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 = 3.5620076 3.5620076 3.5620076 Created orthogonal box = (0.0000000 -66.065399 0.0000000) to (23.357646 66.065399 5.0374395) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9752117 6.1456185 5.0374395 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -66.065399 0.0000000) to (23.357646 66.065399 5.0374395) create_atoms CPU = 0.005 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9752117 6.1456185 5.0374395 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.065399 0.0000000) to (23.357646 66.065399 5.0374395) create_atoms CPU = 0.004 seconds 690 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 7 37 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1378 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_763197941039_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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 7 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 5.121 | 5.121 | 5.121 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5886.162 0 -5886.162 54334.513 36 0 -6053.2434 0 -6053.2434 8500.6536 Loop time of 1.04503 on 1 procs for 36 steps with 1378 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5886.1619625765 -6053.23818470694 -6053.24339713703 Force two-norm initial, final = 203.84692 0.38369516 Force max component initial, final = 50.629429 0.081708196 Final line search alpha, max atom move = 1.0000000 0.081708196 Iterations, force evaluations = 36 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0277 | 1.0277 | 1.0277 | 0.0 | 98.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0089333 | 0.0089333 | 0.0089333 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008395 | | | 0.80 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7817.00 ave 7817 max 7817 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: 192840.0 ave 192840 max 192840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192840 Ave neighs/atom = 139.94194 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 7 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.121 | 5.121 | 5.121 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -6053.2434 0 -6053.2434 8500.6536 15546.87 41 0 -6053.5748 0 -6053.5748 -351.75172 15636.59 Loop time of 0.0703261 on 1 procs for 5 steps with 1378 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 = -6053.24339713704 -6053.57215111571 -6053.57476937795 Force two-norm initial, final = 153.01237 6.7300414 Force max component initial, final = 106.24225 5.9104821 Final line search alpha, max atom move = 0.00013584616 0.00080291627 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.067441 | 0.067441 | 0.067441 | 0.0 | 95.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049087 | 0.00049087 | 0.00049087 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002394 | | | 3.40 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7823.00 ave 7823 max 7823 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: 191848.0 ave 191848 max 191848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191848 Ave neighs/atom = 139.22206 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 7 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 5.259 | 5.259 | 5.259 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6053.5748 0 -6053.5748 -351.75172 Loop time of 2.145e-06 on 1 procs for 0 steps with 1378 atoms 186.5% 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 | | 2.145e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7823.00 ave 7823 max 7823 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: 191652.0 ave 191652 max 191652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191652 Ave neighs/atom = 139.07983 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 7 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 5.259 | 5.259 | 5.259 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 -6053.5748 -6053.5748 23.441647 132.559 5.0320474 -351.75172 -351.75172 -181.43608 -268.85988 -604.9592 2.360465 379.62832 Loop time of 2.635e-06 on 1 procs for 0 steps with 1378 atoms 227.7% 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 | | 2.635e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7823.00 ave 7823 max 7823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95826.0 ave 95826 max 95826 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191652.0 ave 191652 max 191652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191652 Ave neighs/atom = 139.07983 Neighbor list builds = 0 Dangerous builds = 0 1378 -6053.57476937795 eV 2.36046498460603 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01