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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -58.612544 0.0000000) to (20.722664 58.612544 5.1015671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6516355 6.2164819 5.1015671 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.612544 0.0000000) to (20.722664 58.612544 5.1015671) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6516355 6.2164819 5.1015671 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.612544 0.0000000) to (20.722664 58.612544 5.1015671) create_atoms CPU = 0.002 seconds 530 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.146 | 7.146 | 7.146 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3576.9648 0 -3576.9648 25313.235 68 0 -3722.0078 0 -3722.0078 2848.6891 Loop time of 4.89445 on 1 procs for 68 steps with 1056 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 = -3576.96484272189 -3722.00467968051 -3722.00780094727 Force two-norm initial, final = 243.90463 0.22468710 Force max component initial, final = 78.597142 0.025784008 Final line search alpha, max atom move = 1.0000000 0.025784008 Iterations, force evaluations = 68 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8207 | 4.8207 | 4.8207 | 0.0 | 98.49 Neigh | 0.032299 | 0.032299 | 0.032299 | 0.0 | 0.66 Comm | 0.027788 | 0.027788 | 0.027788 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01367 | | | 0.28 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14825.0 ave 14825 max 14825 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: 665092.0 ave 665092 max 665092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665092 Ave neighs/atom = 629.82197 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.146 | 7.146 | 7.146 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -3722.0078 0 -3722.0078 2848.6891 12392.809 75 0 -3722.4175 0 -3722.4175 -20.73515 12417.638 Loop time of 0.535464 on 1 procs for 7 steps with 1056 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 = -3722.00780094725 -3722.41699078196 -3722.41752824811 Force two-norm initial, final = 119.59051 0.73355223 Force max component initial, final = 111.30001 0.52231204 Final line search alpha, max atom move = 0.00029410042 0.00015361219 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52542 | 0.52542 | 0.52542 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020629 | 0.0020629 | 0.0020629 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007981 | | | 1.49 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14858.0 ave 14858 max 14858 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: 664928.0 ave 664928 max 664928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664928 Ave neighs/atom = 629.66667 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.284 | 7.284 | 7.284 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3722.4175 0 -3722.4175 -20.73515 Loop time of 4.07e-06 on 1 procs for 0 steps with 1056 atoms 172.0% 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 | | 4.07e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14868.0 ave 14868 max 14868 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: 663564.0 ave 663564 max 663564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663564 Ave neighs/atom = 628.37500 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.284 | 7.284 | 7.284 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 -3722.4175 -3722.4175 20.639794 117.90004 5.1029309 -20.73515 -20.73515 -67.121428 33.3048 -28.388823 2.3373267 429.5363 Loop time of 5.238e-06 on 1 procs for 0 steps with 1056 atoms 190.9% 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 | | 5.238e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14868.0 ave 14868 max 14868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 331782.0 ave 331782 max 331782 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 663564.0 ave 663564 max 663564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663564 Ave neighs/atom = 628.37500 Neighbor list builds = 0 Dangerous builds = 0 1056 -3722.41752824811 eV 2.33732669047402 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06