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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -40.474043 0.0000000) to (20.234998 40.474043 4.0469996) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6657994 5.6657994 4.0469996 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -40.474043 0.0000000) to (20.234998 40.474043 4.0469996) create_atoms CPU = 0.001 seconds 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6657994 5.6657994 4.0469996 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -40.474043 0.0000000) to (20.234998 40.474043 4.0469996) create_atoms CPU = 0.001 seconds 201 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 23 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 395 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_958395190627_001#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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1307.6579 0 -1307.6579 6766.2952 59 0 -1322.6056 0 -1322.6056 -5598.6952 Loop time of 1.86623 on 1 procs for 59 steps with 395 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 = -1307.65792827644 -1322.60437499123 -1322.60564899787 Force two-norm initial, final = 17.936943 0.097280451 Force max component initial, final = 6.7884296 0.022415493 Final line search alpha, max atom move = 1.0000000 0.022415493 Iterations, force evaluations = 59 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.858 | 1.858 | 1.858 | 0.0 | 99.56 Neigh | 0.0025602 | 0.0025602 | 0.0025602 | 0.0 | 0.14 Comm | 0.0031301 | 0.0031301 | 0.0031301 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002528 | | | 0.14 Nlocal: 395.000 ave 395 max 395 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3575.00 ave 3575 max 3575 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: 33528.0 ave 33528 max 33528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33528 Ave neighs/atom = 84.881013 Neighbor list builds = 1 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -1322.6056 0 -1322.6056 -5598.6952 6628.9218 65 0 -1322.7037 0 -1322.7037 -485.49962 6584.7357 Loop time of 0.154478 on 1 procs for 6 steps with 395 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 = -1322.60564899787 -1322.70234787348 -1322.70365219151 Force two-norm initial, final = 35.754770 0.95379924 Force max component initial, final = 30.414870 0.80414113 Final line search alpha, max atom move = 0.00043268529 0.00034794004 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1532 | 0.1532 | 0.1532 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021794 | 0.00021794 | 0.00021794 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001059 | | | 0.69 Nlocal: 395.000 ave 395 max 395 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3545.00 ave 3545 max 3545 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: 33618.0 ave 33618 max 33618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33618 Ave neighs/atom = 85.108861 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1322.7037 0 -1322.7037 -485.49962 Loop time of 1.96e-06 on 1 procs for 0 steps with 395 atoms 153.1% 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 | | 1.96e-06 | | |100.00 Nlocal: 395.000 ave 395 max 395 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3545.00 ave 3545 max 3545 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: 33648.0 ave 33648 max 33648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33648 Ave neighs/atom = 85.184810 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.586 | 4.586 | 4.586 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 -1322.7037 -1322.7037 20.211239 80.948085 4.0247492 -485.49962 -485.49962 -119.8134 -1142.1002 -194.58526 2.4821881 218.65581 Loop time of 1.669e-06 on 1 procs for 0 steps with 395 atoms 179.7% 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 | | 1.669e-06 | | |100.00 Nlocal: 395.000 ave 395 max 395 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3545.00 ave 3545 max 3545 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16824.0 ave 16824 max 16824 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33648.0 ave 33648 max 33648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33648 Ave neighs/atom = 85.184810 Neighbor list builds = 0 Dangerous builds = 0 395 -1322.70365219151 eV 2.48218806943148 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02