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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -46.119266 0.0000000) to (23.059633 46.119266 2.8601955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9023994 3.9023994 2.8601955 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -46.119266 0.0000000) to (23.059633 46.119266 2.8601955) create_atoms CPU = 0.002 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9023994 3.9023994 2.8601955 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.119266 0.0000000) to (23.059633 46.119266 2.8601955) create_atoms CPU = 0.001 seconds 261 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 521 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.842 | 4.842 | 4.842 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2144.6064 0 -2144.6064 34771.336 31 0 -2219.1875 0 -2219.1875 9609.4914 Loop time of 4.74978 on 1 procs for 31 steps with 521 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 = -2144.60640131849 -2219.18546927672 -2219.18751542134 Force two-norm initial, final = 154.81655 0.18969656 Force max component initial, final = 88.932689 0.049571484 Final line search alpha, max atom move = 1.0000000 0.049571484 Iterations, force evaluations = 31 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7413 | 4.7413 | 4.7413 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041712 | 0.0041712 | 0.0041712 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004266 | | | 0.09 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3327.00 ave 3327 max 3327 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: 30186.0 ave 30186 max 30186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30186 Ave neighs/atom = 57.938580 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.842 | 4.842 | 4.842 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -2219.1875 0 -2219.1875 9609.4914 6083.5976 42 0 -2219.5991 0 -2219.5991 231.72001 6114.1912 Loop time of 1.13411 on 1 procs for 11 steps with 521 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 = -2219.18751542134 -2219.59756064984 -2219.59912836735 Force two-norm initial, final = 91.085622 1.7075479 Force max component initial, final = 89.781943 1.2402099 Final line search alpha, max atom move = 0.00034702129 0.00043037924 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1296 | 1.1296 | 1.1296 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093666 | 0.00093666 | 0.00093666 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0036 | | | 0.32 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3306.00 ave 3306 max 3306 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: 30016.0 ave 30016 max 30016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30016 Ave neighs/atom = 57.612284 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2219.5991 0 -2219.5991 231.72001 Loop time of 6.956e-06 on 1 procs for 0 steps with 521 atoms 172.5% 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 | | 6.956e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3306.00 ave 3306 max 3306 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: 30010.0 ave 30010 max 30010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30010 Ave neighs/atom = 57.600768 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.980 | 4.980 | 4.980 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 -2219.5991 -2219.5991 23.050832 93.148667 2.8475789 231.72001 231.72001 162.34086 328.19412 204.62504 2.271123 264.39088 Loop time of 7.037e-06 on 1 procs for 0 steps with 521 atoms 255.8% 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 | | 7.037e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15005.0 ave 15005 max 15005 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30010.0 ave 30010 max 30010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30010 Ave neighs/atom = 57.600768 Neighbor list builds = 0 Dangerous builds = 0 521 -2219.59912836735 eV 2.27112304595333 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06