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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -65.399776 0.0000000) to (23.122312 65.399776 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2035472 5.5829077 5.1068645 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.399776 0.0000000) to (23.122312 65.399776 5.1068645) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2035472 5.5829077 5.1068645 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.399776 0.0000000) to (23.122312 65.399776 5.1068645) create_atoms CPU = 0.002 seconds 658 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 = 8 41 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 0 atoms, new total = 1314 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_115454747503_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 = 8 41 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5173.0433 0 -5173.0433 65377.85 773 0 -5583.3969 0 -5583.3969 7447.7169 Loop time of 126.234 on 1 procs for 773 steps with 1314 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5173.04333069616 -5583.39168581603 -5583.39686241974 Force two-norm initial, final = 387.26225 0.23173836 Force max component initial, final = 111.47981 0.065323004 Final line search alpha, max atom move = 0.85914784 0.056122117 Iterations, force evaluations = 773 1491 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 125.82 | 125.82 | 125.82 | 0.0 | 99.67 Neigh | 0.18597 | 0.18597 | 0.18597 | 0.0 | 0.15 Comm | 0.12213 | 0.12213 | 0.12213 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1047 | | | 0.08 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6634.00 ave 6634 max 6634 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: 128840.0 ave 128840 max 128840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128840 Ave neighs/atom = 98.051750 Neighbor list builds = 21 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 = 8 41 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 : 773 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press Volume 773 0 -5583.3969 0 -5583.3969 7447.7169 15445.14 791 0 -5587.8375 0 -5587.8375 16.216895 15502.946 Loop time of 1.95707 on 1 procs for 18 steps with 1314 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5583.39686241974 -5587.8373192733 -5587.83752910827 Force two-norm initial, final = 403.04223 1.3328570 Force max component initial, final = 241.22891 0.66227277 Final line search alpha, max atom move = 0.00060875874 0.00040316434 Iterations, force evaluations = 18 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9411 | 1.9411 | 1.9411 | 0.0 | 99.19 Neigh | 0.0085377 | 0.0085377 | 0.0085377 | 0.0 | 0.44 Comm | 0.0013225 | 0.0013225 | 0.0013225 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006079 | | | 0.31 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6688.00 ave 6688 max 6688 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: 128960.0 ave 128960 max 128960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128960 Ave neighs/atom = 98.143075 Neighbor list builds = 1 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 = 8 41 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) = 5.216 | 5.216 | 5.216 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5587.8375 0 -5587.8375 16.216895 Loop time of 2.075e-06 on 1 procs for 0 steps with 1314 atoms 144.6% 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 | | 2.075e-06 | | |100.00 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6661.00 ave 6661 max 6661 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: 129056.0 ave 129056 max 129056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129056 Ave neighs/atom = 98.216134 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 = 8 41 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) = 5.216 | 5.216 | 5.216 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 -5587.8375 -5587.8375 23.327334 132.3436 5.0216469 16.216895 16.216895 69.050506 -21.226356 0.82653608 2.302194 2464.8669 Loop time of 2.226e-06 on 1 procs for 0 steps with 1314 atoms 179.7% 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 | | 2.226e-06 | | |100.00 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6661.00 ave 6661 max 6661 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64528.0 ave 64528 max 64528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129056.0 ave 129056 max 129056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129056 Ave neighs/atom = 98.216134 Neighbor list builds = 0 Dangerous builds = 0 1314 -5587.83752910827 eV 2.30219401057064 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:09