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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -41.488364 0.0000000) to (29.336703 41.488364 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2229371 5.6575042 5.1068646 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.488364 0.0000000) to (29.336703 41.488364 5.1068646) create_atoms CPU = 0.003 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2229371 5.6575042 5.1068646 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.488364 0.0000000) to (29.336703 41.488364 5.1068646) create_atoms CPU = 0.003 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 28 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 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_179158257180_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 = 10 28 2 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) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4122.9557 0 -4122.9557 64352.665 434 0 -4492.4522 0 -4492.4522 5745.1948 Loop time of 33.1677 on 1 procs for 434 steps with 1056 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 = -4122.95566262161 -4492.44837738552 -4492.45221616998 Force two-norm initial, final = 522.04553 0.22311525 Force max component initial, final = 112.10515 0.025616984 Final line search alpha, max atom move = 1.0000000 0.025616984 Iterations, force evaluations = 434 836 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.995 | 32.995 | 32.995 | 0.0 | 99.48 Neigh | 0.076228 | 0.076228 | 0.076228 | 0.0 | 0.23 Comm | 0.047816 | 0.047816 | 0.047816 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04814 | | | 0.15 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4660.00 ave 4660 max 4660 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: 70328.0 ave 70328 max 70328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70328 Ave neighs/atom = 66.598485 Neighbor list builds = 12 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 = 10 28 2 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 : 434 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press Volume 434 0 -4492.4522 0 -4492.4522 5745.1948 12431.455 462 0 -4502.7387 0 -4502.7387 -4.805516 12454.189 Loop time of 1.08916 on 1 procs for 28 steps with 1056 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 = -4492.45221616998 -4502.73690704954 -4502.73871322193 Force two-norm initial, final = 564.03181 1.6683052 Force max component initial, final = 440.12884 0.46292808 Final line search alpha, max atom move = 0.00017452693 8.0793418e-05 Iterations, force evaluations = 28 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0676 | 1.0676 | 1.0676 | 0.0 | 98.02 Neigh | 0.01255 | 0.01255 | 0.01255 | 0.0 | 1.15 Comm | 0.0015291 | 0.0015291 | 0.0015291 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007527 | | | 0.69 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4767.00 ave 4767 max 4767 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: 69528.0 ave 69528 max 69528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69528 Ave neighs/atom = 65.840909 Neighbor list builds = 2 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 = 10 29 2 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) = 4.739 | 4.739 | 4.739 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4502.7387 0 -4502.7387 -4.805516 Loop time of 2.106e-06 on 1 procs for 0 steps with 1056 atoms 189.9% 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 | | 2.106e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4767.00 ave 4767 max 4767 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: 69520.0 ave 69520 max 69520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69520 Ave neighs/atom = 65.833333 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 = 10 29 2 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) = 4.739 | 4.739 | 4.739 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 -4502.7387 -4502.7387 29.308037 85.252175 4.984519 -4.805516 -4.805516 -26.579404 -45.964068 58.126924 2.3713768 2559.4225 Loop time of 2.05e-06 on 1 procs for 0 steps with 1056 atoms 195.1% 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 | | 2.05e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4767.00 ave 4767 max 4767 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34760.0 ave 34760 max 34760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69520.0 ave 69520 max 69520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69520 Ave neighs/atom = 65.833333 Neighbor list builds = 0 Dangerous builds = 0 1056 -4502.73871322193 eV 2.37137680221925 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34