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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -57.215844 0.0000000) to (11.679135 57.215844 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3086978 5.2014403 5.7504086 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.215844 0.0000000) to (11.679135 57.215844 8.6256130) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3086978 5.2014403 5.7504086 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.215844 0.0000000) to (11.679135 57.215844 8.6256130) 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 36 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1052 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_115454747503_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4431.807 0 -4431.807 50275.336 108 0 -4662.9843 0 -4662.9843 2531.32 Loop time of 10.0939 on 1 procs for 108 steps with 1052 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4431.80704808192 -4662.9799106693 -4662.98433246719 Force two-norm initial, final = 368.35657 0.26558588 Force max component initial, final = 88.830512 0.051420340 Final line search alpha, max atom move = 0.82785883 0.042568782 Iterations, force evaluations = 108 206 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.054 | 10.054 | 10.054 | 0.0 | 99.60 Neigh | 0.015882 | 0.015882 | 0.015882 | 0.0 | 0.16 Comm | 0.011384 | 0.011384 | 0.011384 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01283 | | | 0.13 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5318.00 ave 5318 max 5318 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: 91620.0 ave 91620 max 91620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91620 Ave neighs/atom = 87.091255 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.614 | 4.614 | 4.614 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -4662.9843 0 -4662.9843 2531.32 11527.814 112 0 -4663.0518 0 -4663.0518 -15.059398 11543.567 Loop time of 0.333891 on 1 procs for 4 steps with 1052 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 = -4662.98433246719 -4663.05131667567 -4663.05182618727 Force two-norm initial, final = 50.173394 0.85134661 Force max component initial, final = 49.704511 0.50935799 Final line search alpha, max atom move = 0.00017795794 9.0644298e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33212 | 0.33212 | 0.33212 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032056 | 0.00032056 | 0.00032056 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001452 | | | 0.43 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5318.00 ave 5318 max 5318 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: 91680.0 ave 91680 max 91680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91680 Ave neighs/atom = 87.148289 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.752 | 4.752 | 4.752 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4663.0518 0 -4663.0518 -15.059398 Loop time of 2.103e-06 on 1 procs for 0 steps with 1052 atoms 190.2% 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 | | 2.103e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5318.00 ave 5318 max 5318 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: 91572.0 ave 91572 max 91572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91572 Ave neighs/atom = 87.045627 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.752 | 4.752 | 4.752 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 -4663.0518 -4663.0518 11.665587 114.74356 8.6239278 -15.059398 -15.059398 -68.046926 -47.813229 70.68196 2.2198331 395.02544 Loop time of 1.922e-06 on 1 procs for 0 steps with 1052 atoms 208.1% 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 | | 1.922e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5318.00 ave 5318 max 5318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45786.0 ave 45786 max 45786 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91572.0 ave 91572 max 91572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91572 Ave neighs/atom = 87.045627 Neighbor list builds = 0 Dangerous builds = 0 1052 -4663.05182618727 eV 2.21983311827323 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11