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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -36.114597 0.0000000) to (18.055493 36.114597 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0555380 5.0555380 3.6110985 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -36.114597 0.0000000) to (18.055493 36.114597 3.6110985) create_atoms CPU = 0.002 seconds 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0555380 5.0555380 3.6110985 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -36.114597 0.0000000) to (18.055493 36.114597 3.6110985) create_atoms CPU = 0.001 seconds 202 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 22 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, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 400 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1656.3236 0 -1656.3236 33975.478 29 0 -1690.6422 0 -1690.6422 6776.6729 Loop time of 3.25676 on 1 procs for 29 steps with 400 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 = -1656.3236220397 -1690.64057278108 -1690.64221318344 Force two-norm initial, final = 43.209169 0.12338072 Force max component initial, final = 13.265960 0.016634485 Final line search alpha, max atom move = 1.0000000 0.016634485 Iterations, force evaluations = 29 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.242 | 3.242 | 3.242 | 0.0 | 99.55 Neigh | 0.0065268 | 0.0065268 | 0.0065268 | 0.0 | 0.20 Comm | 0.0044278 | 0.0044278 | 0.0044278 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003799 | | | 0.12 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3720.00 ave 3720 max 3720 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: 50236.0 ave 50236 max 50236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50236 Ave neighs/atom = 125.59000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -1690.6422 0 -1690.6422 6776.6729 4709.3552 44 0 -1690.9799 0 -1690.9799 -1812.1297 4732.6459 Loop time of 1.31753 on 1 procs for 15 steps with 400 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1690.64221318344 -1690.97862891572 -1690.97986288946 Force two-norm initial, final = 41.441574 0.58159401 Force max component initial, final = 41.153421 0.10899855 Final line search alpha, max atom move = 0.00058591488 6.3863871e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3101 | 1.3101 | 1.3101 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015552 | 0.0015552 | 0.0015552 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005868 | | | 0.45 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3735.00 ave 3735 max 3735 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: 50188.0 ave 50188 max 50188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50188 Ave neighs/atom = 125.47000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1690.9799 0 -1690.9799 -1812.1297 Loop time of 6.074e-06 on 1 procs for 0 steps with 400 atoms 197.6% 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 | | 6.074e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3765.00 ave 3765 max 3765 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: 47512.0 ave 47512 max 47512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47512 Ave neighs/atom = 118.78000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.590 | 4.590 | 4.590 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 -1690.9799 -1690.9799 17.879623 72.229193 3.6646532 -1812.1297 -1812.1297 27.005719 -5425.9474 -37.447307 2.3023209 155.79493 Loop time of 8.56e-06 on 1 procs for 0 steps with 400 atoms 257.0% 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 | | 8.56e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3765.00 ave 3765 max 3765 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23756.0 ave 23756 max 23756 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47512.0 ave 47512 max 47512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47512 Ave neighs/atom = 118.78000 Neighbor list builds = 0 Dangerous builds = 0 400 -1690.97986288946 eV 2.30232091737914 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05