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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -31.869537 0.0000000) to (6.3733373 31.869537 2.8502431) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8240024 3.8240024 2.8502431 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -31.869537 0.0000000) to (6.3733373 31.869537 2.8502431) create_atoms CPU = 0.001 seconds 51 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8240024 3.8240024 2.8502431 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -31.869537 0.0000000) to (6.3733373 31.869537 2.8502431) create_atoms CPU = 0.000 seconds 51 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 98 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.377 | 4.377 | 4.377 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -416.48722 0 -416.48722 -11832.646 31 0 -417.95521 0 -417.95521 -23380.329 Loop time of 1.02214 on 1 procs for 31 steps with 98 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 = -416.487220438796 -417.954860603935 -417.955208277113 Force two-norm initial, final = 2.4441318 0.050032974 Force max component initial, final = 1.0148839 0.014933459 Final line search alpha, max atom move = 1.0000000 0.014933459 Iterations, force evaluations = 31 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0181 | 1.0181 | 1.0181 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024303 | 0.0024303 | 0.0024303 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001594 | | | 0.16 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1759.00 ave 1759 max 1759 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: 6272.00 ave 6272 max 6272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6272 Ave neighs/atom = 64.000000 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.377 | 4.377 | 4.377 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -417.95521 0 -417.95521 -23380.329 1157.856 45 0 -418.08709 0 -418.08709 -2132.0967 1142.4917 Loop time of 0.334321 on 1 procs for 14 steps with 98 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 = -417.955208277113 -418.087026754027 -418.087085719053 Force two-norm initial, final = 24.352357 0.099036973 Force max component initial, final = 20.232878 0.029808169 Final line search alpha, max atom move = 0.0026670439 7.9499694e-05 Iterations, force evaluations = 14 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33131 | 0.33131 | 0.33131 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007738 | 0.0007738 | 0.0007738 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00224 | | | 0.67 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1759.00 ave 1759 max 1759 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: 6380.00 ave 6380 max 6380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6380 Ave neighs/atom = 65.102041 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -418.08709 0 -418.08709 -2132.0967 Loop time of 6.896e-06 on 1 procs for 0 steps with 98 atoms 174.0% 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 | | 6.896e-06 | | |100.00 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1759.00 ave 1759 max 1759 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: 6416.00 ave 6416 max 6416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6416 Ave neighs/atom = 65.469388 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.515 | 4.515 | 4.515 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 -418.08709 -418.08709 6.3648038 63.739073 2.8161922 -2132.0967 -2132.0967 26.234021 -6444.1073 21.583137 2.3670034 76.88972 Loop time of 6.295e-06 on 1 procs for 0 steps with 98 atoms 254.2% 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 | | 6.295e-06 | | |100.00 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1759.00 ave 1759 max 1759 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3208.00 ave 3208 max 3208 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6416.00 ave 6416 max 6416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6416 Ave neighs/atom = 65.469388 Neighbor list builds = 0 Dangerous builds = 0 98 -418.087085719053 eV 2.36700342124598 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01