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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -52.684169 0.0000000) to (26.340543 52.684169 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9691229 3.9691229 3.0829274 Created 293 atoms using lattice units in orthogonal box = (0.0000000 -52.684169 0.0000000) to (26.340543 52.684169 3.0829274) create_atoms CPU = 0.000 seconds 293 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9691229 3.9691229 3.0829274 Created 293 atoms using lattice units in orthogonal box = (0.0000000 -52.684169 0.0000000) to (26.340543 52.684169 3.0829274) create_atoms CPU = 0.000 seconds 293 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 32 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 584 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.265 | 5.265 | 5.265 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3600.3985 0 -3600.3985 81873.941 135 0 -3789.3499 0 -3789.3499 8060.1045 Loop time of 19.1132 on 1 procs for 135 steps with 584 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 = -3600.39853410776 -3789.34619132886 -3789.34994352405 Force two-norm initial, final = 341.28441 0.27306319 Force max component initial, final = 134.33012 0.093747025 Final line search alpha, max atom move = 0.73629403 0.069025374 Iterations, force evaluations = 135 258 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.092 | 19.092 | 19.092 | 0.0 | 99.89 Neigh | 0.0091231 | 0.0091231 | 0.0091231 | 0.0 | 0.05 Comm | 0.0083144 | 0.0083144 | 0.0083144 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004245 | | | 0.02 Nlocal: 584.000 ave 584 max 584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4356.00 ave 4356 max 4356 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: 43600.0 ave 43600 max 43600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43600 Ave neighs/atom = 74.657534 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 135 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.261 | 5.261 | 5.261 Mbytes Step Temp E_pair E_mol TotEng Press Volume 135 0 -3789.3499 0 -3789.3499 8060.1045 8556.5393 136 0 -3789.3527 0 -3789.3527 6725.3467 8561.7567 Loop time of 0.218394 on 1 procs for 1 steps with 584 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 = -3789.34994352404 -3789.34994352404 -3789.35271785921 Force two-norm initial, final = 11.110038 3.8407795 Force max component initial, final = 10.755452 3.7171042 Final line search alpha, max atom move = 9.2976104e-05 0.00034560187 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21815 | 0.21815 | 0.21815 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.91e-05 | 6.91e-05 | 6.91e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000178 | | | 0.08 Nlocal: 584.000 ave 584 max 584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4346.00 ave 4346 max 4346 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: 43332.0 ave 43332 max 43332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43332 Ave neighs/atom = 74.198630 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.399 | 5.399 | 5.399 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3789.3527 0 -3789.3527 6725.3467 Loop time of 1.9e-06 on 1 procs for 0 steps with 584 atoms 157.9% 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 | | 1.9e-06 | | |100.00 Nlocal: 584.000 ave 584 max 584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4346.00 ave 4346 max 4346 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: 43108.0 ave 43108 max 43108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43108 Ave neighs/atom = 73.815068 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.399 | 5.399 | 5.399 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 -3789.3527 -3789.3527 26.353313 105.36834 3.0833124 6725.3467 6725.3467 173.60047 20698.115 -695.67509 2.5136807 873.84739 Loop time of 2e-06 on 1 procs for 0 steps with 584 atoms 150.0% 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 | | 2e-06 | | |100.00 Nlocal: 584.000 ave 584 max 584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4346.00 ave 4346 max 4346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21554.0 ave 21554 max 21554 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43108.0 ave 43108 max 43108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43108 Ave neighs/atom = 73.815068 Neighbor list builds = 0 Dangerous builds = 0 584 -3789.35271785921 eV 2.5136807309539 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19