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 -31.406493 0.0000000) to (6.4102384 31.406493 7.0220643) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8461430 4.1871502 4.6813762 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -31.406493 0.0000000) to (6.4102384 31.406493 7.0220643) create_atoms CPU = 0.001 seconds 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8461430 4.1871502 4.6813762 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -31.406493 0.0000000) to (6.4102384 31.406493 7.0220643) create_atoms CPU = 0.001 seconds 122 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 = 2 17 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 = 236 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 = 2 17 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) = 4.486 | 4.486 | 4.486 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -985.98301 0 -985.98301 18413.539 55 0 -1002.1921 0 -1002.1921 -24491.565 Loop time of 0.431361 on 1 procs for 55 steps with 236 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -985.983006680262 -1002.19138781404 -1002.19212445666 Force two-norm initial, final = 28.126525 0.10372071 Force max component initial, final = 8.1091198 0.010865573 Final line search alpha, max atom move = 1.0000000 0.010865573 Iterations, force evaluations = 55 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41395 | 0.41395 | 0.41395 | 0.0 | 95.96 Neigh | 0.0059888 | 0.0059888 | 0.0059888 | 0.0 | 1.39 Comm | 0.0068039 | 0.0068039 | 0.0068039 | 0.0 | 1.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004614 | | | 1.07 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3119.00 ave 3119 max 3119 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: 38876.0 ave 38876 max 38876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38876 Ave neighs/atom = 164.72881 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 = 2 17 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -1002.1921 0 -1002.1921 -24491.565 2827.4076 61 0 -1002.3871 0 -1002.3871 -5058.5685 2800.2132 Loop time of 0.0402606 on 1 procs for 6 steps with 236 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1002.19212445666 -1002.38693158325 -1002.38709930471 Force two-norm initial, final = 57.250412 0.50700598 Force max component initial, final = 42.130801 0.14975372 Final line search alpha, max atom move = 0.0013336477 0.00019971869 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.038051 | 0.038051 | 0.038051 | 0.0 | 94.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052537 | 0.00052537 | 0.00052537 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001684 | | | 4.18 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2915.00 ave 2915 max 2915 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: 38948.0 ave 38948 max 38948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38948 Ave neighs/atom = 165.03390 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 = 2 17 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) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1002.3871 0 -1002.3871 -5058.5685 Loop time of 6.254e-06 on 1 procs for 0 steps with 236 atoms 159.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2915.00 ave 2915 max 2915 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: 39004.0 ave 39004 max 39004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39004 Ave neighs/atom = 165.27119 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 = 2 17 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) = 4.622 | 4.622 | 4.622 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 -1002.3871 -1002.3871 6.3782658 62.812986 6.9893863 -5058.5685 -5058.5685 83.77229 -15174.193 -85.284696 2.3673024 277.06843 Loop time of 6.434e-06 on 1 procs for 0 steps with 236 atoms 217.6% 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 | | 6.434e-06 | | |100.00 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2915.00 ave 2915 max 2915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19502.0 ave 19502 max 19502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39004.0 ave 39004 max 39004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39004 Ave neighs/atom = 165.27119 Neighbor list builds = 0 Dangerous builds = 0 236 -1002.38709930471 eV 2.3673024312521 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00