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 -65.512245 0.0000000) to (13.372631 65.512245 9.8763426) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0784687 5.9556587 6.5842284 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -65.512245 0.0000000) to (13.372631 65.512245 9.8763426) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0784687 5.9556587 6.5842284 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -65.512245 0.0000000) to (13.372631 65.512245 9.8763426) create_atoms CPU = 0.001 seconds 530 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 = 4 30 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 0 atoms, new total = 1058 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 = 4 30 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) = 5.119 | 5.119 | 5.119 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3473.895 0 -3473.895 15009.662 70 0 -3546.9007 0 -3546.9007 4805.5168 Loop time of 1.38614 on 1 procs for 70 steps with 1058 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3473.89496364691 -3546.89767899752 -3546.90066998191 Force two-norm initial, final = 83.059786 0.13249705 Force max component initial, final = 19.577583 0.023269207 Final line search alpha, max atom move = 1.0000000 0.023269207 Iterations, force evaluations = 70 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3574 | 1.3574 | 1.3574 | 0.0 | 97.93 Neigh | 0.011807 | 0.011807 | 0.011807 | 0.0 | 0.85 Comm | 0.00852 | 0.00852 | 0.00852 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00838 | | | 0.60 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6864.00 ave 6864 max 6864 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: 186216.0 ave 186216 max 186216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186216 Ave neighs/atom = 176.00756 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 4 30 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 : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.116 | 5.116 | 5.116 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -3546.9007 0 -3546.9007 4805.5168 17304.756 78 0 -3547.1968 0 -3547.1968 79.180859 17404.547 Loop time of 0.107614 on 1 procs for 8 steps with 1058 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3546.90066998191 -3547.19648405399 -3547.19679384572 Force two-norm initial, final = 101.02394 1.5582121 Force max component initial, final = 89.483079 1.1105576 Final line search alpha, max atom move = 0.00051192877 0.00056852640 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10417 | 0.10417 | 0.10417 | 0.0 | 96.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053645 | 0.00053645 | 0.00053645 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002909 | | | 2.70 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6652.00 ave 6652 max 6652 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: 185940.0 ave 185940 max 185940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185940 Ave neighs/atom = 175.74669 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 = 4 30 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) = 5.254 | 5.254 | 5.254 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3547.1968 0 -3547.1968 79.180859 Loop time of 2.099e-06 on 1 procs for 0 steps with 1058 atoms 142.9% 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 | | 2.099e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656.00 ave 6656 max 6656 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: 185712.0 ave 185712 max 185712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185712 Ave neighs/atom = 175.53119 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 = 4 30 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) = 5.254 | 5.254 | 5.254 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 -3547.1968 -3547.1968 13.359493 131.95813 9.8727145 79.180859 79.180859 49.271908 102.96092 85.309743 2.5410126 525.69029 Loop time of 2.646e-06 on 1 procs for 0 steps with 1058 atoms 264.6% 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 | | 2.646e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656.00 ave 6656 max 6656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92856.0 ave 92856 max 92856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 185712.0 ave 185712 max 185712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185712 Ave neighs/atom = 175.53119 Neighbor list builds = 0 Dangerous builds = 0 1058 -3547.19679384572 eV 2.5410126072941 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01