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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -41.049901 0.0000000) to (20.524951 41.049901 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8294001 4.8294001 3.5200000 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.049901 0.0000000) to (20.524951 41.049901 3.5200000) create_atoms CPU = 0.002 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8294001 4.8294001 3.5200000 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.049901 0.0000000) to (20.524951 41.049901 3.5200000) create_atoms CPU = 0.001 seconds 274 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 1 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2377.8115 0 -2377.8115 5987.2389 50 0 -2408.7406 0 -2408.7406 11196.912 Loop time of 1.81582 on 1 procs for 50 steps with 544 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 = -2377.81147681672 -2408.73827914225 -2408.74063408588 Force two-norm initial, final = 20.914710 0.14922914 Force max component initial, final = 3.3564879 0.013836932 Final line search alpha, max atom move = 1.0000000 0.013836932 Iterations, force evaluations = 50 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7706 | 1.7706 | 1.7706 | 0.0 | 97.51 Neigh | 0.02119 | 0.02119 | 0.02119 | 0.0 | 1.17 Comm | 0.014998 | 0.014998 | 0.014998 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009073 | | | 0.50 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6740.00 ave 6740 max 6740 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: 134328.0 ave 134328 max 134328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134328 Ave neighs/atom = 246.92647 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2408.7406 0 -2408.7406 11196.912 5931.5322 58 0 -2409.0321 0 -2409.0321 -93.904708 5969.2134 Loop time of 0.219179 on 1 procs for 8 steps with 544 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 = -2408.74063408588 -2409.03197930102 -2409.03206363241 Force two-norm initial, final = 87.900730 0.94949010 Force max component initial, final = 78.100221 0.86804519 Final line search alpha, max atom move = 0.00088776184 0.00077061740 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21269 | 0.21269 | 0.21269 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016088 | 0.0016088 | 0.0016088 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004878 | | | 2.23 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6764.00 ave 6764 max 6764 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: 134352.0 ave 134352 max 134352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134352 Ave neighs/atom = 246.97059 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2409.0321 0 -2409.0321 -93.904708 Loop time of 6.996e-06 on 1 procs for 0 steps with 544 atoms 171.5% 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 | | 6.996e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6776.00 ave 6776 max 6776 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: 134032.0 ave 134032 max 134032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134032 Ave neighs/atom = 246.38235 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.065 | 5.065 | 5.065 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 -2409.0321 -2409.0321 20.480001 82.665682 3.5258341 -93.904708 -93.904708 4.1675215 -52.506394 -233.37525 2.2387406 271.17994 Loop time of 7.066e-06 on 1 procs for 0 steps with 544 atoms 283.0% 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 | | 7.066e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6776.00 ave 6776 max 6776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67016.0 ave 67016 max 67016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134032.0 ave 134032 max 134032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134032 Ave neighs/atom = 246.38235 Neighbor list builds = 0 Dangerous builds = 0 544 -2409.03206363241 eV 2.23874060611925 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02