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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -47.920251 0.0000000) to (58.690082 47.920251 9.9204345) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7074379 6.1611751 6.6136230 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -47.920251 0.0000000) to (58.690082 47.920251 9.9204345) create_atoms CPU = 0.007 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7074379 6.1611751 6.6136230 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -47.920251 0.0000000) to (58.690082 47.920251 9.9204345) create_atoms CPU = 0.006 seconds 1688 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 16 25 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3348 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.502 | 6.502 | 6.502 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10958.36 0 -10958.36 7793.045 118 0 -11214.422 0 -11214.422 4293.4181 Loop time of 9.20399 on 1 procs for 118 steps with 3348 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 = -10958.3603219517 -11214.4112513764 -11214.4216322665 Force two-norm initial, final = 65.557914 0.33545567 Force max component initial, final = 5.3332582 0.094821277 Final line search alpha, max atom move = 1.0000000 0.094821277 Iterations, force evaluations = 118 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.763 | 8.763 | 8.763 | 0.0 | 95.21 Neigh | 0.3243 | 0.3243 | 0.3243 | 0.0 | 3.52 Comm | 0.047014 | 0.047014 | 0.047014 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06971 | | | 0.76 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9374.00 ave 9374 max 9374 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: 439676.0 ave 439676 max 439676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439676 Ave neighs/atom = 131.32497 Neighbor list builds = 5 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.502 | 6.502 | 6.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -11214.422 0 -11214.422 4293.4181 55801.322 128 0 -11215.851 0 -11215.851 2.165686 56103.463 Loop time of 0.51888 on 1 procs for 10 steps with 3348 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 = -11214.4216322665 -11215.8415487189 -11215.8505393372 Force two-norm initial, final = 336.12809 1.0820719 Force max component initial, final = 324.39946 0.12929706 Final line search alpha, max atom move = 6.1626248e-05 7.9680928e-06 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50387 | 0.50387 | 0.50387 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025934 | 0.0025934 | 0.0025934 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01242 | | | 2.39 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9363.00 ave 9363 max 9363 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: 439672.0 ave 439672 max 439672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439672 Ave neighs/atom = 131.32378 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.639 | 6.639 | 6.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11215.851 0 -11215.851 2.165686 Loop time of 5.903e-06 on 1 procs for 0 steps with 3348 atoms 203.3% 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 | | 5.903e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9244.00 ave 9244 max 9244 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: 439088.0 ave 439088 max 439088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439088 Ave neighs/atom = 131.14934 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.639 | 6.639 | 6.639 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 -11215.851 -11215.851 58.58046 96.775595 9.8962588 2.165686 2.165686 3.0757349 0.71300363 2.7083194 2.6006765 2977.9719 Loop time of 6.716e-06 on 1 procs for 0 steps with 3348 atoms 282.9% 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 | | 6.716e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9244.00 ave 9244 max 9244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 219544.0 ave 219544 max 219544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 439088.0 ave 439088 max 439088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439088 Ave neighs/atom = 131.14934 Neighbor list builds = 0 Dangerous builds = 0 3348 -11215.8505393372 eV 2.60067649758865 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10