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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -36.584441 0.0000000) to (8.6222058 36.584441 4.9780328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7481372 6.0968202 4.9780328 Created 152 atoms using lattice units in orthogonal box = (0.0000000 -36.584441 0.0000000) to (8.6222058 36.584441 4.9780328) create_atoms CPU = 0.001 seconds 152 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7481372 6.0968202 4.9780328 Created 152 atoms using lattice units in orthogonal box = (0.0000000 -36.584441 0.0000000) to (8.6222058 36.584441 4.9780328) create_atoms CPU = 0.001 seconds 152 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 19 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 288 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1281.2515 0 -1281.2515 -1189.3932 3 0 -1281.2575 0 -1281.2575 -1380.6238 Loop time of 0.0183722 on 1 procs for 3 steps with 288 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 = -1281.25149894881 -1281.25667994064 -1281.25748208678 Force two-norm initial, final = 0.26267391 0.062225284 Force max component initial, final = 0.062615980 0.0094820964 Final line search alpha, max atom move = 1.0000000 0.0094820964 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018049 | 0.018049 | 0.018049 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018672 | 0.00018672 | 0.00018672 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001367 | | | 0.74 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3739.00 ave 3739 max 3739 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: 50752.0 ave 50752 max 50752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50752 Ave neighs/atom = 176.22222 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 3 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 3 0 -1281.2575 0 -1281.2575 -1380.6238 3140.5272 4 0 -1281.2581 0 -1281.2581 -464.34547 3138.9337 Loop time of 0.00821515 on 1 procs for 1 steps with 288 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 = -1281.25748208678 -1281.25748208678 -1281.25805139899 Force two-norm initial, final = 3.1524864 0.064556946 Force max component initial, final = 2.2287102 0.012903736 Final line search alpha, max atom move = 0.00044869001 5.7897776e-06 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0078947 | 0.0078947 | 0.0078947 | 0.0 | 96.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.976e-05 | 7.976e-05 | 7.976e-05 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002407 | | | 2.93 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3739.00 ave 3739 max 3739 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: 50752.0 ave 50752 max 50752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50752 Ave neighs/atom = 176.22222 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1281.2581 0 -1281.2581 -464.34547 Loop time of 1.699e-06 on 1 procs for 0 steps with 288 atoms 58.9% 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 | | 1.699e-06 | | |100.00 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3739.00 ave 3739 max 3739 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: 50752.0 ave 50752 max 50752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50752 Ave neighs/atom = 176.22222 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.611 | 4.611 | 4.611 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 -1281.2581 -1281.2581 8.620018 73.168882 4.9767697 -464.34547 -464.34547 -6.5846621 -1379.8671 -6.5846621 2.4833385 99.08247 Loop time of 1.357e-06 on 1 procs for 0 steps with 288 atoms 221.1% 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 | | 1.357e-06 | | |100.00 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3739.00 ave 3739 max 3739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25376.0 ave 25376 max 25376 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50752.0 ave 50752 max 50752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50752 Ave neighs/atom = 176.22222 Neighbor list builds = 0 Dangerous builds = 0 288 -1281.25805139899 eV 2.483338526499 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00