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 = 3.1674131 3.1674131 3.1674131 Created orthogonal box = (0.0000000 -49.479742 0.0000000) to (24.738287 49.479742 3.1674131) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4610026 4.4610026 3.1674131 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -49.479742 0.0000000) to (24.738287 49.479742 3.1674131) create_atoms CPU = 0.002 seconds 245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4610026 4.4610026 3.1674131 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -49.479742 0.0000000) to (24.738287 49.479742 3.1674131) create_atoms CPU = 0.001 seconds 245 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 26 1 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 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 486 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_269937397263_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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3266.9861 0 -3266.9861 8017.0324 32 0 -3300.5608 0 -3300.5608 -5390.112 Loop time of 8.36561 on 1 procs for 32 steps with 486 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 = -3266.9861120012 -3300.55813096696 -3300.56077152079 Force two-norm initial, final = 39.459573 0.17994676 Force max component initial, final = 9.9260911 0.048642110 Final line search alpha, max atom move = 1.0000000 0.048642110 Iterations, force evaluations = 32 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3419 | 8.3419 | 8.3419 | 0.0 | 99.72 Neigh | 0.010907 | 0.010907 | 0.010907 | 0.0 | 0.13 Comm | 0.0074617 | 0.0074617 | 0.0074617 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005331 | | | 0.06 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5040.00 ave 5040 max 5040 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: 65354.0 ave 65354 max 65354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65354 Ave neighs/atom = 134.47325 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -3300.5608 0 -3300.5608 -5390.112 7754.1065 34 0 -3300.5773 0 -3300.5773 -1668.8029 7742.107 Loop time of 0.774701 on 1 procs for 2 steps with 486 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 = -3300.56077152079 -3300.57731059596 -3300.57734679035 Force two-norm initial, final = 29.710578 0.18936012 Force max component initial, final = 23.519268 0.045999696 Final line search alpha, max atom move = 0.0014248568 6.5542982e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77168 | 0.77168 | 0.77168 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066217 | 0.00066217 | 0.00066217 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002358 | | | 0.30 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5040.00 ave 5040 max 5040 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: 65358.0 ave 65358 max 65358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65358 Ave neighs/atom = 134.48148 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3300.5773 0 -3300.5773 -1668.8029 Loop time of 6.124e-06 on 1 procs for 0 steps with 486 atoms 196.0% 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 | | 6.124e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5046.00 ave 5046 max 5046 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: 65376.0 ave 65376 max 65376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65376 Ave neighs/atom = 134.51852 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.627 | 4.627 | 4.627 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 -3300.5773 -3300.5773 24.722952 98.959484 3.1644731 -1668.8029 -1668.8029 -8.0013984 -5000.622 2.2147751 2.475379 110.57018 Loop time of 6.545e-06 on 1 procs for 0 steps with 486 atoms 290.3% 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 | | 6.545e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5046.00 ave 5046 max 5046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32688.0 ave 32688 max 32688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65376.0 ave 65376 max 65376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65376 Ave neighs/atom = 134.51852 Neighbor list builds = 0 Dangerous builds = 0 486 -3300.57734679035 eV 2.47537895276192 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09