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 -58.673406 0.0000000) to (11.976659 58.673406 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4439358 5.3339460 5.8968992 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.673406 0.0000000) to (11.976659 58.673406 8.8453488) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4439358 5.3339460 5.8968992 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.673406 0.0000000) to (11.976659 58.673406 8.8453488) create_atoms CPU = 0.001 seconds 530 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 = 4 37 3 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 2 atoms, new total = 1056 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_179420363944_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 = 4 37 3 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) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4057.6795 0 -4057.6795 68243.388 125 0 -4467.8441 0 -4467.8441 6372.6768 Loop time of 12.3 on 1 procs for 125 steps with 1056 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 = -4057.67947379721 -4467.84036947626 -4467.84414933009 Force two-norm initial, final = 677.46878 0.30156199 Force max component initial, final = 192.39786 0.11045136 Final line search alpha, max atom move = 1.0000000 0.11045136 Iterations, force evaluations = 125 235 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.25 | 12.25 | 12.25 | 0.0 | 99.60 Neigh | 0.023013 | 0.023013 | 0.023013 | 0.0 | 0.19 Comm | 0.012383 | 0.012383 | 0.012383 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01434 | | | 0.12 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4931.00 ave 4931 max 4931 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: 92072.0 ave 92072 max 92072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92072 Ave neighs/atom = 87.189394 Neighbor list builds = 3 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 = 4 37 3 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 : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -4467.8441 0 -4467.8441 6372.6768 12431.454 130 0 -4468.0065 0 -4468.0065 -9.5529524 12477.413 Loop time of 0.416632 on 1 procs for 5 steps with 1056 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 = -4467.84414933008 -4468.00457991604 -4468.00652458772 Force two-norm initial, final = 94.023347 1.0578400 Force max component initial, final = 79.075300 0.73732772 Final line search alpha, max atom move = 8.3839070e-05 6.1816870e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41466 | 0.41466 | 0.41466 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003248 | 0.0003248 | 0.0003248 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001652 | | | 0.40 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4927.00 ave 4927 max 4927 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: 92032.0 ave 92032 max 92032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92032 Ave neighs/atom = 87.151515 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 = 4 37 3 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) = 4.738 | 4.738 | 4.738 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4468.0065 0 -4468.0065 -9.5529524 Loop time of 1.897e-06 on 1 procs for 0 steps with 1056 atoms 210.9% 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 | | 1.897e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4927.00 ave 4927 max 4927 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: 91968.0 ave 91968 max 91968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91968 Ave neighs/atom = 87.090909 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 = 4 37 3 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) = 4.738 | 4.738 | 4.738 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 -4468.0065 -4468.0065 11.987353 117.20466 8.8808878 -9.5529524 -9.5529524 94.761948 -65.693036 -57.72777 2.2140458 656.84054 Loop time of 1.883e-06 on 1 procs for 0 steps with 1056 atoms 212.4% 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 | | 1.883e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4927.00 ave 4927 max 4927 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45984.0 ave 45984 max 45984 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91968.0 ave 91968 max 91968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91968 Ave neighs/atom = 87.090909 Neighbor list builds = 0 Dangerous builds = 0 1056 -4468.00652458772 eV 2.21404579587993 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13