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 -46.879902 0.0000000) to (33.149096 46.879902 4.0498067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9476263 4.5480502 4.0498067 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -46.879902 0.0000000) to (33.149096 46.879902 4.0498067) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9476263 4.5480502 4.0498067 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.879902 0.0000000) to (33.149096 46.879902 4.0498067) create_atoms CPU = 0.001 seconds 538 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1072 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3846.2083 0 -3846.2083 104750.94 81 0 -4584.9111 0 -4584.9111 4970.9092 Loop time of 12.5534 on 1 procs for 81 steps with 1072 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 = -3846.20826553481 -4584.9068171458 -4584.91113934306 Force two-norm initial, final = 1075.9662 0.22932053 Force max component initial, final = 294.79897 0.049507679 Final line search alpha, max atom move = 1.0000000 0.049507679 Iterations, force evaluations = 81 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.519 | 12.519 | 12.519 | 0.0 | 99.72 Neigh | 0.014377 | 0.014377 | 0.014377 | 0.0 | 0.11 Comm | 0.010454 | 0.010454 | 0.010454 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01003 | | | 0.08 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5684.00 ave 5684 max 5684 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: 105920.0 ave 105920 max 105920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105920 Ave neighs/atom = 98.805970 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -4584.9111 0 -4584.9111 4970.9092 12587.013 87 0 -4585.194 0 -4585.194 -47.690372 12623.161 Loop time of 0.72445 on 1 procs for 6 steps with 1072 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4584.91113934306 -4585.19150573749 -4585.19400815244 Force two-norm initial, final = 106.96924 0.75354796 Force max component initial, final = 106.71289 0.52196529 Final line search alpha, max atom move = 0.00014507612 7.5724701e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72191 | 0.72191 | 0.72191 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039892 | 0.00039892 | 0.00039892 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002141 | | | 0.30 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5668.00 ave 5668 max 5668 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: 106064.0 ave 106064 max 106064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106064 Ave neighs/atom = 98.940299 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4585.194 0 -4585.194 -47.690372 Loop time of 2.315e-06 on 1 procs for 0 steps with 1072 atoms 216.0% 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 | | 2.315e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5644.00 ave 5644 max 5644 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: 107184.0 ave 107184 max 107184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107184 Ave neighs/atom = 99.985075 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.125 | 5.125 | 5.125 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 -4585.194 -4585.194 33.115568 94.273683 4.0433881 -47.690372 -47.690372 -22.942245 -53.984178 -66.144693 2.2712997 459.52521 Loop time of 2.452e-06 on 1 procs for 0 steps with 1072 atoms 244.7% 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 | | 2.452e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5644.00 ave 5644 max 5644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53592.0 ave 53592 max 53592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107184.0 ave 107184 max 107184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107184 Ave neighs/atom = 99.985075 Neighbor list builds = 0 Dangerous builds = 0 1072 -4585.19400815244 eV 2.27129966516813 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13