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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -40.504050 0.0000000) to (20.250000 40.504050 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6700000 5.6700000 4.0500000 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.504050 0.0000000) to (20.250000 40.504050 4.0500000) create_atoms CPU = 0.002 seconds 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6700000 5.6700000 4.0500000 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.504050 0.0000000) to (20.250000 40.504050 4.0500000) create_atoms CPU = 0.001 seconds 202 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 396 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_971738391444_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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1313.3084 0 -1313.3084 715.23034 40 0 -1322.1023 0 -1322.1023 -5272.3044 Loop time of 3.53088 on 1 procs for 40 steps with 396 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 = -1313.30836881078 -1322.10144241281 -1322.10232179885 Force two-norm initial, final = 9.0233304 0.076029877 Force max component initial, final = 2.5077133 0.0077216610 Final line search alpha, max atom move = 1.0000000 0.0077216610 Iterations, force evaluations = 40 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5198 | 3.5198 | 3.5198 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058602 | 0.0058602 | 0.0058602 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005237 | | | 0.15 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3150.00 ave 3150 max 3150 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: 30824.0 ave 30824 max 30824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30824 Ave neighs/atom = 77.838384 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1322.1023 0 -1322.1023 -5272.3044 6643.6768 44 0 -1322.1406 0 -1322.1406 -1836.7445 6613.4671 Loop time of 0.37886 on 1 procs for 4 steps with 396 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1322.10232179885 -1322.14025856539 -1322.14058772444 Force two-norm initial, final = 22.869540 0.082206211 Force max component initial, final = 17.998378 0.010949816 Final line search alpha, max atom move = 0.00083729294 9.1682039e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37623 | 0.37623 | 0.37623 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052894 | 0.00052894 | 0.00052894 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002103 | | | 0.56 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3139.00 ave 3139 max 3139 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: 31280.0 ave 31280 max 31280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31280 Ave neighs/atom = 78.989899 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.583 | 4.583 | 4.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1322.1406 0 -1322.1406 -1836.7445 Loop time of 7.638e-06 on 1 procs for 0 steps with 396 atoms 170.2% 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 | | 7.638e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3139.00 ave 3139 max 3139 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: 32272.0 ave 32272 max 32272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32272 Ave neighs/atom = 81.494949 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.583 | 4.583 | 4.583 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 -1322.1406 -1322.1406 20.187134 81.0081 4.044139 -1836.7445 -1836.7445 0.46415458 -5509.2513 -1.4462101 2.3884087 166.54092 Loop time of 9.472e-06 on 1 procs for 0 steps with 396 atoms 211.1% 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 | | 9.472e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3139.00 ave 3139 max 3139 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16136.0 ave 16136 max 16136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32272.0 ave 32272 max 32272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32272 Ave neighs/atom = 81.494949 Neighbor list builds = 0 Dangerous builds = 0 396 -1322.14058772444 eV 2.38840873101711 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04