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 -34.722318 0.0000000) to (28.350654 34.722318 7.0149676) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0500934 4.0155062 4.6766450 Created 588 atoms using lattice units in orthogonal box = (0.0000000 -34.722318 0.0000000) to (28.350654 34.722318 7.0149676) create_atoms CPU = 0.001 seconds 588 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0500934 4.0155062 4.6766450 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -34.722318 0.0000000) to (28.350654 34.722318 7.0149676) create_atoms CPU = 0.001 seconds 590 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 = 5 12 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1172 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 = 5 12 2 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) = 7.499 | 7.499 | 7.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4147.7357 0 -4147.7357 80699.31 112 0 -4857.8674 0 -4857.8674 3964.6375 Loop time of 6.19899 on 1 procs for 112 steps with 1172 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 = -4147.73574646098 -4857.86278276962 -4857.86741677507 Force two-norm initial, final = 929.12661 0.29841144 Force max component initial, final = 280.99162 0.055542910 Final line search alpha, max atom move = 1.0000000 0.055542910 Iterations, force evaluations = 112 206 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0417 | 6.0417 | 6.0417 | 0.0 | 97.46 Neigh | 0.11205 | 0.11205 | 0.11205 | 0.0 | 1.81 Comm | 0.027819 | 0.027819 | 0.027819 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01745 | | | 0.28 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11392.0 ave 11392 max 11392 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: 708072.0 ave 708072 max 708072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 708072 Ave neighs/atom = 604.15700 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 = 5 12 2 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 : 112 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.499 | 7.499 | 7.499 Mbytes Step Temp E_pair E_mol TotEng Press Volume 112 0 -4857.8674 0 -4857.8674 3964.6375 13811.074 121 0 -4858.3928 0 -4858.3928 153.55849 13841.448 Loop time of 0.34523 on 1 procs for 9 steps with 1172 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 = -4857.86741677507 -4858.39274674292 -4858.39283013266 Force two-norm initial, final = 130.86579 2.4825727 Force max component initial, final = 128.23560 1.4444995 Final line search alpha, max atom move = 0.0039470170 0.0057014640 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33975 | 0.33975 | 0.33975 | 0.0 | 98.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010625 | 0.0010625 | 0.0010625 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004422 | | | 1.28 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11425.0 ave 11425 max 11425 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: 708188.0 ave 708188 max 708188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 708188 Ave neighs/atom = 604.25597 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 = 5 12 2 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) = 7.637 | 7.637 | 7.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4858.3928 0 -4858.3928 153.55849 Loop time of 2.209e-06 on 1 procs for 0 steps with 1172 atoms 181.1% 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 | | 2.209e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11420.0 ave 11420 max 11420 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: 706452.0 ave 706452 max 706452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 706452 Ave neighs/atom = 602.77474 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 = 5 12 2 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) = 7.637 | 7.637 | 7.637 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 -4858.3928 -4858.3928 28.251678 69.985879 7.0004642 153.55849 153.55849 166.62011 151.7325 142.32285 2.2977214 1534.8993 Loop time of 2.863e-06 on 1 procs for 0 steps with 1172 atoms 244.5% 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 | | 2.863e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11420.0 ave 11420 max 11420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 353226.0 ave 353226 max 353226 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 706452.0 ave 706452 max 706452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 706452 Ave neighs/atom = 602.77474 Neighbor list builds = 0 Dangerous builds = 0 1172 -4858.39283013266 eV 2.29772136286546 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07