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 -58.673406 0.0000000) to (20.744182 58.673406 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6575041 6.2229370 5.1068645 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.673406 0.0000000) to (20.744182 58.673406 5.1068645) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6575041 6.2229370 5.1068645 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.673406 0.0000000) to (20.744182 58.673406 5.1068645) create_atoms CPU = 0.002 seconds 530 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 = 7 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1052 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 = 7 37 2 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) = 4.634 | 4.634 | 4.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4236.8321 0 -4236.8321 38843.792 461 0 -4490.2077 0 -4490.2077 -4471.9602 Loop time of 65.4451 on 1 procs for 461 steps with 1052 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 = -4236.83210743131 -4490.2036072968 -4490.20768010043 Force two-norm initial, final = 412.20132 0.20770252 Force max component initial, final = 118.39556 0.036145924 Final line search alpha, max atom move = 1.0000000 0.036145924 Iterations, force evaluations = 461 834 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 65.205 | 65.205 | 65.205 | 0.0 | 99.63 Neigh | 0.11729 | 0.11729 | 0.11729 | 0.0 | 0.18 Comm | 0.067364 | 0.067364 | 0.067364 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05526 | | | 0.08 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5743.00 ave 5743 max 5743 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: 111160.0 ave 111160 max 111160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111160 Ave neighs/atom = 105.66540 Neighbor list builds = 16 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 = 7 37 2 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 : 461 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.017 | 5.017 | 5.017 Mbytes Step Temp E_pair E_mol TotEng Press Volume 461 0 -4490.2077 0 -4490.2077 -4471.9602 12431.454 490 0 -4499.62 0 -4499.62 26.090946 12378.608 Loop time of 2.81914 on 1 procs for 29 steps with 1052 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 = -4490.20768010042 -4499.61995740086 -4499.6200426689 Force two-norm initial, final = 559.01078 1.3165989 Force max component initial, final = 487.98608 0.96434252 Final line search alpha, max atom move = 0.0024924437 0.0024035695 Iterations, force evaluations = 29 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8008 | 2.8008 | 2.8008 | 0.0 | 99.35 Neigh | 0.0073808 | 0.0073808 | 0.0073808 | 0.0 | 0.26 Comm | 0.0018298 | 0.0018298 | 0.0018298 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009128 | | | 0.32 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5821.00 ave 5821 max 5821 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: 114684.0 ave 114684 max 114684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114684 Ave neighs/atom = 109.01521 Neighbor list builds = 1 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 = 7 37 2 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) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4499.62 0 -4499.62 26.090946 Loop time of 2.114e-06 on 1 procs for 0 steps with 1052 atoms 189.2% 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 | | 2.114e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5821.00 ave 5821 max 5821 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: 114744.0 ave 114744 max 114744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114744 Ave neighs/atom = 109.07224 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 = 7 37 2 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) = 5.155 | 5.155 | 5.155 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 -4499.62 -4499.62 21.021349 118.59723 4.9651993 26.090946 26.090946 -64.953493 126.14589 17.080439 2.3481194 1192.9723 Loop time of 2.163e-06 on 1 procs for 0 steps with 1052 atoms 231.2% 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 | | 2.163e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5821.00 ave 5821 max 5821 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57372.0 ave 57372 max 57372 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114744.0 ave 114744 max 114744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114744 Ave neighs/atom = 109.07224 Neighbor list builds = 0 Dangerous builds = 0 1052 -4499.6200426689 eV 2.34811937172908 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:08