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 = 3.1674131 3.1674131 3.1674131 Created orthogonal box = (0.0000000 -45.239708 0.0000000) to (31.989304 45.239708 4.4793986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0179301 3.9917390 4.4793986 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -45.239708 0.0000000) to (31.989304 45.239708 4.4793986) create_atoms CPU = 0.001 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0179301 3.9917390 4.4793986 Created 409 atoms using lattice units in orthogonal box = (0.0000000 -45.239708 0.0000000) to (31.989304 45.239708 4.4793986) create_atoms CPU = 0.001 seconds 409 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 23 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 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 812 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_269937397263_001#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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5376.669 0 -5376.669 3118.1533 82 0 -5501.0664 0 -5501.0664 -916.12623 Loop time of 11.0024 on 1 procs for 82 steps with 812 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5376.6689747554 -5501.06318086987 -5501.06644196537 Force two-norm initial, final = 48.833673 0.16815300 Force max component initial, final = 10.136108 0.023030407 Final line search alpha, max atom move = 1.0000000 0.023030407 Iterations, force evaluations = 82 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.982 | 10.982 | 10.982 | 0.0 | 99.82 Neigh | 0.0067614 | 0.0067614 | 0.0067614 | 0.0 | 0.06 Comm | 0.0070304 | 0.0070304 | 0.0070304 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006359 | | | 0.06 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5562.00 ave 5562 max 5562 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: 108744.0 ave 108744 max 108744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108744 Ave neighs/atom = 133.92118 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.948 | 4.948 | 4.948 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -5501.0664 0 -5501.0664 -916.12623 12965.053 84 0 -5501.0853 0 -5501.0853 -2.3298739 12960.056 Loop time of 0.390159 on 1 procs for 2 steps with 812 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 = -5501.06644196535 -5501.08043218557 -5501.08530485213 Force two-norm initial, final = 26.682116 0.33271767 Force max component initial, final = 23.236000 0.20719587 Final line search alpha, max atom move = 4.8070153e-05 9.9599369e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38894 | 0.38894 | 0.38894 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025543 | 0.00025543 | 0.00025543 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009605 | | | 0.25 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6278.00 ave 6278 max 6278 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: 109300.0 ave 109300 max 109300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109300 Ave neighs/atom = 134.60591 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.086 | 5.086 | 5.086 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5501.0853 0 -5501.0853 -2.3298739 Loop time of 1.511e-06 on 1 procs for 0 steps with 812 atoms 198.5% 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 | | 1.511e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6278.00 ave 6278 max 6278 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: 109304.0 ave 109304 max 109304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109304 Ave neighs/atom = 134.61084 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.086 | 5.086 | 5.086 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 -5501.0853 -5501.0853 32.020184 90.460158 4.4743063 -2.3298739 -2.3298739 -14.810601 25.60897 -17.787991 2.5165123 443.15337 Loop time of 1.763e-06 on 1 procs for 0 steps with 812 atoms 170.2% 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 | | 1.763e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6278.00 ave 6278 max 6278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54652.0 ave 54652 max 54652 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109304.0 ave 109304 max 109304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109304 Ave neighs/atom = 134.61084 Neighbor list builds = 0 Dangerous builds = 0 812 -5501.08530485213 eV 2.51651227368002 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11