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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -55.436536 0.0000000) to (33.945651 55.436536 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4751050 5.3644854 5.7481360 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.436536 0.0000000) to (33.945651 55.436536 8.6222040) create_atoms CPU = 0.002 seconds 1493 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4751050 5.3644854 5.7481360 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.436536 0.0000000) to (33.945651 55.436536 8.6222040) create_atoms CPU = 0.002 seconds 1493 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 = 8 27 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 2963 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_103383163946_000#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 = 8 27 3 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) = 7.438 | 7.438 | 7.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13060.006 0 -13060.006 11578.438 24 0 -13145.654 0 -13145.654 -1250.3212 Loop time of 1.15437 on 1 procs for 24 steps with 2963 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 = -13060.0055507415 -13145.6423733658 -13145.6539833309 Force two-norm initial, final = 97.562494 0.35232539 Force max component initial, final = 16.385723 0.030943113 Final line search alpha, max atom move = 1.0000000 0.030943113 Iterations, force evaluations = 24 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1431 | 1.1431 | 1.1431 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046892 | 0.0046892 | 0.0046892 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006542 | | | 0.57 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11990.0 ave 11990 max 11990 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: 662864.0 ave 662864 max 662864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 662864 Ave neighs/atom = 223.71380 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.438 | 7.438 | 7.438 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -13145.654 0 -13145.654 -1250.3212 32451.032 26 0 -13145.675 0 -13145.675 -1265.1198 32451.368 Loop time of 0.145521 on 1 procs for 2 steps with 2963 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 = -13145.6539833307 -13145.6748007474 -13145.674807857 Force two-norm initial, final = 42.550233 0.37620311 Force max component initial, final = 30.252147 0.095279701 Final line search alpha, max atom move = 0.0014252785 0.00013580011 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14306 | 0.14306 | 0.14306 | 0.0 | 98.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042795 | 0.00042795 | 0.00042795 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002031 | | | 1.40 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11993.0 ave 11993 max 11993 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: 665000.0 ave 665000 max 665000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665000 Ave neighs/atom = 224.43469 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 = 8 27 3 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) = 7.576 | 7.576 | 7.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13145.675 0 -13145.675 -1265.1198 Loop time of 1.819e-06 on 1 procs for 0 steps with 2963 atoms 164.9% 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 | | 1.819e-06 | | |100.00 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11993.0 ave 11993 max 11993 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: 665018.0 ave 665018 max 665018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665018 Ave neighs/atom = 224.44077 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 = 8 27 3 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) = 7.576 | 7.576 | 7.576 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 -13145.675 -13145.675 33.969324 110.87307 8.6162843 -1265.1198 -1265.1198 -4.5848634 -3786.0736 -4.7008833 2.1899187 1098.6127 Loop time of 2.162e-06 on 1 procs for 0 steps with 2963 atoms 231.3% 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 | | 2.162e-06 | | |100.00 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11993.0 ave 11993 max 11993 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332509.0 ave 332509 max 332509 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 665018.0 ave 665018 max 665018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665018 Ave neighs/atom = 224.44077 Neighbor list builds = 0 Dangerous builds = 0 2963 -13064.9884173638 eV 2.18991865654854 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01