LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 Created orthogonal box = (0 -43.4309 0) to (21.7134 43.4309 4.03208) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24117 5.24117 4.03208 Created 233 atoms create_atoms CPU = 0.000226021 secs 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24117 5.24117 4.03208 Created 233 atoms create_atoms CPU = 0.00010705 secs 233 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1146) 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 6 23 2 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 456 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 4.467 | 4.467 | 4.467 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1519.617 0 -1519.617 442.83015 50 0 -1526.5027 0 -1526.5027 -7771.7675 Loop time of 0.155211 on 1 procs for 50 steps with 456 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 = -1519.61699648 -1526.50125427 -1526.50265537 Force two-norm initial, final = 12.9073 0.101371 Force max component initial, final = 4.29415 0.0295599 Final line search alpha, max atom move = 1 0.0295599 Iterations, force evaluations = 50 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15128 | 0.15128 | 0.15128 | 0.0 | 97.47 Neigh | 0.0011811 | 0.0011811 | 0.0011811 | 0.0 | 0.76 Comm | 0.0018003 | 0.0018003 | 0.0018003 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009472 | | | 0.61 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4035 ave 4035 max 4035 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49946 ave 49946 max 49946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49946 Ave neighs/atom = 109.531 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.47 | 4.47 | 4.47 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -1526.5027 0 -1526.5027 -7771.7675 7604.7792 55 0 -1526.6213 0 -1526.6213 -1891.6579 7548.0414 Loop time of 0.0162539 on 1 procs for 5 steps with 456 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 = -1526.50265537 -1526.62128333 -1526.62133957 Force two-norm initial, final = 44.7299 0.140756 Force max component initial, final = 31.9114 0.0337071 Final line search alpha, max atom move = 0.0027694 9.33484e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015487 | 0.015487 | 0.015487 | 0.0 | 95.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017977 | 0.00017977 | 0.00017977 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005875 | | | 3.61 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4049 ave 4049 max 4049 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48952 ave 48952 max 48952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48952 Ave neighs/atom = 107.351 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1526.6213 0 -1526.6213 -1891.6579 Loop time of 1.90735e-06 on 1 procs for 0 steps with 456 atoms 104.9% 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 | | 1.907e-06 | | |100.00 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4049 ave 4049 max 4049 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53754 ave 53754 max 53754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53754 Ave neighs/atom = 117.882 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.608 | 4.608 | 4.608 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 -1526.6213 -1526.6213 21.636083 86.861784 4.0163069 -1891.6579 -1891.6579 -6.9553091 -5672.5606 4.5421877 2.5776505 372.3573 Loop time of 9.53674e-07 on 1 procs for 0 steps with 456 atoms 209.7% 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 | | 9.537e-07 | | |100.00 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4049 ave 4049 max 4049 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26877 ave 26877 max 26877 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53754 ave 53754 max 53754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53754 Ave neighs/atom = 117.882 Neighbor list builds = 0 Dangerous builds = 0 456 -1526.62133956576 eV 2.57765049031725 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:00