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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -43.740626 0.0000000) to (53.571108 43.740626 8.8671528) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1369555 5.3926799 5.9114352 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -43.740626 0.0000000) to (53.571108 43.740626 8.8671528) create_atoms CPU = 0.007 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1369555 5.3926799 5.9114352 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -43.740626 0.0000000) to (53.571108 43.740626 8.8671528) create_atoms CPU = 0.006 seconds 1757 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 = 18 30 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 5 atoms, new total = 3503 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_313717476091_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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 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) = 5.682 | 5.682 | 5.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11194.41 0 -11194.41 98635.915 20 0 -12356.288 0 -12356.288 3897.1441 Loop time of 4.1677 on 1 procs for 20 steps with 3503 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11194.4103552543 -12356.2876075616 -12356.2876087168 Force two-norm initial, final = 2041.8178 4.0122844 Force max component initial, final = 410.03194 1.1752451 Final line search alpha, max atom move = 0.10743912 0.12626730 Iterations, force evaluations = 20 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1497 | 4.1497 | 4.1497 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064587 | 0.0064587 | 0.0064587 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01158 | | | 0.28 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8294.00 ave 8294 max 8294 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: 272744.0 ave 272744 max 272744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272744 Ave neighs/atom = 77.860120 Neighbor list builds = 0 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 = 18 30 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.682 | 5.682 | 5.682 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -12356.288 0 -12356.288 3897.1441 41555.624 26 0 -12356.868 0 -12356.868 29.496403 41674.409 Loop time of 1.11754 on 1 procs for 6 steps with 3503 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12356.2876087168 -12356.8674250002 -12356.8684605283 Force two-norm initial, final = 240.56796 4.7305696 Force max component initial, final = 226.55836 2.5710519 Final line search alpha, max atom move = 0.00026979322 0.00069365239 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1062 | 1.1062 | 1.1062 | 0.0 | 98.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017486 | 0.0017486 | 0.0017486 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009549 | | | 0.85 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8249.00 ave 8249 max 8249 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: 271556.0 ave 271556 max 271556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271556 Ave neighs/atom = 77.520982 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 = 18 30 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) = 5.820 | 5.820 | 5.820 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12356.868 0 -12356.868 29.496403 Loop time of 6.505e-06 on 1 procs for 0 steps with 3503 atoms 199.8% 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 | | 6.505e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8252.00 ave 8252 max 8252 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: 271334.0 ave 271334 max 271334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271334 Ave neighs/atom = 77.457608 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 = 18 30 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) = 5.820 | 5.820 | 5.820 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 -12356.868 -12356.868 53.565315 87.93561 8.8475089 29.496403 29.496403 98.833641 -44.821409 34.476975 2.2148119 1592.7139 Loop time of 6.535e-06 on 1 procs for 0 steps with 3503 atoms 306.0% 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 | | 6.535e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8252.00 ave 8252 max 8252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135667.0 ave 135667 max 135667 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 271334.0 ave 271334 max 271334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271334 Ave neighs/atom = 77.457608 Neighbor list builds = 0 Dangerous builds = 0 3503 -12356.8684605283 eV 2.21481187517137 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06