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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -55.425424 0.0000000) to (33.938847 55.425424 8.6204757) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4740075 5.3634101 5.7469838 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.425424 0.0000000) to (33.938847 55.425424 8.6204757) create_atoms CPU = 0.002 seconds 1493 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4740075 5.3634101 5.7469838 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.425424 0.0000000) to (33.938847 55.425424 8.6204757) create_atoms CPU = 0.002 seconds 1493 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 2952 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.937 | 6.937 | 6.937 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13030.464 0 -13030.464 8502.8759 85 0 -13096.848 0 -13096.848 -8377.8044 Loop time of 3.92396 on 1 procs for 85 steps with 2952 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13030.4637518565 -13096.8363020264 -13096.8478633047 Force two-norm initial, final = 102.78694 0.40054494 Force max component initial, final = 19.163218 0.032857132 Final line search alpha, max atom move = 1.0000000 0.032857132 Iterations, force evaluations = 85 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8536 | 3.8536 | 3.8536 | 0.0 | 98.21 Neigh | 0.033859 | 0.033859 | 0.033859 | 0.0 | 0.86 Comm | 0.016414 | 0.016414 | 0.016414 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02008 | | | 0.51 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10377.0 ave 10377 max 10377 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: 514292.0 ave 514292 max 514292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514292 Ave neighs/atom = 174.21816 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.937 | 6.937 | 6.937 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -13096.848 0 -13096.848 -8377.8044 32431.522 88 0 -13097.12 0 -13097.12 -1994.4745 32314.663 Loop time of 0.137579 on 1 procs for 3 steps with 2952 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 = -13096.8478633046 -13097.120190259 -13097.1204225289 Force two-norm initial, final = 213.15538 0.44747902 Force max component initial, final = 156.91473 0.039317624 Final line search alpha, max atom move = 0.00031045785 1.2206465e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13476 | 0.13476 | 0.13476 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004518 | 0.0004518 | 0.0004518 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002363 | | | 1.72 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10380.0 ave 10380 max 10380 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: 513996.0 ave 513996 max 513996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513996 Ave neighs/atom = 174.11789 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.075 | 7.075 | 7.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13097.12 0 -13097.12 -1994.4745 Loop time of 1.739e-06 on 1 procs for 0 steps with 2952 atoms 115.0% 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 | | 1.739e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10395.0 ave 10395 max 10395 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: 514208.0 ave 514208 max 514208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514208 Ave neighs/atom = 174.18970 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.075 | 7.075 | 7.075 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 -13097.12 -13097.12 33.871636 110.85085 8.6064577 -1994.4745 -1994.4745 1.7488646 -5983.833 -1.3395079 2.2164235 975.01928 Loop time of 2.642e-06 on 1 procs for 0 steps with 2952 atoms 227.1% 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 | | 2.642e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10395.0 ave 10395 max 10395 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257104.0 ave 257104 max 257104 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 514208.0 ave 514208 max 514208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514208 Ave neighs/atom = 174.18970 Neighbor list builds = 0 Dangerous builds = 0 2952 -13097.1204225289 eV 2.21642348741967 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04