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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -34.601564 0.0000000) to (42.378088 34.601564 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0636523 4.2659462 4.6763140 Created 872 atoms using lattice units in orthogonal box = (0.0000000 -34.601564 0.0000000) to (42.378088 34.601564 7.0144710) create_atoms CPU = 0.001 seconds 872 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0636523 4.2659462 4.6763140 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -34.601564 0.0000000) to (42.378088 34.601564 7.0144710) create_atoms CPU = 0.001 seconds 878 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 22 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1738 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_179420363944_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.122 | 5.122 | 5.122 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6737.1216 0 -6737.1216 66398.476 76 0 -7414.7521 0 -7414.7521 -4297.3264 Loop time of 16.6277 on 1 procs for 76 steps with 1738 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6737.12155930295 -7414.74520830041 -7414.75207737699 Force two-norm initial, final = 771.65082 0.26676696 Force max component initial, final = 139.85632 0.050889431 Final line search alpha, max atom move = 1.0000000 0.050889431 Iterations, force evaluations = 76 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.582 | 16.582 | 16.582 | 0.0 | 99.72 Neigh | 0.024316 | 0.024316 | 0.024316 | 0.0 | 0.15 Comm | 0.0085898 | 0.0085898 | 0.0085898 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01282 | | | 0.08 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5907.00 ave 5907 max 5907 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: 188066.0 ave 188066 max 188066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188066 Ave neighs/atom = 108.20829 Neighbor list builds = 2 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.122 | 5.122 | 5.122 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -7414.7521 0 -7414.7521 -4297.3264 20571.313 79 0 -7414.8557 0 -7414.8557 -6.4501274 20519.379 Loop time of 0.772306 on 1 procs for 3 steps with 1738 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7414.752077377 -7414.8511871282 -7414.85573661683 Force two-norm initial, final = 103.69729 1.8926818 Force max component initial, final = 86.670078 1.5923031 Final line search alpha, max atom move = 5.7109671e-05 9.0935904e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77018 | 0.77018 | 0.77018 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003138 | 0.0003138 | 0.0003138 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001814 | | | 0.23 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5907.00 ave 5907 max 5907 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: 188420.0 ave 188420 max 188420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188420 Ave neighs/atom = 108.41197 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.260 | 5.260 | 5.260 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7414.8557 0 -7414.8557 -6.4501274 Loop time of 2.15e-06 on 1 procs for 0 steps with 1738 atoms 186.0% 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 | | 2.15e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5907.00 ave 5907 max 5907 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: 188522.0 ave 188522 max 188522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188522 Ave neighs/atom = 108.47066 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.260 | 5.260 | 5.260 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 -7414.8557 -7414.8557 42.353101 69.216693 6.9995183 -6.4501274 -6.4501274 -124.25553 66.262559 38.642592 2.2725088 1726.1064 Loop time of 2.332e-06 on 1 procs for 0 steps with 1738 atoms 257.3% 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 | | 2.332e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5907.00 ave 5907 max 5907 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94261.0 ave 94261 max 94261 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188522.0 ave 188522 max 188522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188522 Ave neighs/atom = 108.47066 Neighbor list builds = 0 Dangerous builds = 0 1738 -7414.85573661683 eV 2.27250884777751 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18