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 = 2.8553249 2.8553249 2.8553249 Created orthogonal box = (0.0000000 -43.114460 0.0000000) to (30.486527 43.114460 4.0380392) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8136622 4.9165613 4.0380392 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -43.114460 0.0000000) to (30.486527 43.114460 4.0380392) create_atoms CPU = 0.002 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8136622 4.9165613 4.0380392 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.114460 0.0000000) to (30.486527 43.114460 4.0380392) create_atoms CPU = 0.002 seconds 458 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 = 9 24 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 2 atoms, new total = 912 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 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) = 4.977 | 4.977 | 4.977 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3000.9247 0 -3000.9247 171001.67 121 0 -3740.2411 0 -3740.2411 6112.1488 Loop time of 1.53706 on 1 procs for 121 steps with 912 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3000.92465514478 -3740.23818594774 -3740.24108856838 Force two-norm initial, final = 1798.9909 0.20690083 Force max component initial, final = 497.86698 0.053714051 Final line search alpha, max atom move = 1.0000000 0.053714051 Iterations, force evaluations = 121 213 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4865 | 1.4865 | 1.4865 | 0.0 | 96.71 Neigh | 0.025022 | 0.025022 | 0.025022 | 0.0 | 1.63 Comm | 0.013705 | 0.013705 | 0.013705 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01183 | | | 0.77 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6187.00 ave 6187 max 6187 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: 125104.0 ave 125104 max 125104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125104 Ave neighs/atom = 137.17544 Neighbor list builds = 3 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 = 9 24 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 : 121 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.977 | 4.977 | 4.977 Mbytes Step Temp E_pair E_mol TotEng Press Volume 121 0 -3740.2411 0 -3740.2411 6112.1488 10615.28 126 0 -3740.3901 0 -3740.3901 -23.8147 10652.977 Loop time of 0.0578528 on 1 procs for 5 steps with 912 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 = -3740.24108856838 -3740.38993306589 -3740.39005465037 Force two-norm initial, final = 84.522750 0.71365223 Force max component initial, final = 78.341622 0.46849005 Final line search alpha, max atom move = 0.00048708107 0.00022819263 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05531 | 0.05531 | 0.05531 | 0.0 | 95.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040497 | 0.00040497 | 0.00040497 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002138 | | | 3.70 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6177.00 ave 6177 max 6177 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: 124932.0 ave 124932 max 124932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124932 Ave neighs/atom = 136.98684 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 = 9 24 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) = 5.115 | 5.115 | 5.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3740.3901 0 -3740.3901 -23.8147 Loop time of 1.804e-06 on 1 procs for 0 steps with 912 atoms 166.3% 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 | | 1.804e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6177.00 ave 6177 max 6177 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: 124752.0 ave 124752 max 124752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124752 Ave neighs/atom = 136.78947 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 = 9 24 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) = 5.115 | 5.115 | 5.115 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 -3740.3901 -3740.3901 30.499589 86.556869 4.0352966 -23.8147 -23.8147 47.117106 -48.149532 -70.411675 2.2299317 578.44365 Loop time of 8.409e-06 on 1 procs for 0 steps with 912 atoms 118.9% 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 | | 8.409e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6177.00 ave 6177 max 6177 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62376.0 ave 62376 max 62376 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 124752.0 ave 124752 max 124752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124752 Ave neighs/atom = 136.78947 Neighbor list builds = 0 Dangerous builds = 0 912 -3740.39005465037 eV 2.22993168813078 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01