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 = 3.5898365 3.5898365 3.5898365 Created orthogonal box = (0.0000000 -41.864328 0.0000000) to (14.801275 41.864328 5.0767954) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0946426 6.1565188 5.0767954 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.864328 0.0000000) to (14.801275 41.864328 5.0767954) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0946426 6.1565188 5.0767954 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.864328 0.0000000) to (14.801275 41.864328 5.0767954) create_atoms CPU = 0.001 seconds 274 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 4 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 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_115316750986_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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1750.6252 0 -1750.6252 70497.272 108 0 -1914.5466 0 -1914.5466 9630.9468 Loop time of 1.76542 on 1 procs for 108 steps with 546 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1750.62524591069 -1914.54476104151 -1914.54655266329 Force two-norm initial, final = 330.64114 0.13526945 Force max component initial, final = 105.78191 0.036184979 Final line search alpha, max atom move = 1.0000000 0.036184979 Iterations, force evaluations = 108 209 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7423 | 1.7423 | 1.7423 | 0.0 | 98.69 Neigh | 0.0057557 | 0.0057557 | 0.0057557 | 0.0 | 0.33 Comm | 0.010228 | 0.010228 | 0.010228 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007161 | | | 0.41 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4702.00 ave 4702 max 4702 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: 87864.0 ave 87864 max 87864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87864 Ave neighs/atom = 160.92308 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -1914.5466 0 -1914.5466 9630.9468 6291.6261 114 0 -1914.72 0 -1914.72 139.91772 6335.7318 Loop time of 0.0660129 on 1 procs for 6 steps with 546 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 = -1914.54655266329 -1914.71953900968 -1914.71998482723 Force two-norm initial, final = 69.599952 1.3581772 Force max component initial, final = 56.969237 1.2547115 Final line search alpha, max atom move = 0.00038560334 0.00048382095 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064371 | 0.064371 | 0.064371 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029815 | 0.00029815 | 0.00029815 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001343 | | | 2.03 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4689.00 ave 4689 max 4689 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: 89192.0 ave 89192 max 89192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89192 Ave neighs/atom = 163.35531 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.666 | 4.666 | 4.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1914.72 0 -1914.72 139.91772 Loop time of 1.716e-06 on 1 procs for 0 steps with 546 atoms 116.6% 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 | | 1.716e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676.00 ave 4676 max 4676 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: 83784.0 ave 83784 max 83784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83784 Ave neighs/atom = 153.45055 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.666 | 4.666 | 4.666 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 -1914.72 -1914.72 14.875902 83.810629 5.0817625 139.91772 139.91772 318.89055 123.41892 -22.55631 2.4021226 479.9702 Loop time of 1.853e-06 on 1 procs for 0 steps with 546 atoms 161.9% 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 | | 1.853e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676.00 ave 4676 max 4676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41892.0 ave 41892 max 41892 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 83784.0 ave 83784 max 83784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83784 Ave neighs/atom = 153.45055 Neighbor list builds = 0 Dangerous builds = 0 546 -1914.71998482723 eV 2.40212260534874 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02