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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -63.945570 0.0000000) to (36.916902 63.945570 6.2700240) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6795234 5.7383801 6.2700240 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -63.945570 0.0000000) to (36.916902 63.945570 6.2700240) create_atoms CPU = 0.007 seconds 1252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6795234 5.7383801 6.2700240 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -63.945570 0.0000000) to (36.916902 63.945570 6.2700240) create_atoms CPU = 0.006 seconds 1252 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 33 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2480 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.532 | 6.532 | 6.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8724.8005 0 -8724.8005 133.28859 26 0 -8756.4256 0 -8756.4256 -2523.3084 Loop time of 2.14131 on 1 procs for 26 steps with 2480 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8724.80053009175 -8756.41880473523 -8756.42556413068 Force two-norm initial, final = 27.241555 0.22119627 Force max component initial, final = 3.8855636 0.035379352 Final line search alpha, max atom move = 1.0000000 0.035379352 Iterations, force evaluations = 26 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1166 | 2.1166 | 2.1166 | 0.0 | 98.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012885 | 0.012885 | 0.012885 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01185 | | | 0.55 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11932.0 ave 11932 max 11932 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: 432128.0 ave 432128 max 432128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432128 Ave neighs/atom = 174.24516 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.532 | 6.532 | 6.532 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -8756.4256 0 -8756.4256 -2523.3084 29602.944 28 0 -8756.4776 0 -8756.4776 32.861201 29546.797 Loop time of 0.180017 on 1 procs for 2 steps with 2480 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 = -8756.42556413065 -8756.47662968958 -8756.47756688768 Force two-norm initial, final = 76.648543 3.2161769 Force max component initial, final = 63.166030 3.2082400 Final line search alpha, max atom move = 0.00011045457 0.00035436478 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1755 | 0.1755 | 0.1755 | 0.0 | 97.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085529 | 0.00085529 | 0.00085529 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003664 | | | 2.04 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11944.0 ave 11944 max 11944 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: 432424.0 ave 432424 max 432424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432424 Ave neighs/atom = 174.36452 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.670 | 6.670 | 6.670 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8756.4776 0 -8756.4776 32.861201 Loop time of 6.066e-06 on 1 procs for 0 steps with 2480 atoms 197.8% 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 | | 6.066e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12009.0 ave 12009 max 12009 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: 432496.0 ave 432496 max 432496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432496 Ave neighs/atom = 174.39355 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.670 | 6.670 | 6.670 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 -8756.4776 -8756.4776 36.891414 127.89114 6.2624555 32.861201 32.861201 173.84686 -73.502173 -1.761089 2.3404809 983.81796 Loop time of 3.504e-06 on 1 procs for 0 steps with 2480 atoms 199.8% 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 | | 3.504e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12009.0 ave 12009 max 12009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 216248.0 ave 216248 max 216248 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 432496.0 ave 432496 max 432496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432496 Ave neighs/atom = 174.39355 Neighbor list builds = 0 Dangerous builds = 0 2480 -8756.47756688768 eV 2.34048091325683 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03