave 9341 max 9341 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 200833.0 ave 200833 max 200833 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 401666.0 ave 401666 max 401666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401666 Ave neighs/atom = 167.64023 Neighbor list builds = 0 Dangerous builds = 0 2396 -8463.69393970498 eV 2.36737643565937 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06