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 -38.431593 0.0000000) to (38.427978 38.431593 3.6150001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1010590 5.1010590 3.6150001 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -38.431593 0.0000000) to (38.427978 38.431593 3.6150001) create_atoms CPU = 0.001 seconds 453 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1010590 5.1010590 3.6150001 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -38.431593 0.0000000) to (38.427978 38.431593 3.6150001) create_atoms CPU = 0.001 seconds 453 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 18 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 900 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_266134052596_000#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.391 | 5.391 | 5.391 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3124.1554 0 -3124.1554 22426.931 70 0 -3178.3277 0 -3178.3277 -3111.7327 Loop time of 1.31746 on 1 procs for 70 steps with 900 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 = -3124.15535337121 -3178.32494596514 -3178.32770299988 Force two-norm initial, final = 43.919220 0.15992791 Force max component initial, final = 11.029206 0.041738962 Final line search alpha, max atom move = 1.0000000 0.041738962 Iterations, force evaluations = 70 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.289 | 1.289 | 1.289 | 0.0 | 97.84 Neigh | 0.012244 | 0.012244 | 0.012244 | 0.0 | 0.93 Comm | 0.0095241 | 0.0095241 | 0.0095241 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006673 | | | 0.51 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7934.00 ave 7934 max 7934 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: 202864.0 ave 202864 max 202864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202864 Ave neighs/atom = 225.40444 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -3178.3277 0 -3178.3277 -3111.7327 10677.614 72 0 -3178.3464 0 -3178.3464 -674.3559 10658.874 Loop time of 0.0432055 on 1 procs for 2 steps with 900 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 = -3178.32770299988 -3178.34360512299 -3178.34635707043 Force two-norm initial, final = 25.583967 4.9771622 Force max component initial, final = 23.493315 4.2967884 Final line search alpha, max atom move = 0.00019071164 0.00081944757 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042169 | 0.042169 | 0.042169 | 0.0 | 97.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022569 | 0.00022569 | 0.00022569 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008111 | | | 1.88 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7942.00 ave 7942 max 7942 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: 202308.0 ave 202308 max 202308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202308 Ave neighs/atom = 224.78667 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.529 | 5.529 | 5.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3178.3464 0 -3178.3464 -674.3559 Loop time of 1.731e-06 on 1 procs for 0 steps with 900 atoms 115.5% 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 | | 1.731e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7953.00 ave 7953 max 7953 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: 202344.0 ave 202344 max 202344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202344 Ave neighs/atom = 224.82667 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.529 | 5.529 | 5.529 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 -3178.3464 -3178.3464 38.359592 76.863186 3.6150886 -674.3559 -674.3559 376.10452 -3045.0549 645.8827 2.3129076 146.05611 Loop time of 1.984e-06 on 1 procs for 0 steps with 900 atoms 201.6% 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 | | 1.984e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7953.00 ave 7953 max 7953 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101172.0 ave 101172 max 101172 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 202344.0 ave 202344 max 202344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202344 Ave neighs/atom = 224.82667 Neighbor list builds = 0 Dangerous builds = 0 900 -3178.34635707042 eV 2.31290758474244 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01