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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -48.718841 0.0000000) to (59.668151 48.718841 9.8763426) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7216035 6.0064325 6.5842284 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -48.718841 0.0000000) to (59.668151 48.718841 9.8763426) create_atoms CPU = 0.003 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7216035 6.0064325 6.5842284 Created 1753 atoms using lattice units in orthogonal box = (0.0000000 -48.718841 0.0000000) to (59.668151 48.718841 9.8763426) create_atoms CPU = 0.002 seconds 1753 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 14 22 3 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 3476 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 7.384 | 7.384 | 7.384 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10975.307 0 -10975.307 19820.322 103 0 -11653.349 0 -11653.349 -3079.7983 Loop time of 5.34775 on 1 procs for 103 steps with 3476 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10975.3066856431 -11653.3387445798 -11653.3494117247 Force two-norm initial, final = 568.95313 0.24760020 Force max component initial, final = 105.27670 0.032911720 Final line search alpha, max atom move = 1.0000000 0.032911720 Iterations, force evaluations = 103 162 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.044 | 5.044 | 5.044 | 0.0 | 94.32 Neigh | 0.2402 | 0.2402 | 0.2402 | 0.0 | 4.49 Comm | 0.029029 | 0.029029 | 0.029029 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03447 | | | 0.64 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11502.0 ave 11502 max 11502 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: 610774.0 ave 610774 max 610774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610774 Ave neighs/atom = 175.71174 Neighbor list builds = 6 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.387 | 7.387 | 7.387 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -11653.349 0 -11653.349 -3079.7983 57420.328 107 0 -11653.655 0 -11653.655 -254.33464 57217.057 Loop time of 0.177371 on 1 procs for 4 steps with 3476 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 = -11653.3494117247 -11653.6478841415 -11653.6554503124 Force two-norm initial, final = 201.47087 17.785809 Force max component initial, final = 161.33601 15.745251 Final line search alpha, max atom move = 6.8925359e-05 0.0010852471 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17372 | 0.17372 | 0.17372 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053159 | 0.00053159 | 0.00053159 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003116 | | | 1.76 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11586.0 ave 11586 max 11586 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: 610584.0 ave 610584 max 610584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610584 Ave neighs/atom = 175.65708 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 7.525 | 7.525 | 7.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11653.655 0 -11653.655 -254.33464 Loop time of 2.415e-06 on 1 procs for 0 steps with 3476 atoms 165.6% 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 | | 2.415e-06 | | |100.00 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11586.0 ave 11586 max 11586 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: 611300.0 ave 611300 max 611300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 611300 Ave neighs/atom = 175.86306 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 7.525 | 7.525 | 7.525 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 -11653.655 -11653.655 59.647322 97.116005 9.8774255 -254.33464 -254.33464 -136.93515 -439.4387 -186.63006 2.6499969 1929.8893 Loop time of 5.321e-06 on 1 procs for 0 steps with 3476 atoms 206.7% 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 | | 5.321e-06 | | |100.00 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11586.0 ave 11586 max 11586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 305650.0 ave 305650 max 305650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 611300.0 ave 611300 max 611300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 611300 Ave neighs/atom = 175.86306 Neighbor list builds = 0 Dangerous builds = 0 3476 -11653.6554503124 eV 2.649996858023 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06