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 = 2.8553128 2.8553128 2.8553128 Created orthogonal box = (0.0000000 -37.880005 0.0000000) to (23.196671 37.880005 6.9940594) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2175765 4.3045460 4.6627062 Created 525 atoms using lattice units in orthogonal box = (0.0000000 -37.880005 0.0000000) to (23.196671 37.880005 6.9940594) create_atoms CPU = 0.001 seconds 525 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2175765 4.3045460 4.6627062 Created 531 atoms using lattice units in orthogonal box = (0.0000000 -37.880005 0.0000000) to (23.196671 37.880005 6.9940594) create_atoms CPU = 0.001 seconds 531 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1055 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2702.3237 0 -2702.3237 284808.2 105 0 -4209.6729 0 -4209.6729 8314.8854 Loop time of 1.47803 on 1 procs for 105 steps with 1055 atoms 93.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2702.323655531 -4209.66885394479 -4209.67292649797 Force two-norm initial, final = 2587.8728 0.22995054 Force max component initial, final = 468.59849 0.048565627 Final line search alpha, max atom move = 1.0000000 0.048565627 Iterations, force evaluations = 105 183 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3972 | 1.3972 | 1.3972 | 0.0 | 94.53 Neigh | 0.048551 | 0.048551 | 0.048551 | 0.0 | 3.28 Comm | 0.022753 | 0.022753 | 0.022753 | 0.0 | 1.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009536 | | | 0.65 Nlocal: 1055.00 ave 1055 max 1055 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5381.00 ave 5381 max 5381 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: 143824.0 ave 143824 max 143824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143824 Ave neighs/atom = 136.32607 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 105 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press Volume 105 0 -4209.6729 0 -4209.6729 8314.8854 12291.22 112 0 -4210.0262 0 -4210.0262 -206.24052 12353.117 Loop time of 0.0709561 on 1 procs for 7 steps with 1055 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 = -4209.67292649795 -4210.02479430138 -4210.02615274796 Force two-norm initial, final = 129.31899 2.8680243 Force max component initial, final = 118.61098 1.9971342 Final line search alpha, max atom move = 0.00018767345 0.00037480907 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068358 | 0.068358 | 0.068358 | 0.0 | 96.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039921 | 0.00039921 | 0.00039921 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002198 | | | 3.10 Nlocal: 1055.00 ave 1055 max 1055 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5361.00 ave 5361 max 5361 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: 143784.0 ave 143784 max 143784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143784 Ave neighs/atom = 136.28815 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.167 | 5.167 | 5.167 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4210.0262 0 -4210.0262 -206.24052 Loop time of 2.087e-06 on 1 procs for 0 steps with 1055 atoms 143.7% 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 | | 2.087e-06 | | |100.00 Nlocal: 1055.00 ave 1055 max 1055 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5361.00 ave 5361 max 5361 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: 143574.0 ave 143574 max 143574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143574 Ave neighs/atom = 136.08910 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.167 | 5.167 | 5.167 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 -4210.0262 -4210.0262 23.170824 76.246138 6.9922543 -206.24052 -206.24052 -258.73601 -141.71011 -218.27543 2.2379449 844.27519 Loop time of 2.407e-06 on 1 procs for 0 steps with 1055 atoms 207.7% 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 | | 2.407e-06 | | |100.00 Nlocal: 1055.00 ave 1055 max 1055 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5361.00 ave 5361 max 5361 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71787.0 ave 71787 max 71787 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 143574.0 ave 143574 max 143574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143574 Ave neighs/atom = 136.08910 Neighbor list builds = 0 Dangerous builds = 0 1055 -4210.02615274796 eV 2.2379449431837 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01