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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -47.230830 0.0000000) to (23.615415 47.230830 4.0500102) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5565682 5.5565682 4.0500102 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -47.230830 0.0000000) to (23.615415 47.230830 4.0500102) create_atoms CPU = 0.002 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5565682 5.5565682 4.0500102 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -47.230830 0.0000000) to (23.615415 47.230830 4.0500102) create_atoms CPU = 0.001 seconds 274 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 25 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 540 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_120808805541_005#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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1750.788 0 -1750.788 20452.603 83 0 -1824.3421 0 -1824.3421 -1221.1035 Loop time of 1.30262 on 1 procs for 83 steps with 540 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 = -1750.78795008751 -1824.34058540483 -1824.34213525877 Force two-norm initial, final = 165.16711 0.089445457 Force max component initial, final = 56.662495 0.016797150 Final line search alpha, max atom move = 1.0000000 0.016797150 Iterations, force evaluations = 83 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2503 | 1.2503 | 1.2503 | 0.0 | 95.99 Neigh | 0.019037 | 0.019037 | 0.019037 | 0.0 | 1.46 Comm | 0.01851 | 0.01851 | 0.01851 | 0.0 | 1.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01474 | | | 1.13 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4080.00 ave 4080 max 4080 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: 61824.0 ave 61824 max 61824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61824 Ave neighs/atom = 114.48889 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -1824.3421 0 -1824.3421 -1221.1035 9034.5654 86 0 -1824.3517 0 -1824.3517 -103.89207 9021.3062 Loop time of 0.0775273 on 1 procs for 3 steps with 540 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 = -1824.34213525878 -1824.35128302039 -1824.35167428865 Force two-norm initial, final = 12.502015 1.2067386 Force max component initial, final = 9.4372355 1.0889787 Final line search alpha, max atom move = 0.00090401474 0.00098445282 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072744 | 0.072744 | 0.072744 | 0.0 | 93.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093127 | 0.00093127 | 0.00093127 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003852 | | | 4.97 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4088.00 ave 4088 max 4088 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: 64024.0 ave 64024 max 64024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64024 Ave neighs/atom = 118.56296 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.630 | 4.630 | 4.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1824.3517 0 -1824.3517 -103.89207 Loop time of 1.2068e-05 on 1 procs for 0 steps with 540 atoms 124.3% 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 | | 1.207e-05 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4088.00 ave 4088 max 4088 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: 64956.0 ave 64956 max 64956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64956 Ave neighs/atom = 120.28889 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.630 | 4.630 | 4.630 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 -1824.3517 -1824.3517 23.580032 94.361842 4.054419 -103.89207 -103.89207 -193.11194 -83.051885 -35.512376 2.590702 333.25611 Loop time of 1.2309e-05 on 1 procs for 0 steps with 540 atoms 178.7% 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 | | 1.231e-05 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4088.00 ave 4088 max 4088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32478.0 ave 32478 max 32478 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64956.0 ave 64956 max 64956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64956 Ave neighs/atom = 120.28889 Neighbor list builds = 0 Dangerous builds = 0 540 -1824.35167428865 eV 2.59070198768009 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01