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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2931087 4.2931087 3.1465590 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) create_atoms CPU = 0.002 seconds 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2931087 4.2931087 3.1465590 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) create_atoms CPU = 0.001 seconds 261 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 35 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 518 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.458 | 4.458 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3494.1649 0 -3494.1649 7190.8074 25 0 -3508.8447 0 -3508.8447 -1480.451 Loop time of 1.45017 on 1 procs for 25 steps with 518 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3494.16491198381 -3508.84180992065 -3508.84468713241 Force two-norm initial, final = 17.385289 0.18033209 Force max component initial, final = 4.9588491 0.021757208 Final line search alpha, max atom move = 1.0000000 0.021757208 Iterations, force evaluations = 25 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4428 | 1.4428 | 1.4428 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036768 | 0.0036768 | 0.0036768 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003728 | | | 0.26 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3239.00 ave 3239 max 3239 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: 29760.0 ave 29760 max 29760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29760 Ave neighs/atom = 57.451737 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.458 | 4.458 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -3508.8447 0 -3508.8447 -1480.451 8100.4268 28 0 -3508.901 0 -3508.901 2615.8658 8087.8362 Loop time of 0.178449 on 1 procs for 3 steps with 518 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 = -3508.84468713242 -3508.89783806985 -3508.90103027737 Force two-norm initial, final = 49.177450 3.3639015 Force max component initial, final = 48.895235 3.0840102 Final line search alpha, max atom move = 0.00010861759 0.00033497776 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17599 | 0.17599 | 0.17599 | 0.0 | 98.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049123 | 0.00049123 | 0.00049123 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001969 | | | 1.10 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3265.00 ave 3265 max 3265 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: 29772.0 ave 29772 max 29772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29772 Ave neighs/atom = 57.474903 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3508.901 0 -3508.901 2615.8658 Loop time of 7.618e-06 on 1 procs for 0 steps with 518 atoms 170.6% 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 | | 7.618e-06 | | |100.00 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3261.00 ave 3261 max 3261 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: 29770.0 ave 29770 max 29770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29770 Ave neighs/atom = 57.471042 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.596 | 4.596 | 4.596 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 -3508.901 -3508.901 25.386064 101.47977 3.1394785 2615.8658 2615.8658 -263.4572 8720.613 -609.55858 2.3794053 271.59991 Loop time of 8.329e-06 on 1 procs for 0 steps with 518 atoms 264.1% 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 | | 8.329e-06 | | |100.00 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3261.00 ave 3261 max 3261 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14885.0 ave 14885 max 14885 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29770.0 ave 29770 max 29770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29770 Ave neighs/atom = 57.471042 Neighbor list builds = 0 Dangerous builds = 0 518 -3508.90103027737 eV 2.37940531988381 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02