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 = 3.5184747 3.5184747 3.5184747 Created orthogonal box = (0.0000000 -36.565061 0.0000000) to (25.855403 36.565061 4.9758746) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7456450 4.7399153 4.9758746 Created 430 atoms using lattice units in orthogonal box = (0.0000000 -36.565061 0.0000000) to (25.855403 36.565061 4.9758746) create_atoms CPU = 0.001 seconds 430 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7456450 4.7399153 4.9758746 Created 438 atoms using lattice units in orthogonal box = (0.0000000 -36.565061 0.0000000) to (25.855403 36.565061 4.9758746) create_atoms CPU = 0.001 seconds 438 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 ghost atom cutoff = 8 binsize = 4, bins = 7 19 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 864 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_922363340570_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 ghost atom cutoff = 8 binsize = 4, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.990 | 4.990 | 4.990 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3616.0839 0 -3616.0839 60795.372 53 0 -3736.8694 0 -3736.8694 7223.5504 Loop time of 0.825479 on 1 procs for 53 steps with 864 atoms 95.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3616.08387219914 -3736.86610534447 -3736.86939792592 Force two-norm initial, final = 203.85952 0.19613016 Force max component initial, final = 30.497904 0.018804941 Final line search alpha, max atom move = 1.0000000 0.018804941 Iterations, force evaluations = 53 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80617 | 0.80617 | 0.80617 | 0.0 | 97.66 Neigh | 0.0096031 | 0.0096031 | 0.0096031 | 0.0 | 1.16 Comm | 0.0053117 | 0.0053117 | 0.0053117 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004395 | | | 0.53 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6357.00 ave 6357 max 6357 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: 171550.0 ave 171550 max 171550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171550 Ave neighs/atom = 198.55324 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.990 | 4.990 | 4.990 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -3736.8694 0 -3736.8694 7223.5504 9408.4272 59 0 -3737.0666 0 -3737.0666 -382.11156 9447.5397 Loop time of 0.0646594 on 1 procs for 6 steps with 864 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 = -3736.86939792592 -3737.06497016065 -3737.06661783772 Force two-norm initial, final = 85.579124 4.1133063 Force max component initial, final = 76.488575 2.7679007 Final line search alpha, max atom move = 0.00018386101 0.00050890901 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062729 | 0.062729 | 0.062729 | 0.0 | 97.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036976 | 0.00036976 | 0.00036976 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00156 | | | 2.41 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6357.00 ave 6357 max 6357 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: 171694.0 ave 171694 max 171694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171694 Ave neighs/atom = 198.71991 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 ghost atom cutoff = 8 binsize = 4, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.128 | 5.128 | 5.128 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3737.0666 0 -3737.0666 -382.11156 Loop time of 1.6e-06 on 1 procs for 0 steps with 864 atoms 125.0% 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 | | 1.6e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6357.00 ave 6357 max 6357 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: 171440.0 ave 171440 max 171440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171440 Ave neighs/atom = 198.42593 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 ghost atom cutoff = 8 binsize = 4, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.128 | 5.128 | 5.128 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 -3737.0666 -3737.0666 25.82201 73.535906 4.9754142 -382.11156 -382.11156 -467.55063 -209.42853 -469.35554 2.2936844 515.00631 Loop time of 1.533e-06 on 1 procs for 0 steps with 864 atoms 130.5% 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 | | 1.533e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6357.00 ave 6357 max 6357 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85720.0 ave 85720 max 85720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171440.0 ave 171440 max 171440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171440 Ave neighs/atom = 198.42593 Neighbor list builds = 0 Dangerous builds = 0 864 -3737.06661783772 eV 2.29368442976308 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01