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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -38.034547 0.0000000) to (13.446229 38.034547 4.0541907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8895380 4.3217818 4.0541907 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -38.034547 0.0000000) to (13.446229 38.034547 4.0541907) create_atoms CPU = 0.001 seconds 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8895380 4.3217818 4.0541907 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -38.034547 0.0000000) to (13.446229 38.034547 4.0541907) create_atoms CPU = 0.000 seconds 178 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 348 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.464 | 4.464 | 4.464 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1461.6066 0 -1461.6066 13764.436 47 0 -1479.0816 0 -1479.0816 -9973.4956 Loop time of 0.237367 on 1 procs for 47 steps with 348 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 = -1461.60660756101 -1479.08068698402 -1479.08162871952 Force two-norm initial, final = 43.922408 0.12033186 Force max component initial, final = 15.255715 0.017752873 Final line search alpha, max atom move = 1.0000000 0.017752873 Iterations, force evaluations = 47 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22982 | 0.22982 | 0.22982 | 0.0 | 96.82 Neigh | 0.003381 | 0.003381 | 0.003381 | 0.0 | 1.42 Comm | 0.0025513 | 0.0025513 | 0.0025513 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001611 | | | 0.68 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4097.00 ave 4097 max 4097 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: 57648.0 ave 57648 max 57648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57648 Ave neighs/atom = 165.65517 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.464 | 4.464 | 4.464 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1479.0816 0 -1479.0816 -9973.4956 4146.7985 51 0 -1479.1474 0 -1479.1474 -333.81694 4128.851 Loop time of 0.0193253 on 1 procs for 4 steps with 348 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 = -1479.08162871952 -1479.14733814969 -1479.14741079749 Force two-norm initial, final = 42.066201 0.20482430 Force max component initial, final = 33.337051 0.037284682 Final line search alpha, max atom move = 0.0010942848 4.0800059e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018362 | 0.018362 | 0.018362 | 0.0 | 95.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019805 | 0.00019805 | 0.00019805 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007655 | | | 3.96 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4177.00 ave 4177 max 4177 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: 57756.0 ave 57756 max 57756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57756 Ave neighs/atom = 165.96552 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1479.1474 0 -1479.1474 -333.81694 Loop time of 1.714e-06 on 1 procs for 0 steps with 348 atoms 116.7% 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 | | 1.714e-06 | | |100.00 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4177.00 ave 4177 max 4177 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: 57768.0 ave 57768 max 57768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57768 Ave neighs/atom = 166.00000 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.602 | 4.602 | 4.602 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 -1479.1474 -1479.1474 13.423785 76.069094 4.0433932 -333.81694 -333.81694 -13.510319 -997.39209 9.4515924 2.3181975 282.05586 Loop time of 1.494e-06 on 1 procs for 0 steps with 348 atoms 133.9% 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 | | 1.494e-06 | | |100.00 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4177.00 ave 4177 max 4177 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28884.0 ave 28884 max 28884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57768.0 ave 57768 max 57768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57768 Ave neighs/atom = 166.00000 Neighbor list builds = 0 Dangerous builds = 0 348 -1479.14741079749 eV 2.31819747129241 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00