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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -35.423850 0.0000000) to (16.698963 35.423850 4.0500934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9114597 4.8620970 4.0500934 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -35.423850 0.0000000) to (16.698963 35.423850 4.0500934) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9114597 4.8620970 4.0500934 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -35.423850 0.0000000) to (16.698963 35.423850 4.0500934) 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 12 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 406 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.341 | 5.341 | 5.341 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1541.6567 0 -1541.6567 58956.603 119 0 -1685.978 0 -1685.978 -1419.0264 Loop time of 2.36652 on 1 procs for 119 steps with 406 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1541.65674309302 -1685.97669844633 -1685.97799808067 Force two-norm initial, final = 270.13437 0.13652259 Force max component initial, final = 81.134703 0.021660119 Final line search alpha, max atom move = 1.0000000 0.021660119 Iterations, force evaluations = 119 214 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3088 | 2.3088 | 2.3088 | 0.0 | 97.56 Neigh | 0.037347 | 0.037347 | 0.037347 | 0.0 | 1.58 Comm | 0.013959 | 0.013959 | 0.013959 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006449 | | | 0.27 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8189.00 ave 8189 max 8189 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: 245324.0 ave 245324 max 245324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245324 Ave neighs/atom = 604.24631 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.336 | 5.336 | 5.336 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -1685.978 0 -1685.978 -1419.0264 4791.5971 125 0 -1686.1384 0 -1686.1384 -20.798194 4787.4503 Loop time of 0.0893421 on 1 procs for 6 steps with 406 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 = -1685.97799808068 -1686.13824457108 -1686.13841374565 Force two-norm initial, final = 50.597772 0.43506962 Force max component initial, final = 39.999489 0.21318980 Final line search alpha, max atom move = 0.00091277991 0.00019459537 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087068 | 0.087068 | 0.087068 | 0.0 | 97.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047874 | 0.00047874 | 0.00047874 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001796 | | | 2.01 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8168.00 ave 8168 max 8168 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: 245528.0 ave 245528 max 245528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245528 Ave neighs/atom = 604.74877 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.473 | 5.473 | 5.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1686.1384 0 -1686.1384 -20.798194 Loop time of 1.667e-06 on 1 procs for 0 steps with 406 atoms 120.0% 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 | | 1.667e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8121.00 ave 8121 max 8121 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: 245496.0 ave 245496 max 245496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245496 Ave neighs/atom = 604.66995 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.473 | 5.473 | 5.473 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 -1686.1384 -1686.1384 16.762513 70.88333 4.0292204 -20.798194 -20.798194 24.036836 -71.382354 -15.049065 2.3110539 313.59693 Loop time of 1.984e-06 on 1 procs for 0 steps with 406 atoms 201.6% 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 | | 1.984e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8121.00 ave 8121 max 8121 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122748.0 ave 122748 max 122748 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 245496.0 ave 245496 max 245496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245496 Ave neighs/atom = 604.66995 Neighbor list builds = 0 Dangerous builds = 0 406 -1686.13841374565 eV 2.3110538573479 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02