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 -36.404345 0.0000000) to (8.5805864 36.404345 4.0449272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7669924 4.0449272 4.0449272 Created 108 atoms using lattice units in orthogonal box = (0.0000000 -36.404345 0.0000000) to (8.5805864 36.404345 4.0449272) create_atoms CPU = 0.001 seconds 108 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7669924 4.0449272 4.0449272 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -36.404345 0.0000000) to (8.5805864 36.404345 4.0449272) create_atoms CPU = 0.000 seconds 110 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 = 4 28 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 = 218 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 = 4 28 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) = 4.399 | 4.399 | 4.399 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -610.53606 0 -610.53606 185472.56 54 0 -926.9897 0 -926.9897 24758.343 Loop time of 1.50577 on 1 procs for 54 steps with 218 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 = -610.536059901297 -926.988861072207 -926.989702175933 Force two-norm initial, final = 675.79011 0.11982722 Force max component initial, final = 196.60653 0.024649227 Final line search alpha, max atom move = 1.0000000 0.024649227 Iterations, force evaluations = 54 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4941 | 1.4941 | 1.4941 | 0.0 | 99.22 Neigh | 0.0082143 | 0.0082143 | 0.0082143 | 0.0 | 0.55 Comm | 0.0017195 | 0.0017195 | 0.0017195 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001768 | | | 0.12 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1739.00 ave 1739 max 1739 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: 12568.0 ave 12568 max 12568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12568 Ave neighs/atom = 57.651376 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 28 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.399 | 4.399 | 4.399 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -926.9897 0 -926.9897 24758.343 2527.0329 73 0 -927.50872 0 -927.50872 -142.03387 2563.0274 Loop time of 0.386407 on 1 procs for 19 steps with 218 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -926.989702175932 -927.508594376011 -927.508719726658 Force two-norm initial, final = 75.339909 0.54190967 Force max component initial, final = 66.143877 0.36500906 Final line search alpha, max atom move = 0.00096922956 0.00035377758 Iterations, force evaluations = 19 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37498 | 0.37498 | 0.37498 | 0.0 | 97.04 Neigh | 0.0087481 | 0.0087481 | 0.0087481 | 0.0 | 2.26 Comm | 0.0005164 | 0.0005164 | 0.0005164 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002161 | | | 0.56 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1725.00 ave 1725 max 1725 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: 12540.0 ave 12540 max 12540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12540 Ave neighs/atom = 57.522936 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 28 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) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -927.50872 0 -927.50872 -142.03387 Loop time of 1.686e-06 on 1 procs for 0 steps with 218 atoms 118.6% 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 | | 1.686e-06 | | |100.00 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1725.00 ave 1725 max 1725 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: 12548.0 ave 12548 max 12548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12548 Ave neighs/atom = 57.559633 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 = 4 28 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) = 4.537 | 4.537 | 4.537 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 -927.50872 -927.50872 8.5714693 74.051438 4.037983 -142.03387 -142.03387 -49.348539 -148.97364 -227.77944 2.3098228 179.03777 Loop time of 1.643e-06 on 1 procs for 0 steps with 218 atoms 121.7% 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 | | 1.643e-06 | | |100.00 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6274.00 ave 6274 max 6274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12548.0 ave 12548 max 12548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12548 Ave neighs/atom = 57.559633 Neighbor list builds = 0 Dangerous builds = 0 218 -927.508719726658 eV 2.30982281986895 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02