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 = 3.1599882 3.1599882 3.1599882 Created orthogonal box = (0.0000000 -50.953279 0.0000000) to (25.476639 50.953279 3.1599882) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5275347 3.5275347 3.1599882 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -50.953279 0.0000000) to (25.476639 50.953279 3.1599882) create_atoms CPU = 0.001 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5275347 3.5275347 3.1599882 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.953279 0.0000000) to (25.476639 50.953279 3.1599882) create_atoms CPU = 0.000 seconds 261 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 8 31 1 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 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 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_698578166685_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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 8 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11411.316 0 -11411.316 37280.748 60 0 -11656.232 0 -11656.232 20394.003 Loop time of 17.4207 on 1 procs for 60 steps with 521 atoms 95.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11411.31642225 -11656.2229402667 -11656.2324596251 Force two-norm initial, final = 259.41832 0.32298004 Force max component initial, final = 91.927424 0.032636757 Final line search alpha, max atom move = 1.0000000 0.032636757 Iterations, force evaluations = 60 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.406 | 17.406 | 17.406 | 0.0 | 99.92 Neigh | 0.0056987 | 0.0056987 | 0.0056987 | 0.0 | 0.03 Comm | 0.0046069 | 0.0046069 | 0.0046069 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004062 | | | 0.02 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4058.00 ave 4058 max 4058 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: 33654.0 ave 33654 max 33654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33654 Ave neighs/atom = 64.595010 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 8 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.483 | 4.483 | 4.483 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -11656.232 0 -11656.232 20394.003 8204.0771 69 0 -11657.047 0 -11657.047 77.805809 8267.5906 Loop time of 2.39861 on 1 procs for 9 steps with 521 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11656.2324596251 -11657.0419344607 -11657.0466938816 Force two-norm initial, final = 213.54123 0.87834022 Force max component initial, final = 197.10230 0.58315316 Final line search alpha, max atom move = 0.00010409726 6.0704646e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3957 | 2.3957 | 2.3957 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053912 | 0.00053912 | 0.00053912 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002378 | | | 0.10 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4385.00 ave 4385 max 4385 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: 33432.0 ave 33432 max 33432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33432 Ave neighs/atom = 64.168906 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11657.047 0 -11657.047 77.805809 Loop time of 3.451e-06 on 1 procs for 0 steps with 521 atoms 173.9% 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 | | 3.451e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4385.00 ave 4385 max 4385 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: 33392.0 ave 33392 max 33392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33392 Ave neighs/atom = 64.092131 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.622 | 4.622 | 4.622 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 -11657.047 -11657.047 25.464835 102.78783 3.1586129 77.805809 77.805809 47.226907 73.230446 112.96008 2.5294479 137.9825 Loop time of 3.22e-06 on 1 procs for 0 steps with 521 atoms 186.3% 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 | | 3.22e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4385.00 ave 4385 max 4385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16696.0 ave 16696 max 16696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33392.0 ave 33392 max 33392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33392 Ave neighs/atom = 64.092131 Neighbor list builds = 0 Dangerous builds = 0 521 -2656.3570610332 eV 2.52944786129276 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21