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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -39.358325 0.0000000) to (7.8709610 39.358325 3.5200008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7225766 4.7225766 3.5200008 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.358325 0.0000000) to (7.8709610 39.358325 3.5200008) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7225766 4.7225766 3.5200008 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.358325 0.0000000) to (7.8709610 39.358325 3.5200008) create_atoms CPU = 0.000 seconds 102 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 198 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -867.7379 0 -867.7379 3664.3331 76 0 -875.65973 0 -875.65973 -3957.8201 Loop time of 0.297368 on 1 procs for 76 steps with 198 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 = -867.73789916232 -875.659086529944 -875.659732709369 Force two-norm initial, final = 14.945756 0.13142129 Force max component initial, final = 4.3331505 0.052438554 Final line search alpha, max atom move = 1.0000000 0.052438554 Iterations, force evaluations = 76 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29164 | 0.29164 | 0.29164 | 0.0 | 98.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038235 | 0.0038235 | 0.0038235 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001907 | | | 0.64 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3663.00 ave 3663 max 3663 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: 34624.0 ave 34624 max 34624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34624 Ave neighs/atom = 174.86869 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 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 76 0 -875.65973 0 -875.65973 -3957.8201 2180.9069 79 0 -875.66892 0 -875.66892 358.06246 2175.8715 Loop time of 0.012041 on 1 procs for 3 steps with 198 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 = -875.659732709367 -875.66874414492 -875.668918500785 Force two-norm initial, final = 10.235272 0.15680853 Force max component initial, final = 8.5924914 0.065599819 Final line search alpha, max atom move = 0.0015294450 0.00010033132 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011352 | 0.011352 | 0.011352 | 0.0 | 94.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015347 | 0.00015347 | 0.00015347 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005353 | | | 4.45 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3723.00 ave 3723 max 3723 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: 34736.0 ave 34736 max 34736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34736 Ave neighs/atom = 175.43434 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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 -875.66892 0 -875.66892 358.06246 Loop time of 1.549e-06 on 1 procs for 0 steps with 198 atoms 129.1% 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 | | 1.549e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3729.00 ave 3729 max 3729 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: 34756.0 ave 34756 max 34756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34756 Ave neighs/atom = 175.53535 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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 -875.66892 -875.66892 7.8567522 78.71665 3.5182248 358.06246 358.06246 9.249923 1082.3157 -17.37823 2.2883031 126.2574 Loop time of 1.395e-06 on 1 procs for 0 steps with 198 atoms 143.4% 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 | | 1.395e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3729.00 ave 3729 max 3729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17378.0 ave 17378 max 17378 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34756.0 ave 34756 max 34756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34756 Ave neighs/atom = 175.53535 Neighbor list builds = 0 Dangerous builds = 0 198 -875.668918500785 eV 2.28830313002266 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00