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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -59.885664 0.0000000) to (42.345559 59.885664 5.1733334) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3202327 5.8098032 5.1733334 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -59.885664 0.0000000) to (42.345559 59.885664 5.1733334) create_atoms CPU = 0.002 seconds 1071 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3202327 5.8098032 5.1733334 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -59.885664 0.0000000) to (42.345559 59.885664 5.1733334) create_atoms CPU = 0.002 seconds 1079 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2128 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.640 | 5.640 | 5.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8221.0128 0 -8221.0128 3055.0436 918 0 -8414.004 0 -8414.004 -79040.928 Loop time of 27.5561 on 1 procs for 918 steps with 2128 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8221.01281674326 -8413.99584716458 -8414.00403184855 Force two-norm initial, final = 66.054312 0.28950120 Force max component initial, final = 11.617102 0.039216673 Final line search alpha, max atom move = 1.0000000 0.039216673 Iterations, force evaluations = 918 1786 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.805 | 26.805 | 26.805 | 0.0 | 97.28 Neigh | 0.35966 | 0.35966 | 0.35966 | 0.0 | 1.31 Comm | 0.20259 | 0.20259 | 0.20259 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1883 | | | 0.68 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10161.0 ave 10161 max 10161 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: 287024.0 ave 287024 max 287024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287024 Ave neighs/atom = 134.87970 Neighbor list builds = 19 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 918 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.642 | 5.642 | 5.642 Mbytes Step Temp E_pair E_mol TotEng Press Volume 918 0 -8414.004 0 -8414.004 -79040.928 26238.029 972 0 -8488.9355 0 -8488.9355 524.06792 24802.271 Loop time of 0.967711 on 1 procs for 54 steps with 2128 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8414.00403184857 -8488.9296456685 -8488.9355091554 Force two-norm initial, final = 2582.2067 22.207528 Force max component initial, final = 1914.7892 21.780747 Final line search alpha, max atom move = 0.00020099308 0.0043777794 Iterations, force evaluations = 54 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87553 | 0.87553 | 0.87553 | 0.0 | 90.47 Neigh | 0.058357 | 0.058357 | 0.058357 | 0.0 | 6.03 Comm | 0.0056977 | 0.0056977 | 0.0056977 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02812 | | | 2.91 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10702.0 ave 10702 max 10702 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: 298900.0 ave 298900 max 298900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298900 Ave neighs/atom = 140.46053 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.172 | 6.172 | 6.172 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8488.9355 0 -8488.9355 524.06792 Loop time of 1.923e-06 on 1 procs for 0 steps with 2128 atoms 208.0% 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 | | 1.923e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10715.0 ave 10715 max 10715 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: 298996.0 ave 298996 max 298996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298996 Ave neighs/atom = 140.50564 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.172 | 6.172 | 6.172 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 -8488.9355 -8488.9355 40.965599 122.55709 4.940077 524.06792 524.06792 67.44705 161.20332 1343.5534 2.2722008 5409.3701 Loop time of 2.597e-06 on 1 procs for 0 steps with 2128 atoms 269.5% 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 | | 2.597e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10715.0 ave 10715 max 10715 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149498.0 ave 149498 max 149498 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 298996.0 ave 298996 max 298996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298996 Ave neighs/atom = 140.50564 Neighbor list builds = 0 Dangerous builds = 0 2128 -8187.99029346802 eV 2.27220077330159 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29