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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -37.915080 0.0000000) to (18.955780 37.915080 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5755331 4.5755331 3.5200000 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -37.915080 0.0000000) to (18.955780 37.915080 3.5200000) create_atoms CPU = 0.001 seconds 234 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5755331 4.5755331 3.5200000 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -37.915080 0.0000000) to (18.955780 37.915080 3.5200000) create_atoms CPU = 0.000 seconds 234 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 456 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.900 | 4.900 | 4.900 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2011.3488 0 -2011.3488 -3481.4502 42 0 -2016.9523 0 -2016.9523 -14817.143 Loop time of 0.580328 on 1 procs for 42 steps with 456 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 = -2011.34876334255 -2016.95035350843 -2016.95225140745 Force two-norm initial, final = 8.7373645 0.13245305 Force max component initial, final = 2.5454015 0.020381525 Final line search alpha, max atom move = 1.0000000 0.020381525 Iterations, force evaluations = 42 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.574 | 0.574 | 0.574 | 0.0 | 98.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038978 | 0.0038978 | 0.0038978 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002429 | | | 0.42 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5412.00 ave 5412 max 5412 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: 111396.0 ave 111396 max 111396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111396 Ave neighs/atom = 244.28947 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.900 | 4.900 | 4.900 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -2016.9523 0 -2016.9523 -14817.143 5059.7178 48 0 -2017.0852 0 -2017.0852 -3071.2353 5025.3706 Loop time of 0.0774503 on 1 procs for 6 steps with 456 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 = -2016.95225140745 -2017.08483958326 -2017.0852212235 Force two-norm initial, final = 56.190066 2.5795941 Force max component initial, final = 42.066200 1.9655012 Final line search alpha, max atom move = 0.082456370 0.16206809 Iterations, force evaluations = 6 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.074996 | 0.074996 | 0.074996 | 0.0 | 96.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045445 | 0.00045445 | 0.00045445 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002 | | | 2.58 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5412.00 ave 5412 max 5412 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: 111864.0 ave 111864 max 111864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111864 Ave neighs/atom = 245.31579 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.038 | 5.038 | 5.038 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2017.0852 0 -2017.0852 -3071.2353 Loop time of 2.331e-06 on 1 procs for 0 steps with 456 atoms 171.6% 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 | | 2.331e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5412.00 ave 5412 max 5412 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: 111944.0 ave 111944 max 111944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111944 Ave neighs/atom = 245.49123 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.038 | 5.038 | 5.038 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 -2017.0852 -2017.0852 18.919748 75.83016 3.5027631 -3071.2353 -3071.2353 529.39701 -10366.671 623.5678 2.2080619 286.00141 Loop time of 2.514e-06 on 1 procs for 0 steps with 456 atoms 198.9% 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 | | 2.514e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5412.00 ave 5412 max 5412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55972.0 ave 55972 max 55972 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111944.0 ave 111944 max 111944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111944 Ave neighs/atom = 245.49123 Neighbor list builds = 0 Dangerous builds = 0 456 -2017.0852212235 eV 2.20806188069845 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01