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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -46.567967 0.0000000) to (38.020017 46.567967 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6873993 4.4651197 5.1383093 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -46.567967 0.0000000) to (38.020017 46.567967 7.7074639) create_atoms CPU = 0.004 seconds 878 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6873993 4.4651197 5.1383093 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -46.567967 0.0000000) to (38.020017 46.567967 7.7074639) create_atoms CPU = 0.004 seconds 878 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1738 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.040 | 5.040 | 5.040 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11690.631 0 -11690.631 3594.9806 53 0 -11765.423 0 -11765.423 -9216.7807 Loop time of 7.1227 on 1 procs for 53 steps with 1738 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 = -11690.6310728529 -11765.4185228988 -11765.4233640956 Force two-norm initial, final = 37.828155 1.2218616 Force max component initial, final = 6.5773123 0.38403056 Final line search alpha, max atom move = 0.21505349 0.082587112 Iterations, force evaluations = 53 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0638 | 7.0638 | 7.0638 | 0.0 | 99.17 Neigh | 0.033366 | 0.033366 | 0.033366 | 0.0 | 0.47 Comm | 0.0094629 | 0.0094629 | 0.0094629 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01609 | | | 0.23 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4639.00 ave 4639 max 4639 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: 99540.0 ave 99540 max 99540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99540 Ave neighs/atom = 57.272727 Neighbor list builds = 2 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.040 | 5.040 | 5.040 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -11765.423 0 -11765.423 -9216.7807 27292.359 57 0 -11765.785 0 -11765.785 -840.07047 27204.869 Loop time of 0.609352 on 1 procs for 4 steps with 1738 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11765.4233640956 -11765.7784924037 -11765.7851564166 Force two-norm initial, final = 250.84151 1.2427657 Force max component initial, final = 228.46387 0.36988844 Final line search alpha, max atom move = 3.1482885e-05 1.1645155e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60538 | 0.60538 | 0.60538 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006603 | 0.0006603 | 0.0006603 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003314 | | | 0.54 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4633.00 ave 4633 max 4633 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: 99556.0 ave 99556 max 99556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99556 Ave neighs/atom = 57.281933 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.178 | 5.178 | 5.178 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11765.785 0 -11765.785 -840.07047 Loop time of 6.104e-06 on 1 procs for 0 steps with 1738 atoms 180.2% 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 | | 6.104e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4639.00 ave 4639 max 4639 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: 99576.0 ave 99576 max 99576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99576 Ave neighs/atom = 57.293441 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.178 | 5.178 | 5.178 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 -11765.785 -11765.785 37.901624 93.135934 7.7067549 -840.07047 -840.07047 1.1628743 -2515.8924 -5.4818803 2.3210502 1535.2272 Loop time of 6.666e-06 on 1 procs for 0 steps with 1738 atoms 285.0% 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 | | 6.666e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4639.00 ave 4639 max 4639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49788.0 ave 49788 max 49788 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 99576.0 ave 99576 max 99576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99576 Ave neighs/atom = 57.293441 Neighbor list builds = 0 Dangerous builds = 0 1738 -11765.7851564166 eV 2.32105023451929 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08