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 = 2.8669669 2.8669669 2.8669669 Created orthogonal box = (0.0000000 -56.765917 0.0000000) to (34.760127 56.765917 7.0226061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0198786 4.0545035 4.6817374 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.765917 0.0000000) to (34.760127 56.765917 7.0226061) create_atoms CPU = 0.002 seconds 1182 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0198786 4.0545035 4.6817374 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.765917 0.0000000) to (34.760127 56.765917 7.0226061) create_atoms CPU = 0.002 seconds 1182 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 13 atoms, new total = 2351 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.489 | 6.489 | 6.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9217.5815 0 -9217.5815 19045.269 307 0 -9474.0978 0 -9474.0978 -65862.52 Loop time of 9.85249 on 1 procs for 307 steps with 2351 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 = -9217.58147871654 -9474.08887814614 -9474.0978317444 Force two-norm initial, final = 155.33275 0.35237532 Force max component initial, final = 30.833739 0.10763739 Final line search alpha, max atom move = 0.89660878 0.096508633 Iterations, force evaluations = 307 603 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6825 | 9.6825 | 9.6825 | 0.0 | 98.27 Neigh | 0.064493 | 0.064493 | 0.064493 | 0.0 | 0.65 Comm | 0.051561 | 0.051561 | 0.051561 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05393 | | | 0.55 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9781.00 ave 9781 max 9781 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: 369208.0 ave 369208 max 369208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369208 Ave neighs/atom = 157.04296 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 307 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.112 | 6.112 | 6.112 Mbytes Step Temp E_pair E_mol TotEng Press Volume 307 0 -9474.0978 0 -9474.0978 -65862.52 27713.879 332 0 -9497.8419 0 -9497.8419 -16218.116 26514.881 Loop time of 0.44155 on 1 procs for 25 steps with 2351 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 = -9474.0978317444 -9497.83869927545 -9497.84185075824 Force two-norm initial, final = 1489.6457 10.253037 Force max component initial, final = 1136.2069 5.3014766 Final line search alpha, max atom move = 9.1849776e-05 0.00048693944 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4289 | 0.4289 | 0.4289 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001839 | 0.001839 | 0.001839 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01081 | | | 2.45 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9790.00 ave 9790 max 9790 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: 368856.0 ave 368856 max 368856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368856 Ave neighs/atom = 156.89324 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.251 | 6.251 | 6.251 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9497.8419 0 -9497.8419 -16218.116 Loop time of 1.776e-06 on 1 procs for 0 steps with 2351 atoms 168.9% 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 | | 1.776e-06 | | |100.00 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10046.0 ave 10046 max 10046 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: 381136.0 ave 381136 max 381136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 381136 Ave neighs/atom = 162.11655 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.251 | 6.251 | 6.251 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 -9497.8419 -9497.8419 34.087691 113.53183 6.8513229 -16218.116 -16218.116 258.88778 -49225.768 312.5314 2.2525659 9103.0307 Loop time of 1.926e-06 on 1 procs for 0 steps with 2351 atoms 207.7% 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 | | 1.926e-06 | | |100.00 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10046.0 ave 10046 max 10046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 190568.0 ave 190568 max 190568 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 381136.0 ave 381136 max 381136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 381136 Ave neighs/atom = 162.11655 Neighbor list builds = 0 Dangerous builds = 0 2351 -9497.84185075824 eV 2.2525659300295 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10