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 -59.443983 0.0000000) to (21.016622 59.443983 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4487538 6.6048870 5.7200000 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.443983 0.0000000) to (21.016622 59.443983 5.7200000) create_atoms CPU = 0.002 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4487538 6.6048870 5.7200000 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.443983 0.0000000) to (21.016622 59.443983 5.7200000) create_atoms CPU = 0.001 seconds 434 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 = 7 37 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 6 atoms, new total = 860 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_616482358807_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 = 7 37 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2795.0456 0 -2795.0456 15311.379 59 0 -2881.5474 0 -2881.5474 502.65036 Loop time of 3.14789 on 1 procs for 59 steps with 860 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2795.04564401887 -2881.54531804896 -2881.54742412405 Force two-norm initial, final = 169.16962 0.10560738 Force max component initial, final = 46.909622 0.012168643 Final line search alpha, max atom move = 1.0000000 0.012168643 Iterations, force evaluations = 59 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1324 | 3.1324 | 3.1324 | 0.0 | 99.51 Neigh | 0.0043224 | 0.0043224 | 0.0043224 | 0.0 | 0.14 Comm | 0.0051608 | 0.0051608 | 0.0051608 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005992 | | | 0.19 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4175.00 ave 4175 max 4175 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: 65752.0 ave 65752 max 65752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65752 Ave neighs/atom = 76.455814 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 37 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -2881.5474 0 -2881.5474 502.65036 14292.126 62 0 -2881.5669 0 -2881.5669 -39.713145 14302.105 Loop time of 0.142498 on 1 procs for 3 steps with 860 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 = -2881.54742412405 -2881.56553203707 -2881.566949662 Force two-norm initial, final = 16.258718 0.74297090 Force max component initial, final = 14.328310 0.66602567 Final line search alpha, max atom move = 0.00015271584 0.00010171267 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14144 | 0.14144 | 0.14144 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017716 | 0.00017716 | 0.00017716 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008758 | | | 0.61 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4076.00 ave 4076 max 4076 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: 65964.0 ave 65964 max 65964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65964 Ave neighs/atom = 76.702326 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 = 7 37 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) = 4.712 | 4.712 | 4.712 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2881.5669 0 -2881.5669 -39.713145 Loop time of 1.995e-06 on 1 procs for 0 steps with 860 atoms 200.5% 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 | | 1.995e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4076.00 ave 4076 max 4076 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: 65944.0 ave 65944 max 65944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65944 Ave neighs/atom = 76.679070 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 = 7 37 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) = 4.712 | 4.712 | 4.712 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 -2881.5669 -2881.5669 21.023662 119.11668 5.7110902 -39.713145 -39.713145 -32.136518 -12.508389 -74.494528 2.5869586 584.22888 Loop time of 3.402e-06 on 1 procs for 0 steps with 860 atoms 176.4% 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 | | 3.402e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4076.00 ave 4076 max 4076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32972.0 ave 32972 max 32972 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65944.0 ave 65944 max 65944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65944 Ave neighs/atom = 76.679070 Neighbor list builds = 0 Dangerous builds = 0 860 -2881.566949662 eV 2.58695859279334 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03