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 = 2.8669669 2.8669669 2.8669669 Created orthogonal box = (0.0000000 -30.613697 0.0000000) to (21.645126 30.613697 4.0545035) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1771295 4.8332890 4.0545035 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.613697 0.0000000) to (21.645126 30.613697 4.0545035) create_atoms CPU = 0.002 seconds 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1771295 4.8332890 4.0545035 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.613697 0.0000000) to (21.645126 30.613697 4.0545035) create_atoms CPU = 0.001 seconds 230 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 17 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 452 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1782.758 0 -1782.758 7141.6208 163 0 -1814.5434 0 -1814.5434 -60605.553 Loop time of 2.60637 on 1 procs for 163 steps with 452 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 = -1782.75804994495 -1814.54158759729 -1814.54335033009 Force two-norm initial, final = 27.101538 0.14205572 Force max component initial, final = 7.2224404 0.028144091 Final line search alpha, max atom move = 1.0000000 0.028144091 Iterations, force evaluations = 163 318 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5405 | 2.5405 | 2.5405 | 0.0 | 97.47 Neigh | 0.010433 | 0.010433 | 0.010433 | 0.0 | 0.40 Comm | 0.031473 | 0.031473 | 0.031473 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02395 | | | 0.92 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4338.00 ave 4338 max 4338 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: 71776.0 ave 71776 max 71776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71776 Ave neighs/atom = 158.79646 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 163 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press Volume 163 0 -1814.5434 0 -1814.5434 -60605.553 5373.3308 359 0 -1826.2816 0 -1826.2816 -13602.846 4981.823 Loop time of 1.88992 on 1 procs for 196 steps with 452 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 = -1814.54335033009 -1826.28008074798 -1826.28164024508 Force two-norm initial, final = 295.90596 3.6398920 Force max component initial, final = 239.89394 2.5442533 Final line search alpha, max atom move = 0.00032859601 0.00083603149 Iterations, force evaluations = 196 219 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7883 | 1.7883 | 1.7883 | 0.0 | 94.63 Neigh | 0.01048 | 0.01048 | 0.01048 | 0.0 | 0.55 Comm | 0.020271 | 0.020271 | 0.020271 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07083 | | | 3.75 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4438.00 ave 4438 max 4438 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: 73988.0 ave 73988 max 73988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73988 Ave neighs/atom = 163.69027 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1826.2816 0 -1826.2816 -13602.846 Loop time of 6.385e-06 on 1 procs for 0 steps with 452 atoms 187.9% 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 | | 6.385e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4458.00 ave 4458 max 4458 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: 74324.0 ave 74324 max 74324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74324 Ave neighs/atom = 164.43363 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.615 | 4.615 | 4.615 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 -1826.2816 -1826.2816 20.41179 61.227395 3.9862214 -13602.846 -13602.846 185.40327 -40189.477 -804.46314 2.2578671 1312.1597 Loop time of 6.665e-06 on 1 procs for 0 steps with 452 atoms 300.1% 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 | | 6.665e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4458.00 ave 4458 max 4458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37162.0 ave 37162 max 37162 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74324.0 ave 74324 max 74324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74324 Ave neighs/atom = 164.43363 Neighbor list builds = 0 Dangerous builds = 0 452 -1826.28164024508 eV 2.25786706052386 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05