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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -35.421342 0.0000000) to (11.807114 35.421342 2.8636458) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.4726806 3.4726806 2.8636458 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -35.421342 0.0000000) to (11.807114 35.421342 2.8636458) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.4726806 3.4726806 2.8636458 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -35.421342 0.0000000) to (11.807114 35.421342 2.8636458) create_atoms CPU = 0.001 seconds 103 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 22 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 205 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_115454747503_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -834.42901 0 -834.42901 62797.95 29 0 -874.42074 0 -874.42074 17805.89 Loop time of 2.53232 on 1 procs for 29 steps with 205 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 = -834.429007289126 -874.419936704701 -874.420735924568 Force two-norm initial, final = 107.03271 0.085499057 Force max component initial, final = 46.932596 0.029768669 Final line search alpha, max atom move = 1.0000000 0.029768669 Iterations, force evaluations = 29 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5262 | 2.5262 | 2.5262 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0034075 | 0.0034075 | 0.0034075 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002712 | | | 0.11 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2578.00 ave 2578 max 2578 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: 22790.0 ave 22790 max 22790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22790 Ave neighs/atom = 111.17073 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -874.42074 0 -874.42074 17805.89 2395.2898 47 0 -874.83466 0 -874.83466 -6.8760331 2419.212 Loop time of 0.980904 on 1 procs for 18 steps with 205 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 = -874.420735924567 -874.834394058424 -874.834659490831 Force two-norm initial, final = 55.901617 0.41214022 Force max component initial, final = 51.604737 0.13745439 Final line search alpha, max atom move = 0.0017690419 0.00024316257 Iterations, force evaluations = 18 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97241 | 0.97241 | 0.97241 | 0.0 | 99.13 Neigh | 0.003211 | 0.003211 | 0.003211 | 0.0 | 0.33 Comm | 0.0013326 | 0.0013326 | 0.0013326 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003955 | | | 0.40 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2577.00 ave 2577 max 2577 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: 22296.0 ave 22296 max 22296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22296 Ave neighs/atom = 108.76098 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -874.83466 0 -874.83466 -6.8760331 Loop time of 6.004e-06 on 1 procs for 0 steps with 205 atoms 183.2% 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 | | 6.004e-06 | | |100.00 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2577.00 ave 2577 max 2577 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: 22282.0 ave 22282 max 22282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22282 Ave neighs/atom = 108.69268 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.545 | 4.545 | 4.545 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 -874.83466 -874.83466 11.819349 72.072262 2.8399599 -6.8760331 -6.8760331 -8.1997588 -92.612192 80.183852 2.3174593 152.55244 Loop time of 6.395e-06 on 1 procs for 0 steps with 205 atoms 234.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2577.00 ave 2577 max 2577 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11141.0 ave 11141 max 11141 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22282.0 ave 22282 max 22282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22282 Ave neighs/atom = 108.69268 Neighbor list builds = 0 Dangerous builds = 0 205 -874.834659490831 eV 2.31745929746405 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04