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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -56.178259 0.0000000) to (34.402017 56.178259 8.7381211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5487124 5.4366057 5.8254141 Created 1485 atoms using lattice units in orthogonal box = (0.0000000 -56.178259 0.0000000) to (34.402017 56.178259 8.7381211) create_atoms CPU = 0.002 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5487124 5.4366057 5.8254141 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -56.178259 0.0000000) to (34.402017 56.178259 8.7381211) create_atoms CPU = 0.002 seconds 1491 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 41 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 13 atoms, new total = 2963 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 41 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.192 | 5.192 | 5.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11947.144 0 -11947.144 36191.645 110 0 -12499.879 0 -12499.879 36429.399 Loop time of 14.8576 on 1 procs for 110 steps with 2963 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 = -11947.1435430189 -12499.8677661973 -12499.8792106006 Force two-norm initial, final = 595.01644 0.46533684 Force max component initial, final = 93.646601 0.069339792 Final line search alpha, max atom move = 1.0000000 0.069339792 Iterations, force evaluations = 110 197 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.79 | 14.79 | 14.79 | 0.0 | 99.55 Neigh | 0.016065 | 0.016065 | 0.016065 | 0.0 | 0.11 Comm | 0.018509 | 0.018509 | 0.018509 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03301 | | | 0.22 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7041.00 ave 7041 max 7041 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: 165666.0 ave 165666 max 165666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165666 Ave neighs/atom = 55.911576 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 41 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.191 | 5.191 | 5.191 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -12499.879 0 -12499.879 36429.399 33775.379 117 0 -12504.2 0 -12504.2 -415.78778 34139.356 Loop time of 0.685224 on 1 procs for 7 steps with 2963 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 = -12499.8792106006 -12504.1978278814 -12504.2003400208 Force two-norm initial, final = 1342.9447 17.201400 Force max component initial, final = 854.78907 12.619069 Final line search alpha, max atom move = 5.5300599e-05 0.00069784209 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68049 | 0.68049 | 0.68049 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053113 | 0.00053113 | 0.00053113 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0042 | | | 0.61 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6972.00 ave 6972 max 6972 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: 171214.0 ave 171214 max 171214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171214 Ave neighs/atom = 57.784003 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 41 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.328 | 5.328 | 5.328 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12504.2 0 -12504.2 -415.78778 Loop time of 2.014e-06 on 1 procs for 0 steps with 2963 atoms 198.6% 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 | | 2.014e-06 | | |100.00 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6902.00 ave 6902 max 6902 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: 167520.0 ave 167520 max 167520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167520 Ave neighs/atom = 56.537293 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 41 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.328 | 5.328 | 5.328 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 -12504.2 -12504.2 34.429497 112.83323 8.787951 -415.78778 -415.78778 -592.69207 -519.98548 -134.6858 2.3343982 1513.8066 Loop time of 1.0601e-05 on 1 procs for 0 steps with 2963 atoms 169.8% 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 | | 1.06e-05 | | |100.00 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6902.00 ave 6902 max 6902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 83760.0 ave 83760 max 83760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 167520.0 ave 167520 max 167520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167520 Ave neighs/atom = 56.537293 Neighbor list builds = 0 Dangerous builds = 0 2963 -12504.2003400208 eV 2.33439821109923 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16