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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -39.962389 0.0000000) to (23.070516 39.962389 5.3397869) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9436820 4.7570602 5.3397869 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -39.962389 0.0000000) to (23.070516 39.962389 5.3397869) create_atoms CPU = 0.001 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9436820 4.7570602 5.3397869 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -39.962389 0.0000000) to (23.070516 39.962389 5.3397869) create_atoms CPU = 0.001 seconds 339 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 24 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 7 atoms, new total = 672 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.284 | 5.284 | 5.284 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4225.448 0 -4225.448 57578.003 84 0 -4361.4664 0 -4361.4664 6160.9776 Loop time of 27.4271 on 1 procs for 84 steps with 672 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 = -4225.44803021232 -4361.46249567511 -4361.46639124253 Force two-norm initial, final = 158.93232 0.27801315 Force max component initial, final = 27.957121 0.053556732 Final line search alpha, max atom move = 1.0000000 0.053556732 Iterations, force evaluations = 84 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.396 | 27.396 | 27.396 | 0.0 | 99.89 Neigh | 0.021404 | 0.021404 | 0.021404 | 0.0 | 0.08 Comm | 0.0049828 | 0.0049828 | 0.0049828 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004728 | | | 0.02 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3721.00 ave 3721 max 3721 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: 51604.0 ave 51604 max 51604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51604 Ave neighs/atom = 76.791667 Neighbor list builds = 1 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.284 | 5.284 | 5.284 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -4361.4664 0 -4361.4664 6160.9776 9846.0642 88 0 -4361.5919 0 -4361.5919 2023.596 9864.4309 Loop time of 1.03634 on 1 procs for 4 steps with 672 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 = -4361.46639124253 -4361.59060161259 -4361.59189421547 Force two-norm initial, final = 77.032554 1.9256261 Force max component initial, final = 76.563442 1.7898939 Final line search alpha, max atom move = 0.00014154564 0.00025335167 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0354 | 1.0354 | 1.0354 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001718 | 0.0001718 | 0.0001718 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000738 | | | 0.07 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3692.00 ave 3692 max 3692 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: 50814.0 ave 50814 max 50814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50814 Ave neighs/atom = 75.616071 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.422 | 5.422 | 5.422 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4361.5919 0 -4361.5919 2023.596 Loop time of 1.665e-06 on 1 procs for 0 steps with 672 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 | | 1.665e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3686.00 ave 3686 max 3686 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: 50716.0 ave 50716 max 50716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50716 Ave neighs/atom = 75.470238 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.422 | 5.422 | 5.422 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 -4361.5919 -4361.5919 23.04217 79.924778 5.3563286 2023.596 2023.596 86.749722 5692.4238 291.61435 2.5454994 1699.3358 Loop time of 1.519e-06 on 1 procs for 0 steps with 672 atoms 131.7% 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 | | 1.519e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3686.00 ave 3686 max 3686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25358.0 ave 25358 max 25358 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50716.0 ave 50716 max 50716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50716 Ave neighs/atom = 75.470238 Neighbor list builds = 0 Dangerous builds = 0 672 -4361.59189421547 eV 2.54549936302139 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29