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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -63.669004 0.0000000) to (36.757236 63.669004 6.2429061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6549593 5.7135615 6.2429061 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -63.669004 0.0000000) to (36.757236 63.669004 6.2429061) create_atoms CPU = 0.002 seconds 1252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6549593 5.7135615 6.2429061 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -63.669004 0.0000000) to (36.757236 63.669004 6.2429061) create_atoms CPU = 0.002 seconds 1252 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 42 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2472 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.316 | 5.316 | 5.316 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10427.928 0 -10427.928 -2707.9723 175 0 -10474.838 0 -10474.838 -13610.464 Loop time of 27.6447 on 1 procs for 175 steps with 2472 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 = -10427.9278730613 -10474.8283910091 -10474.8379031349 Force two-norm initial, final = 26.828557 0.32478315 Force max component initial, final = 6.0427121 0.043656888 Final line search alpha, max atom move = 1.0000000 0.043656888 Iterations, force evaluations = 175 333 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.516 | 27.516 | 27.516 | 0.0 | 99.53 Neigh | 0.065942 | 0.065942 | 0.065942 | 0.0 | 0.24 Comm | 0.027508 | 0.027508 | 0.027508 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03523 | | | 0.13 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8209.00 ave 8209 max 8209 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: 188528.0 ave 188528 max 188528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188528 Ave neighs/atom = 76.265372 Neighbor list builds = 5 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 175 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.315 | 5.315 | 5.315 Mbytes Step Temp E_pair E_mol TotEng Press Volume 175 0 -10474.838 0 -10474.838 -13610.464 29220.504 186 0 -10477.139 0 -10477.139 1160.2029 28946.537 Loop time of 1.15355 on 1 procs for 11 steps with 2472 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 = -10474.8379031348 -10477.1309561586 -10477.1390011247 Force two-norm initial, final = 469.85972 3.0896061 Force max component initial, final = 446.34986 2.2449073 Final line search alpha, max atom move = 6.2007061e-05 0.00013920010 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1476 | 1.1476 | 1.1476 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007787 | 0.0007787 | 0.0007787 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005213 | | | 0.45 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8212.00 ave 8212 max 8212 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: 188440.0 ave 188440 max 188440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188440 Ave neighs/atom = 76.229773 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.452 | 5.452 | 5.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10477.139 0 -10477.139 1160.2029 Loop time of 1.659e-06 on 1 procs for 0 steps with 2472 atoms 180.8% 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 | | 1.659e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8235.00 ave 8235 max 8235 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: 188800.0 ave 188800 max 188800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188800 Ave neighs/atom = 76.375405 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.452 | 5.452 | 5.452 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 -10477.139 -10477.139 36.371507 127.33801 6.2499605 1160.2029 1160.2029 -122.95058 3714.0396 -110.48024 2.2388489 1733.006 Loop time of 1.994e-06 on 1 procs for 0 steps with 2472 atoms 200.6% 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 | | 1.994e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8235.00 ave 8235 max 8235 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94400.0 ave 94400 max 94400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188800.0 ave 188800 max 188800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188800 Ave neighs/atom = 76.375405 Neighbor list builds = 0 Dangerous builds = 0 2472 -10477.1390011247 eV 2.23884885420201 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29