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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -73.251741 0.0000000) to (25.898401 73.251741 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9483516 6.2531974 5.7200000 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -73.251741 0.0000000) to (25.898401 73.251741 5.7200000) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9483516 6.2531974 5.7200000 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -73.251741 0.0000000) to (25.898401 73.251741 5.7200000) create_atoms CPU = 0.002 seconds 658 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 46 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1314 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_876687166519_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4215.9147 0 -4215.9147 21828.535 90 0 -4407.4175 0 -4407.4175 3194.3571 Loop time of 10.9511 on 1 procs for 90 steps with 1314 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4215.91471684367 -4407.41359888523 -4407.41751565035 Force two-norm initial, final = 277.28675 0.15049315 Force max component initial, final = 71.746205 0.016827823 Final line search alpha, max atom move = 1.0000000 0.016827823 Iterations, force evaluations = 90 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.884 | 10.884 | 10.884 | 0.0 | 99.39 Neigh | 0.028078 | 0.028078 | 0.028078 | 0.0 | 0.26 Comm | 0.018675 | 0.018675 | 0.018675 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01996 | | | 0.18 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5656.00 ave 5656 max 5656 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: 101200.0 ave 101200 max 101200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101200 Ave neighs/atom = 77.016743 Neighbor list builds = 2 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.060 | 5.060 | 5.060 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -4407.4175 0 -4407.4175 3194.3571 21702.858 96 0 -4407.6218 0 -4407.6218 -176.02946 21794.465 Loop time of 0.794611 on 1 procs for 6 steps with 1314 atoms 93.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4407.41751565034 -4407.61903961796 -4407.62182787225 Force two-norm initial, final = 86.749593 4.2671426 Force max component initial, final = 78.536152 2.8911974 Final line search alpha, max atom move = 0.00015201359 0.00043950130 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78881 | 0.78881 | 0.78881 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092711 | 0.00092711 | 0.00092711 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004872 | | | 0.61 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6204.00 ave 6204 max 6204 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: 101212.0 ave 101212 max 101212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101212 Ave neighs/atom = 77.025875 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.198 | 5.198 | 5.198 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4407.6218 0 -4407.6218 -176.02946 Loop time of 7.186e-06 on 1 procs for 0 steps with 1314 atoms 180.9% 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 | | 7.186e-06 | | |100.00 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6197.00 ave 6197 max 6197 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: 101068.0 ave 101068 max 101068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101068 Ave neighs/atom = 76.916286 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.198 | 5.198 | 5.198 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 -4407.6218 -4407.6218 25.894521 147.34111 5.7123447 -176.02946 -176.02946 -198.65314 -117.17909 -212.25614 2.5980642 487.30196 Loop time of 4.49e-06 on 1 procs for 0 steps with 1314 atoms 200.4% 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 | | 4.49e-06 | | |100.00 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6197.00 ave 6197 max 6197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50534.0 ave 50534 max 50534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101068.0 ave 101068 max 101068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101068 Ave neighs/atom = 76.916286 Neighbor list builds = 0 Dangerous builds = 0 1314 -4407.62182787225 eV 2.5980641873077 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12