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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -42.209135 0.0000000) to (51.695422 42.209135 8.7381211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9080482 5.4268888 5.8254141 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -42.209135 0.0000000) to (51.695422 42.209135 8.7381211) create_atoms CPU = 0.003 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9080482 5.4268888 5.8254141 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -42.209135 0.0000000) to (51.695422 42.209135 8.7381211) create_atoms CPU = 0.002 seconds 1686 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3348 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_058735400462_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.197 | 5.197 | 5.197 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13570.97 0 -13570.97 40733.4 113 0 -14112.865 0 -14112.865 43041.321 Loop time of 18.3026 on 1 procs for 113 steps with 3348 atoms 93.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13570.9696609423 -14112.8525336423 -14112.8648510667 Force two-norm initial, final = 412.70877 0.57376471 Force max component initial, final = 77.774758 0.11919058 Final line search alpha, max atom move = 0.68718691 0.081906209 Iterations, force evaluations = 113 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.196 | 18.196 | 18.196 | 0.0 | 99.42 Neigh | 0.051416 | 0.051416 | 0.051416 | 0.0 | 0.28 Comm | 0.018959 | 0.018959 | 0.018959 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03608 | | | 0.20 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7111.00 ave 7111 max 7111 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: 195574.0 ave 195574 max 195574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195574 Ave neighs/atom = 58.415173 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.578 | 5.578 | 5.578 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -14112.865 0 -14112.865 43041.321 38133.493 125 0 -14121.312 0 -14121.312 -102.92963 38646.075 Loop time of 1.22433 on 1 procs for 12 steps with 3348 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 = -14112.8648510666 -14121.3057729943 -14121.3122258783 Force two-norm initial, final = 1830.5087 7.7939713 Force max component initial, final = 1343.0390 6.9793463 Final line search alpha, max atom move = 1.7572868e-05 0.00012264713 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2167 | 1.2167 | 1.2167 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085061 | 0.00085061 | 0.00085061 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006799 | | | 0.56 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7065.00 ave 7065 max 7065 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: 196322.0 ave 196322 max 196322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196322 Ave neighs/atom = 58.638590 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.334 | 5.334 | 5.334 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14121.312 0 -14121.312 -102.92963 Loop time of 2.319e-06 on 1 procs for 0 steps with 3348 atoms 215.6% 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 | | 2.319e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7037.00 ave 7037 max 7037 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: 190502.0 ave 190502 max 190502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190502 Ave neighs/atom = 56.900239 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.334 | 5.334 | 5.334 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 -14121.312 -14121.312 51.585284 85.341035 8.7785273 -102.92963 -102.92963 -0.87378137 -17.229631 -290.68547 2.3627352 2719.1633 Loop time of 2.486e-06 on 1 procs for 0 steps with 3348 atoms 281.6% 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 | | 2.486e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7037.00 ave 7037 max 7037 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95251.0 ave 95251 max 95251 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 190502.0 ave 190502 max 190502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190502 Ave neighs/atom = 56.900239 Neighbor list builds = 0 Dangerous builds = 0 3348 -14121.3122258783 eV 2.36273518057689 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20