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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -47.913158 0.0000000) to (33.879719 47.913158 5.1666087) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3032035 6.1284272 5.1666087 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -47.913158 0.0000000) to (33.879719 47.913158 5.1666087) create_atoms CPU = 0.006 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3032035 6.1284272 5.1666087 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -47.913158 0.0000000) to (33.879719 47.913158 5.1666087) create_atoms CPU = 0.005 seconds 694 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1374 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_673777079812_004#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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.903 | 5.903 | 5.903 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4390.3809 0 -4390.3809 15071.57 106 0 -4481.0617 0 -4481.0617 -3383.5184 Loop time of 6.1114 on 1 procs for 106 steps with 1374 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 = -4390.3808798444 -4481.05772668116 -4481.06167218574 Force two-norm initial, final = 93.619457 0.23221017 Force max component initial, final = 15.045035 0.016272472 Final line search alpha, max atom move = 1.0000000 0.016272472 Iterations, force evaluations = 106 203 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9899 | 5.9899 | 5.9899 | 0.0 | 98.01 Neigh | 0.043797 | 0.043797 | 0.043797 | 0.0 | 0.72 Comm | 0.04458 | 0.04458 | 0.04458 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03307 | | | 0.54 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9652.00 ave 9652 max 9652 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: 309628.0 ave 309628 max 309628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309628 Ave neighs/atom = 225.34789 Neighbor list builds = 1 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.902 | 5.902 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -4481.0617 0 -4481.0617 -3383.5184 16773.75 113 0 -4481.675 0 -4481.675 -24.994514 16726.914 Loop time of 0.273259 on 1 procs for 7 steps with 1374 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4481.06167218576 -4481.67473658101 -4481.6749719768 Force two-norm initial, final = 172.19676 0.68339121 Force max component initial, final = 148.45815 0.35152764 Final line search alpha, max atom move = 0.00040363877 0.00014189018 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26538 | 0.26538 | 0.26538 | 0.0 | 97.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017786 | 0.0017786 | 0.0017786 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006104 | | | 2.23 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9511.00 ave 9511 max 9511 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: 311040.0 ave 311040 max 311040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311040 Ave neighs/atom = 226.37555 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.040 | 6.040 | 6.040 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4481.675 0 -4481.675 -24.994514 Loop time of 6.565e-06 on 1 procs for 0 steps with 1374 atoms 182.8% 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 | | 6.565e-06 | | |100.00 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9539.00 ave 9539 max 9539 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: 311384.0 ave 311384 max 311384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311384 Ave neighs/atom = 226.62591 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.040 | 6.040 | 6.040 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 -4481.675 -4481.675 34.010379 95.243424 5.1637993 -24.994514 -24.994514 -23.949424 -17.381584 -33.652535 2.4266503 1450.9259 Loop time of 7.006e-06 on 1 procs for 0 steps with 1374 atoms 271.2% 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 | | 7.006e-06 | | |100.00 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9539.00 ave 9539 max 9539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155692.0 ave 155692 max 155692 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 311384.0 ave 311384 max 311384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311384 Ave neighs/atom = 226.62591 Neighbor list builds = 0 Dangerous builds = 0 1374 -4481.6749719768 eV 2.42665033583418 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07