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 = 4.0816549 4.0816549 4.0816549 Created orthogonal box = (0.0000000 -41.624876 0.0000000) to (20.812438 41.624876 4.0816549) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8028703 4.8028703 4.0816549 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -41.624876 0.0000000) to (20.812438 41.624876 4.0816549) create_atoms CPU = 0.002 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8028703 4.8028703 4.0816549 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -41.624876 0.0000000) to (20.812438 41.624876 4.0816549) create_atoms CPU = 0.001 seconds 210 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 14 1 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 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_049243498555_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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 4.921 | 4.921 | 4.921 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1456.8916 0 -1456.8916 3123.5962 56 0 -1470.8855 0 -1470.8855 -2764.5022 Loop time of 2.88351 on 1 procs for 56 steps with 412 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1456.89157629876 -1470.88441340681 -1470.88545646568 Force two-norm initial, final = 29.847680 0.058677954 Force max component initial, final = 10.507031 0.0059917276 Final line search alpha, max atom move = 1.0000000 0.0059917276 Iterations, force evaluations = 56 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.837 | 2.837 | 2.837 | 0.0 | 98.39 Neigh | 0.019942 | 0.019942 | 0.019942 | 0.0 | 0.69 Comm | 0.017317 | 0.017317 | 0.017317 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00926 | | | 0.32 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7060.00 ave 7060 max 7060 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: 175008.0 ave 175008 max 175008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175008 Ave neighs/atom = 424.77670 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.921 | 4.921 | 4.921 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -1470.8855 0 -1470.8855 -2764.5022 7071.9991 58 0 -1470.9042 0 -1470.9042 78.579361 7050.1002 Loop time of 0.110475 on 1 procs for 2 steps with 412 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 = -1470.88545646567 -1470.90389260599 -1470.90419134222 Force two-norm initial, final = 21.196136 1.1474563 Force max component initial, final = 13.410168 1.0440268 Final line search alpha, max atom move = 0.00048898696 0.00051051549 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10829 | 0.10829 | 0.10829 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067386 | 0.00067386 | 0.00067386 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001507 | | | 1.36 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7064.00 ave 7064 max 7064 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: 175248.0 ave 175248 max 175248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175248 Ave neighs/atom = 425.35922 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.059 | 5.059 | 5.059 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1470.9042 0 -1470.9042 78.579361 Loop time of 6.685e-06 on 1 procs for 0 steps with 412 atoms 194.5% 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 | | 6.685e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7085.00 ave 7085 max 7085 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: 175432.0 ave 175432 max 175432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175432 Ave neighs/atom = 425.80583 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.059 | 5.059 | 5.059 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 -1470.9042 -1470.9042 20.794498 83.164766 4.0766881 78.579361 78.579361 237.05667 75.080722 -76.399312 2.5986207 251.02931 Loop time of 6.726e-06 on 1 procs for 0 steps with 412 atoms 252.8% 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 | | 6.726e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7085.00 ave 7085 max 7085 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87716.0 ave 87716 max 87716 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 175432.0 ave 175432 max 175432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175432 Ave neighs/atom = 425.80583 Neighbor list builds = 0 Dangerous builds = 0 412 -1470.90419134222 eV 2.59862070212933 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03