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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -44.666233 0.0000000) to (14.888744 44.666233 3.6110509) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3790424 4.3790424 3.6110509 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -44.666233 0.0000000) to (14.888744 44.666233 3.6110509) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3790424 4.3790424 3.6110509 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.666233 0.0000000) to (14.888744 44.666233 3.6110509) create_atoms CPU = 0.001 seconds 206 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 18 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, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 4.929 | 4.929 | 4.929 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1623.5933 0 -1623.5933 34737.478 49 0 -1683.2112 0 -1683.2112 9672.4752 Loop time of 0.782917 on 1 procs for 49 steps with 408 atoms 93.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1623.59330146608 -1683.21003631047 -1683.21118014398 Force two-norm initial, final = 130.21625 0.13887587 Force max component initial, final = 41.292689 0.020941417 Final line search alpha, max atom move = 1.0000000 0.020941417 Iterations, force evaluations = 49 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76514 | 0.76514 | 0.76514 | 0.0 | 97.73 Neigh | 0.0086769 | 0.0086769 | 0.0086769 | 0.0 | 1.11 Comm | 0.0062258 | 0.0062258 | 0.0062258 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002875 | | | 0.37 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7405.00 ave 7405 max 7405 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: 154740.0 ave 154740 max 154740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154740 Ave neighs/atom = 379.26471 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.931 | 4.931 | 4.931 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1683.2112 0 -1683.2112 9672.4752 4802.8719 55 0 -1683.3329 0 -1683.3329 -323.05753 4830.7166 Loop time of 0.0578996 on 1 procs for 6 steps with 408 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1683.21118014398 -1683.33213148547 -1683.33291321392 Force two-norm initial, final = 53.041720 2.4577279 Force max component initial, final = 41.924587 1.7191516 Final line search alpha, max atom move = 0.00026478538 0.00045520620 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055361 | 0.055361 | 0.055361 | 0.0 | 95.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055807 | 0.00055807 | 0.00055807 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001981 | | | 3.42 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7366.00 ave 7366 max 7366 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: 154824.0 ave 154824 max 154824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154824 Ave neighs/atom = 379.47059 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.069 | 5.069 | 5.069 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1683.3329 0 -1683.3329 -323.05753 Loop time of 1.774e-06 on 1 procs for 0 steps with 408 atoms 112.7% 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 | | 1.774e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7366.00 ave 7366 max 7366 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: 154728.0 ave 154728 max 154728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154728 Ave neighs/atom = 379.23529 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.069 | 5.069 | 5.069 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 -1683.3329 -1683.3329 14.877383 89.808429 3.6154963 -323.05753 -323.05753 -569.7462 156.89271 -556.31909 2.297591 199.28347 Loop time of 1.529e-06 on 1 procs for 0 steps with 408 atoms 130.8% 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 | | 1.529e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7366.00 ave 7366 max 7366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77364.0 ave 77364 max 77364 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 154728.0 ave 154728 max 154728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154728 Ave neighs/atom = 379.23529 Neighbor list builds = 0 Dangerous builds = 0 408 -1683.33291321392 eV 2.29759096861068 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01