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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -65.439930 0.0000000) to (23.136509 65.439930 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2073561 5.5863354 5.1100000 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.439930 0.0000000) to (23.136509 65.439930 5.1100000) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2073561 5.5863354 5.1100000 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.439930 0.0000000) to (23.136509 65.439930 5.1100000) create_atoms CPU = 0.002 seconds 658 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 39 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_694335101831_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.081 | 5.081 | 5.081 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4421.4253 0 -4421.4253 39151.49 62 0 -4637.1133 0 -4637.1133 2608.1942 Loop time of 5.10991 on 1 procs for 62 steps with 1312 atoms 90.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4421.42534000902 -4637.10887319802 -4637.11325235882 Force two-norm initial, final = 297.99503 0.19060524 Force max component initial, final = 77.041314 0.042827802 Final line search alpha, max atom move = 1.0000000 0.042827802 Iterations, force evaluations = 62 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0586 | 5.0586 | 5.0586 | 0.0 | 99.00 Neigh | 0.032532 | 0.032532 | 0.032532 | 0.0 | 0.64 Comm | 0.0099565 | 0.0099565 | 0.0099565 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008835 | | | 0.17 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6710.00 ave 6710 max 6710 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: 169860.0 ave 169860 max 169860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169860 Ave neighs/atom = 129.46646 Neighbor list builds = 2 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.081 | 5.081 | 5.081 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -4637.1133 0 -4637.1133 2608.1942 15473.606 65 0 -4637.1658 0 -4637.1658 146.75603 15500.294 Loop time of 0.212773 on 1 procs for 3 steps with 1312 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4637.11325235881 -4637.16521384226 -4637.16575880045 Force two-norm initial, final = 50.724378 2.6502379 Force max component initial, final = 41.838797 2.1644612 Final line search alpha, max atom move = 0.00041468681 0.00089757352 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21108 | 0.21108 | 0.21108 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030839 | 0.00030839 | 0.00030839 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001385 | | | 0.65 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6703.00 ave 6703 max 6703 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: 169548.0 ave 169548 max 169548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169548 Ave neighs/atom = 129.22866 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.219 | 5.219 | 5.219 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4637.1658 0 -4637.1658 146.75603 Loop time of 2.026e-06 on 1 procs for 0 steps with 1312 atoms 148.1% 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 | | 2.026e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6703.00 ave 6703 max 6703 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: 168736.0 ave 168736 max 168736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168736 Ave neighs/atom = 128.60976 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.219 | 5.219 | 5.219 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 -4637.1658 -4637.1658 23.150961 131.15723 5.1047992 146.75603 146.75603 132.45559 224.20209 83.61043 2.3885002 470.97419 Loop time of 2.66e-06 on 1 procs for 0 steps with 1312 atoms 225.6% 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 | | 2.66e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6703.00 ave 6703 max 6703 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84368.0 ave 84368 max 84368 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 168736.0 ave 168736 max 168736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168736 Ave neighs/atom = 128.60976 Neighbor list builds = 0 Dangerous builds = 0 1312 -4637.16575880045 eV 2.38850023168244 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05