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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -68.179517 0.0000000) to (34.087952 68.179517 3.6133157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9791390 4.9791390 3.6133157 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -68.179517 0.0000000) to (34.087952 68.179517 3.6133157) create_atoms CPU = 0.003 seconds 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9791390 4.9791390 3.6133157 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -68.179517 0.0000000) to (34.087952 68.179517 3.6133157) create_atoms CPU = 0.002 seconds 714 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1416 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4970.7972 0 -4970.7972 5555.601 68 0 -4999.5447 0 -4999.5447 -2612.4344 Loop time of 11.7783 on 1 procs for 68 steps with 1416 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 = -4970.79716935017 -4999.54001292385 -4999.54468976446 Force two-norm initial, final = 41.336121 0.23888702 Force max component initial, final = 10.743289 0.047746285 Final line search alpha, max atom move = 1.0000000 0.047746285 Iterations, force evaluations = 68 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.734 | 11.734 | 11.734 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.023435 | 0.023435 | 0.023435 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02085 | | | 0.18 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8207.00 ave 8207 max 8207 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: 121776.0 ave 121776 max 121776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121776 Ave neighs/atom = 86.000000 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -4999.5447 0 -4999.5447 -2612.4344 16795.415 70 0 -4999.5786 0 -4999.5786 280.01463 16760.819 Loop time of 0.380868 on 1 procs for 2 steps with 1416 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 = -4999.54468976446 -4999.57839031459 -4999.57856113401 Force two-norm initial, final = 47.706149 1.7808370 Force max component initial, final = 35.025090 1.7632621 Final line search alpha, max atom move = 0.00040101720 0.00070709842 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37803 | 0.37803 | 0.37803 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066616 | 0.00066616 | 0.00066616 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002172 | | | 0.57 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8208.00 ave 8208 max 8208 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: 121776.0 ave 121776 max 121776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121776 Ave neighs/atom = 86.000000 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.225 | 5.225 | 5.225 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4999.5786 0 -4999.5786 280.01463 Loop time of 6.856e-06 on 1 procs for 0 steps with 1416 atoms 189.6% 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 | | 6.856e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8216.00 ave 8216 max 8216 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: 121784.0 ave 121784 max 121784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121784 Ave neighs/atom = 86.005650 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.225 | 5.225 | 5.225 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 -4999.5786 -4999.5786 34.053836 136.35903 3.6094853 280.01463 280.01463 168.38257 670.8393 0.82201553 2.2976235 477.90754 Loop time of 6.776e-06 on 1 procs for 0 steps with 1416 atoms 280.4% 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 | | 6.776e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8216.00 ave 8216 max 8216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60892.0 ave 60892 max 60892 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121784.0 ave 121784 max 121784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121784 Ave neighs/atom = 86.005650 Neighbor list builds = 0 Dangerous builds = 0 1416 -4999.57856113401 eV 2.29762348092813 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12