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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -38.597639 0.0000000) to (27.292652 38.597639 5.1123821) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2670030 6.0943640 5.1123821 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.597639 0.0000000) to (27.292652 38.597639 5.1123821) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2670030 6.0943640 5.1123821 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.597639 0.0000000) to (27.292652 38.597639 5.1123821) create_atoms CPU = 0.001 seconds 458 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 8 21 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_346334655118_005#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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2887.7807 0 -2887.7807 88016.785 90 0 -3199.8257 0 -3199.8257 2147.6678 Loop time of 1.14499 on 1 procs for 90 steps with 908 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2887.78074479021 -3199.82284220683 -3199.82570469996 Force two-norm initial, final = 841.92303 0.17898845 Force max component initial, final = 265.11921 0.032143749 Final line search alpha, max atom move = 1.0000000 0.032143749 Iterations, force evaluations = 90 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1012 | 1.1012 | 1.1012 | 0.0 | 96.18 Neigh | 0.025478 | 0.025478 | 0.025478 | 0.0 | 2.23 Comm | 0.010007 | 0.010007 | 0.010007 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008279 | | | 0.72 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5393.00 ave 5393 max 5393 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: 127332.0 ave 127332 max 127332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127332 Ave neighs/atom = 140.23348 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -3199.8257 0 -3199.8257 2147.6678 10771.093 93 0 -3199.8525 0 -3199.8525 53.97462 10787.402 Loop time of 0.0363596 on 1 procs for 3 steps with 908 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 = -3199.82570469997 -3199.85243569873 -3199.85247028819 Force two-norm initial, final = 30.580715 0.77514249 Force max component initial, final = 28.310859 0.61674538 Final line search alpha, max atom move = 0.0010932954 0.00067428487 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035086 | 0.035086 | 0.035086 | 0.0 | 96.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024456 | 0.00024456 | 0.00024456 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001029 | | | 2.83 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5377.00 ave 5377 max 5377 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: 127332.0 ave 127332 max 127332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127332 Ave neighs/atom = 140.23348 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.117 | 5.117 | 5.117 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3199.8525 0 -3199.8525 53.97462 Loop time of 1.778e-06 on 1 procs for 0 steps with 908 atoms 168.7% 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 | | 1.778e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5377.00 ave 5377 max 5377 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: 127292.0 ave 127292 max 127292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127292 Ave neighs/atom = 140.18943 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.117 | 5.117 | 5.117 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 -3199.8525 -3199.8525 27.294329 77.343666 5.1099856 53.97462 53.97462 7.4508629 62.915107 91.557891 2.3525557 665.18693 Loop time of 1.801e-06 on 1 procs for 0 steps with 908 atoms 166.6% 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 | | 1.801e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5377.00 ave 5377 max 5377 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63646.0 ave 63646 max 63646 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127292.0 ave 127292 max 127292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127292 Ave neighs/atom = 140.18943 Neighbor list builds = 0 Dangerous builds = 0 908 -3199.85228786306 eV 2.35255572957709 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01