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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -62.546062 0.0000000) to (25.534323 62.546062 8.8453489) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1282375 5.4206587 5.8968993 Created 1194 atoms using lattice units in orthogonal box = (0.0000000 -62.546062 0.0000000) to (25.534323 62.546062 8.8453489) create_atoms CPU = 0.002 seconds 1194 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1282375 5.4206587 5.8968993 Created 1202 atoms using lattice units in orthogonal box = (0.0000000 -62.546062 0.0000000) to (25.534323 62.546062 8.8453489) create_atoms CPU = 0.002 seconds 1202 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 ghost atom cutoff = 6 binsize = 3, bins = 9 42 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2396 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_150993986463_000#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 ghost atom cutoff = 6 binsize = 3, bins = 9 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.133 | 5.133 | 5.133 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9454.2576 0 -9454.2576 45898.005 609 0 -10183.327 0 -10183.327 -1320.8468 Loop time of 94.863 on 1 procs for 609 steps with 2396 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 = -9454.25764115961 -10183.3176581634 -10183.3269355325 Force two-norm initial, final = 930.99501 0.25493672 Force max component initial, final = 183.21469 0.043511390 Final line search alpha, max atom move = 0.79886918 0.034759908 Iterations, force evaluations = 609 1142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 94.338 | 94.338 | 94.338 | 0.0 | 99.45 Neigh | 0.29309 | 0.29309 | 0.29309 | 0.0 | 0.31 Comm | 0.094502 | 0.094502 | 0.094502 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1375 | | | 0.14 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7026.00 ave 7026 max 7026 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: 165694.0 ave 165694 max 165694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165694 Ave neighs/atom = 69.154424 Neighbor list builds = 18 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 ghost atom cutoff = 6 binsize = 3, bins = 9 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 609 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.136 | 5.136 | 5.136 Mbytes Step Temp E_pair E_mol TotEng Press Volume 609 0 -10183.327 0 -10183.327 -1320.8468 28253.307 638 0 -10200.251 0 -10200.251 17.152284 28201.942 Loop time of 2.5624 on 1 procs for 29 steps with 2396 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 = -10183.3269355325 -10200.2505972288 -10200.2507909145 Force two-norm initial, final = 987.44794 2.0438336 Force max component initial, final = 809.97395 1.3651403 Final line search alpha, max atom move = 0.00084180678 0.0011491843 Iterations, force evaluations = 29 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5137 | 2.5137 | 2.5137 | 0.0 | 98.10 Neigh | 0.031416 | 0.031416 | 0.031416 | 0.0 | 1.23 Comm | 0.0024271 | 0.0024271 | 0.0024271 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01482 | | | 0.58 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6931.00 ave 6931 max 6931 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: 163840.0 ave 163840 max 163840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163840 Ave neighs/atom = 68.380634 Neighbor list builds = 2 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 ghost atom cutoff = 6 binsize = 3, bins = 9 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.274 | 5.274 | 5.274 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10200.251 0 -10200.251 17.152284 Loop time of 1.987e-06 on 1 procs for 0 steps with 2396 atoms 201.3% 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 | | 1.987e-06 | | |100.00 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6931.00 ave 6931 max 6931 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: 163852.0 ave 163852 max 163852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163852 Ave neighs/atom = 68.385643 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 ghost atom cutoff = 6 binsize = 3, bins = 9 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.274 | 5.274 | 5.274 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 -10200.251 -10200.251 24.82339 127.42857 8.915611 17.152284 17.152284 3.2335154 -29.947498 78.170834 2.3832722 14313.574 Loop time of 2.429e-06 on 1 procs for 0 steps with 2396 atoms 205.8% 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 | | 2.429e-06 | | |100.00 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6931.00 ave 6931 max 6931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81926.0 ave 81926 max 81926 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163852.0 ave 163852 max 163852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163852 Ave neighs/atom = 68.385643 Neighbor list builds = 0 Dangerous builds = 0 2396 -10200.2507909145 eV 2.38327224200251 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:38