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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -66.464415 0.0000000) to (33.230405 66.464415 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0822973 5.0822973 3.6043435 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -66.464415 0.0000000) to (33.230405 66.464415 3.6043435) create_atoms CPU = 0.001 seconds 681 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0822973 5.0822973 3.6043435 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -66.464415 0.0000000) to (33.230405 66.464415 3.6043435) create_atoms CPU = 0.001 seconds 681 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 3 atoms, new total = 1359 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_492310898779_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) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5714.4278 0 -5714.4278 10632.235 43 0 -5763.4092 0 -5763.4092 163.16323 Loop time of 3.24379 on 1 procs for 43 steps with 1359 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5714.42778805581 -5763.40379779267 -5763.40920513122 Force two-norm initial, final = 36.770699 0.23437611 Force max component initial, final = 9.7068474 0.079118935 Final line search alpha, max atom move = 1.0000000 0.079118935 Iterations, force evaluations = 43 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2254 | 3.2254 | 3.2254 | 0.0 | 99.43 Neigh | 0.0075545 | 0.0075545 | 0.0075545 | 0.0 | 0.23 Comm | 0.0053118 | 0.0053118 | 0.0053118 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005491 | | | 0.17 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6721.00 ave 6721 max 6721 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: 105296.0 ave 105296 max 105296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105296 Ave neighs/atom = 77.480500 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 = 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 : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -5763.4092 0 -5763.4092 163.16323 15921.39 51 0 -5763.6656 0 -5763.6656 -2303.1627 15945.328 Loop time of 0.461493 on 1 procs for 8 steps with 1359 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 = -5763.40920513122 -5763.66524003971 -5763.66555989825 Force two-norm initial, final = 54.388123 0.36117415 Force max component initial, final = 43.614486 0.067439900 Final line search alpha, max atom move = 0.00065401806 4.4106913e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45825 | 0.45825 | 0.45825 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052746 | 0.00052746 | 0.00052746 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002711 | | | 0.59 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6717.00 ave 6717 max 6717 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: 105582.0 ave 105582 max 105582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105582 Ave neighs/atom = 77.690949 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) = 5.189 | 5.189 | 5.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5763.6656 0 -5763.6656 -2303.1627 Loop time of 1.986e-06 on 1 procs for 0 steps with 1359 atoms 151.1% 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 | | 1.986e-06 | | |100.00 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6733.00 ave 6733 max 6733 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: 105616.0 ave 105616 max 105616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105616 Ave neighs/atom = 77.715968 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) = 5.189 | 5.189 | 5.189 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 -5763.6656 -5763.6656 33.040833 132.92883 3.6304736 -2303.1627 -2303.1627 2.5219206 -6907.4019 -4.6081511 2.2937088 154.50665 Loop time of 2.073e-06 on 1 procs for 0 steps with 1359 atoms 241.2% 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 | | 2.073e-06 | | |100.00 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6733.00 ave 6733 max 6733 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52808.0 ave 52808 max 52808 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105616.0 ave 105616 max 105616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105616 Ave neighs/atom = 77.715968 Neighbor list builds = 0 Dangerous builds = 0 1359 -5763.66555989825 eV 2.29370880396756 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04