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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -67.456915 0.0000000) to (33.728457 67.456915 3.6583649) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1584700 5.1584700 3.6583649 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -67.456915 0.0000000) to (33.728457 67.456915 3.6583649) create_atoms CPU = 0.001 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1584700 5.1584700 3.6583649 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -67.456915 0.0000000) to (33.728457 67.456915 3.6583649) create_atoms CPU = 0.001 seconds 682 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 36 1 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 0 atoms, new total = 1362 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_267721408934_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 36 1 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) = 5.113 | 5.113 | 5.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5172.8315 0 -5172.8315 59434.578 299 0 -5457.2267 0 -5457.2267 -8690.7389 Loop time of 5.78788 on 1 procs for 299 steps with 1362 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 = -5172.83148077855 -5457.22126312737 -5457.22670449943 Force two-norm initial, final = 513.44535 0.22466367 Force max component initial, final = 110.27611 0.061444353 Final line search alpha, max atom move = 1.0000000 0.061444353 Iterations, force evaluations = 299 586 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6654 | 5.6654 | 5.6654 | 0.0 | 97.88 Neigh | 0.047012 | 0.047012 | 0.047012 | 0.0 | 0.81 Comm | 0.041858 | 0.041858 | 0.041858 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03363 | | | 0.58 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9628.00 ave 9628 max 9628 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: 202264.0 ave 202264 max 202264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202264 Ave neighs/atom = 148.50514 Neighbor list builds = 4 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 36 1 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 : 299 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.495 | 5.495 | 5.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 299 0 -5457.2267 0 -5457.2267 -8690.7389 16647.153 370 0 -5494.843 0 -5494.843 -104.6397 16477.876 Loop time of 0.843886 on 1 procs for 71 steps with 1362 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 = -5457.22670449944 -5494.83900562956 -5494.84298388685 Force two-norm initial, final = 880.19145 10.105726 Force max component initial, final = 616.80395 8.1127130 Final line search alpha, max atom move = 0.00015642648 0.0012690431 Iterations, force evaluations = 71 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75252 | 0.75252 | 0.75252 | 0.0 | 89.17 Neigh | 0.059201 | 0.059201 | 0.059201 | 0.0 | 7.02 Comm | 0.0062288 | 0.0062288 | 0.0062288 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02594 | | | 3.07 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9793.00 ave 9793 max 9793 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: 207044.0 ave 207044 max 207044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207044 Ave neighs/atom = 152.01468 Neighbor list builds = 5 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 35 2 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) = 5.620 | 5.620 | 5.620 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5494.843 0 -5494.843 -104.6397 Loop time of 1.745e-06 on 1 procs for 0 steps with 1362 atoms 171.9% 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 | | 1.745e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9798.00 ave 9798 max 9798 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: 207168.0 ave 207168 max 207168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207168 Ave neighs/atom = 152.10573 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 35 2 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) = 5.620 | 5.620 | 5.620 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 -5494.843 -5494.843 32.588604 129.80142 3.8954357 -104.6397 -104.6397 232.51965 293.49353 -839.93227 2.2362306 377.51781 Loop time of 2.251e-06 on 1 procs for 0 steps with 1362 atoms 177.7% 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 | | 2.251e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9798.00 ave 9798 max 9798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103584.0 ave 103584 max 103584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 207168.0 ave 207168 max 207168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207168 Ave neighs/atom = 152.10573 Neighbor list builds = 0 Dangerous builds = 0 1362 -5494.84298388685 eV 2.23623064451435 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06