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 = 3.5937292 3.5937292 3.5937292 Created orthogonal box = (0.0000000 -63.477914 0.0000000) to (36.648990 63.477914 6.2245215) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6383062 5.6967358 6.2245215 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -63.477914 0.0000000) to (36.648990 63.477914 6.2245215) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6383062 5.6967358 6.2245215 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.477914 0.0000000) to (36.648990 63.477914 6.2245215) create_atoms CPU = 0.002 seconds 1249 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 2493 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.117 | 6.117 | 6.117 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9856.1729 0 -9856.1729 85563.185 66 0 -10621.037 0 -10621.037 2750.8111 Loop time of 17.903 on 1 procs for 66 steps with 2493 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9856.17286548424 -10621.0279288809 -10621.0369320262 Force two-norm initial, final = 907.55720 0.38365075 Force max component initial, final = 163.14590 0.13307751 Final line search alpha, max atom move = 0.57966485 0.077140353 Iterations, force evaluations = 66 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.844 | 17.844 | 17.844 | 0.0 | 99.67 Neigh | 0.021438 | 0.021438 | 0.021438 | 0.0 | 0.12 Comm | 0.019223 | 0.019223 | 0.019223 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01829 | | | 0.10 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10284.0 ave 10284 max 10284 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: 331178.0 ave 331178 max 331178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331178 Ave neighs/atom = 132.84316 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.117 | 6.117 | 6.117 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -10621.037 0 -10621.037 2750.8111 28961.472 69 0 -10621.116 0 -10621.116 -25.801824 29010.464 Loop time of 0.893757 on 1 procs for 3 steps with 2493 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 = -10621.0369320262 -10621.1152899984 -10621.1155074673 Force two-norm initial, final = 97.103020 1.7845217 Force max component initial, final = 86.324593 1.4732602 Final line search alpha, max atom move = 0.00023642483 0.00034831528 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89012 | 0.89012 | 0.89012 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054277 | 0.00054277 | 0.00054277 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003096 | | | 0.35 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10272.0 ave 10272 max 10272 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: 331368.0 ave 331368 max 331368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331368 Ave neighs/atom = 132.91937 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.254 | 6.254 | 6.254 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10621.116 0 -10621.116 -25.801824 Loop time of 2.346e-06 on 1 procs for 0 steps with 2493 atoms 213.1% 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 | | 2.346e-06 | | |100.00 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10272.0 ave 10272 max 10272 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: 331266.0 ave 331266 max 331266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331266 Ave neighs/atom = 132.87846 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.254 | 6.254 | 6.254 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 -10621.116 -10621.116 36.641453 127.19877 6.2244227 -25.801824 -25.801824 -81.347798 -33.996043 37.93837 2.2910879 1047.3359 Loop time of 2.576e-06 on 1 procs for 0 steps with 2493 atoms 310.6% 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 | | 2.576e-06 | | |100.00 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10272.0 ave 10272 max 10272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165633.0 ave 165633 max 165633 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 331266.0 ave 331266 max 331266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331266 Ave neighs/atom = 132.87846 Neighbor list builds = 0 Dangerous builds = 0 2493 -10621.1155074673 eV 2.29108789472178 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19