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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -35.308402 0.0000000) to (12.482393 35.308402 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5987764 3.7163725 4.0498230 Created 154 atoms using lattice units in orthogonal box = (0.0000000 -35.308402 0.0000000) to (12.482393 35.308402 4.0498230) create_atoms CPU = 0.002 seconds 154 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5987764 3.7163725 4.0498230 Created 154 atoms using lattice units in orthogonal box = (0.0000000 -35.308402 0.0000000) to (12.482393 35.308402 4.0498230) create_atoms CPU = 0.001 seconds 154 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 300 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.420 | 4.420 | 4.420 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1274.0213 0 -1274.0213 -2286.1022 14 0 -1278.8883 0 -1278.8883 -11831.006 Loop time of 0.415787 on 1 procs for 14 steps with 300 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 = -1274.02126273657 -1278.8871922576 -1278.88828875894 Force two-norm initial, final = 10.124634 0.77025355 Force max component initial, final = 3.2428701 0.33552154 Final line search alpha, max atom move = 0.50908056 0.17080749 Iterations, force evaluations = 14 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41307 | 0.41307 | 0.41307 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013679 | 0.0013679 | 0.0013679 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001344 | | | 0.32 Nlocal: 300.000 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2332.00 ave 2332 max 2332 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: 17220.0 ave 17220 max 17220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17220 Ave neighs/atom = 57.400000 Neighbor list builds = 0 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 14 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.421 | 4.421 | 4.421 Mbytes Step Temp E_pair E_mol TotEng Press Volume 14 0 -1278.8883 0 -1278.8883 -11831.006 3569.7842 18 0 -1278.9648 0 -1278.9648 -1606.4031 3548.0784 Loop time of 0.107142 on 1 procs for 4 steps with 300 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1278.88828875894 -1278.96451554769 -1278.96482844775 Force two-norm initial, final = 35.570862 0.84153368 Force max component initial, final = 26.071312 0.33474277 Final line search alpha, max atom move = 0.00059086983 0.00019778940 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10573 | 0.10573 | 0.10573 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033246 | 0.00033246 | 0.00033246 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001078 | | | 1.01 Nlocal: 300.000 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2344.00 ave 2344 max 2344 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: 17400.0 ave 17400 max 17400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17400 Ave neighs/atom = 58.000000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1278.9648 0 -1278.9648 -1606.4031 Loop time of 6.334e-06 on 1 procs for 0 steps with 300 atoms 142.1% 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 | | 6.334e-06 | | |100.00 Nlocal: 300.000 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2344.00 ave 2344 max 2344 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: 17400.0 ave 17400 max 17400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17400 Ave neighs/atom = 58.000000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.558 | 4.558 | 4.558 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 -1278.9648 -1278.9648 12.446768 70.616805 4.0367194 -1606.4031 -1606.4031 150.72562 -5030.2719 60.337054 2.3219588 258.12884 Loop time of 6.785e-06 on 1 procs for 0 steps with 300 atoms 191.6% 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 | | 6.785e-06 | | |100.00 Nlocal: 300.000 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2344.00 ave 2344 max 2344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8700.00 ave 8700 max 8700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17400.0 ave 17400 max 17400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17400 Ave neighs/atom = 58.000000 Neighbor list builds = 0 Dangerous builds = 0 300 -1278.96482844775 eV 2.32195882109495 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00