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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -66.539752 0.0000000) to (33.268072 66.539752 3.6084290) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0880581 5.0880581 3.6084290 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -66.539752 0.0000000) to (33.268072 66.539752 3.6084290) create_atoms CPU = 0.003 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0880581 5.0880581 3.6084290 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -66.539752 0.0000000) to (33.268072 66.539752 3.6084290) create_atoms CPU = 0.002 seconds 682 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 = 12 45 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 8 atoms, new total = 1356 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_549900287421_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 = 12 45 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) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5718.9238 0 -5718.9238 7212.0239 72 0 -5761.4814 0 -5761.4814 -3124.2199 Loop time of 14.3588 on 1 procs for 72 steps with 1356 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 = -5718.92380869087 -5761.47577442848 -5761.48136066557 Force two-norm initial, final = 30.411053 0.22011661 Force max component initial, final = 8.2930604 0.063238578 Final line search alpha, max atom move = 1.0000000 0.063238578 Iterations, force evaluations = 72 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.318 | 14.318 | 14.318 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019863 | 0.019863 | 0.019863 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02083 | | | 0.15 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6692.00 ave 6692 max 6692 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: 105368.0 ave 105368 max 105368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105368 Ave neighs/atom = 77.705015 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 = 12 45 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 : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -5761.4814 0 -5761.4814 -3124.2199 15975.593 76 0 -5761.5605 0 -5761.5605 -1077.9111 15956.017 Loop time of 0.665634 on 1 procs for 4 steps with 1356 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 = -5761.48136066557 -5761.55710634167 -5761.56047325434 Force two-norm initial, final = 48.867092 8.5818426 Force max component initial, final = 48.864521 8.3302425 Final line search alpha, max atom move = 9.1737923e-05 0.00076419915 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6616 | 0.6616 | 0.6616 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088685 | 0.00088685 | 0.00088685 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003147 | | | 0.47 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6716.00 ave 6716 max 6716 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: 105384.0 ave 105384 max 105384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105384 Ave neighs/atom = 77.716814 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 = 12 45 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) = 5.191 | 5.191 | 5.191 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5761.5605 0 -5761.5605 -1077.9111 Loop time of 6.255e-06 on 1 procs for 0 steps with 1356 atoms 191.8% 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 | | 6.255e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6720.00 ave 6720 max 6720 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: 105384.0 ave 105384 max 105384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105384 Ave neighs/atom = 77.716814 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 = 12 45 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) = 5.191 | 5.191 | 5.191 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 -5761.5605 -5761.5605 33.167592 133.0795 3.6149258 -1077.9111 -1077.9111 205.16843 -4276.8644 837.96276 2.2968843 146.13292 Loop time of 7.036e-06 on 1 procs for 0 steps with 1356 atoms 270.0% 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 | | 7.036e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6720.00 ave 6720 max 6720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52692.0 ave 52692 max 52692 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105384.0 ave 105384 max 105384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105384 Ave neighs/atom = 77.716814 Neighbor list builds = 0 Dangerous builds = 0 1356 -5761.56047325434 eV 2.29688428752058 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15