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 = 3.6147282 3.6147282 3.6147282 Created orthogonal box = (0.0000000 -56.463859 0.0000000) to (28.231929 56.463859 3.6147282) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0910037 5.0910037 3.6147282 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.463859 0.0000000) to (28.231929 56.463859 3.6147282) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0910037 5.0910037 3.6147282 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.463859 0.0000000) to (28.231929 56.463859 3.6147282) create_atoms CPU = 0.001 seconds 490 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 27 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_942551040047_005#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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.436 | 5.436 | 5.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3287.3945 0 -3287.3945 45584.865 91 0 -3440.4349 0 -3440.4349 6267.3397 Loop time of 1.94523 on 1 procs for 91 steps with 978 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 = -3287.3945426358 -3440.43253142113 -3440.43486257453 Force two-norm initial, final = 212.55369 0.17078737 Force max component initial, final = 41.653900 0.030240199 Final line search alpha, max atom move = 1.0000000 0.030240199 Iterations, force evaluations = 91 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8924 | 1.8924 | 1.8924 | 0.0 | 97.28 Neigh | 0.027121 | 0.027121 | 0.027121 | 0.0 | 1.39 Comm | 0.015819 | 0.015819 | 0.015819 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009899 | | | 0.51 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9960.00 ave 9960 max 9960 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: 219392.0 ave 219392 max 219392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219392 Ave neighs/atom = 224.32720 Neighbor list builds = 2 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.437 | 5.437 | 5.437 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -3440.4349 0 -3440.4349 6267.3397 11524.358 96 0 -3440.598 0 -3440.598 -321.87142 11578.092 Loop time of 0.0807811 on 1 procs for 5 steps with 978 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 = -3440.43486257453 -3440.59765957733 -3440.59804287105 Force two-norm initial, final = 87.853899 4.9037317 Force max component initial, final = 71.292464 4.0048362 Final line search alpha, max atom move = 0.00021535915 0.00086247813 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.078228 | 0.078228 | 0.078228 | 0.0 | 96.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050126 | 0.00050126 | 0.00050126 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002052 | | | 2.54 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9978.00 ave 9978 max 9978 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: 219376.0 ave 219376 max 219376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219376 Ave neighs/atom = 224.31084 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.574 | 5.574 | 5.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3440.598 0 -3440.598 -321.87142 Loop time of 2.13e-06 on 1 procs for 0 steps with 978 atoms 187.8% 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 | | 2.13e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9960.00 ave 9960 max 9960 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: 219076.0 ave 219076 max 219076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219076 Ave neighs/atom = 224.00409 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.574 | 5.574 | 5.574 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 -3440.598 -3440.598 28.192054 113.35401 3.6230423 -321.87142 -321.87142 -553.40652 -391.71188 -20.495853 2.3094306 156.73317 Loop time of 2.79e-06 on 1 procs for 0 steps with 978 atoms 215.1% 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 | | 2.79e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9960.00 ave 9960 max 9960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109538.0 ave 109538 max 109538 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 219076.0 ave 219076 max 219076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219076 Ave neighs/atom = 224.00409 Neighbor list builds = 0 Dangerous builds = 0 978 -3440.59804287105 eV 2.30943062137203 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02