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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -42.031851 0.0000000) to (29.721007 42.031851 5.1737632) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3044560 5.7316160 5.1737632 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -42.031851 0.0000000) to (29.721007 42.031851 5.1737632) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3044560 5.7316160 5.1737632 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -42.031851 0.0000000) to (29.721007 42.031851 5.1737632) create_atoms CPU = 0.001 seconds 532 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1060 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.422 | 5.422 | 5.422 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3800.8766 0 -3800.8766 95782.911 412 0 -4163.4144 0 -4163.4144 -59825.862 Loop time of 10.797 on 1 procs for 412 steps with 1060 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3800.87659604826 -4163.41067174531 -4163.41437249646 Force two-norm initial, final = 473.90128 0.22639331 Force max component initial, final = 104.47295 0.024756437 Final line search alpha, max atom move = 1.0000000 0.024756437 Iterations, force evaluations = 412 798 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.591 | 10.591 | 10.591 | 0.0 | 98.09 Neigh | 0.076494 | 0.076494 | 0.076494 | 0.0 | 0.71 Comm | 0.073516 | 0.073516 | 0.073516 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05627 | | | 0.52 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7559.00 ave 7559 max 7559 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: 217852.0 ave 217852 max 217852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217852 Ave neighs/atom = 205.52075 Neighbor list builds = 5 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 412 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.423 | 5.423 | 5.423 Mbytes Step Temp E_pair E_mol TotEng Press Volume 412 0 -4163.4144 0 -4163.4144 -59825.862 12926.429 454 0 -4185.0798 0 -4185.0798 -30.294568 12378.003 Loop time of 0.636132 on 1 procs for 42 steps with 1060 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 = -4163.41437249644 -4185.0768790437 -4185.07978081734 Force two-norm initial, final = 956.17213 6.2588313 Force max component initial, final = 728.76577 3.6028795 Final line search alpha, max atom move = 0.00031930420 0.0011504145 Iterations, force evaluations = 42 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60223 | 0.60223 | 0.60223 | 0.0 | 94.67 Neigh | 0.015477 | 0.015477 | 0.015477 | 0.0 | 2.43 Comm | 0.0031448 | 0.0031448 | 0.0031448 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01528 | | | 2.40 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7845.00 ave 7845 max 7845 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: 229672.0 ave 229672 max 229672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229672 Ave neighs/atom = 216.67170 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.563 | 5.563 | 5.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4185.0798 0 -4185.0798 -30.294568 Loop time of 2.098e-06 on 1 procs for 0 steps with 1060 atoms 190.7% 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 | | 2.098e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7841.00 ave 7841 max 7841 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: 229548.0 ave 229548 max 229548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229548 Ave neighs/atom = 216.55472 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.563 | 5.563 | 5.563 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 -4185.0798 -4185.0798 29.078755 85.560703 4.9750843 -30.294568 -30.294568 361.92422 -474.65201 21.844086 2.3533997 3511.5124 Loop time of 2.763e-06 on 1 procs for 0 steps with 1060 atoms 217.2% 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 | | 2.763e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7841.00 ave 7841 max 7841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114774.0 ave 114774 max 114774 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229548.0 ave 229548 max 229548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229548 Ave neighs/atom = 216.55472 Neighbor list builds = 0 Dangerous builds = 0 1060 -4185.07978081734 eV 2.35339970068385 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11