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 -35.182745 0.0000000) to (17.234413 35.182745 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5958435 4.2215518 5.1383093 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -35.182745 0.0000000) to (17.234413 35.182745 7.7074639) create_atoms CPU = 0.002 seconds 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5958435 4.2215518 5.1383093 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -35.182745 0.0000000) to (17.234413 35.182745 7.7074639) create_atoms CPU = 0.001 seconds 306 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 = 6 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 588 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 = 6 25 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3954.3136 0 -3954.3136 -25516.783 29 0 -3973.1117 0 -3973.1117 -36322.349 Loop time of 1.67117 on 1 procs for 29 steps with 588 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 = -3954.31363644547 -3973.10863696127 -3973.11172476806 Force two-norm initial, final = 17.834269 0.16728157 Force max component initial, final = 3.0682331 0.013192246 Final line search alpha, max atom move = 1.0000000 0.013192246 Iterations, force evaluations = 29 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6634 | 1.6634 | 1.6634 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032634 | 0.0032634 | 0.0032634 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004535 | | | 0.27 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2518.00 ave 2518 max 2518 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: 33264.0 ave 33264 max 33264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33264 Ave neighs/atom = 56.571429 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 25 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.464 | 4.464 | 4.464 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -3973.1117 0 -3973.1117 -36322.349 9346.9026 36 0 -3974.1989 0 -3974.1989 -7975.0315 9242.1861 Loop time of 0.273884 on 1 procs for 7 steps with 588 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 = -3973.11172476806 -3974.19568864144 -3974.19886576679 Force two-norm initial, final = 270.49940 4.1578372 Force max component initial, final = 206.89838 4.0097955 Final line search alpha, max atom move = 7.4941339e-05 0.00030049944 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27134 | 0.27134 | 0.27134 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004444 | 0.0004444 | 0.0004444 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002097 | | | 0.77 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2389.00 ave 2389 max 2389 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: 33576.0 ave 33576 max 33576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33576 Ave neighs/atom = 57.102041 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 = 6 25 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) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3974.1989 0 -3974.1989 -7975.0315 Loop time of 6.405e-06 on 1 procs for 0 steps with 588 atoms 171.7% 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 | | 6.405e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2419.00 ave 2419 max 2419 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: 33576.0 ave 33576 max 33576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33576 Ave neighs/atom = 57.102041 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 = 6 25 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) = 4.602 | 4.602 | 4.602 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 -3974.1989 -3974.1989 17.123337 70.36549 7.6705514 -7975.0315 -7975.0315 -182.36059 -24434.522 691.7879 2.5140105 480.16736 Loop time of 6.255e-06 on 1 procs for 0 steps with 588 atoms 255.8% 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 | | 6.255e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2419.00 ave 2419 max 2419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16788.0 ave 16788 max 16788 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33576.0 ave 33576 max 33576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33576 Ave neighs/atom = 57.102041 Neighbor list builds = 0 Dangerous builds = 0 588 -3974.19886576679 eV 2.51401054748084 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02