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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -43.970565 0.0000000) to (53.852724 43.970565 8.9137664) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1639599 5.4210286 5.9425109 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -43.970565 0.0000000) to (53.852724 43.970565 8.9137664) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1639599 5.4210286 5.9425109 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -43.970565 0.0000000) to (53.852724 43.970565 8.9137664) create_atoms CPU = 0.002 seconds 1755 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 ghost atom cutoff = 8 binsize = 4, bins = 14 22 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 3478 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_748636486270_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 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.385 | 7.385 | 7.385 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8862.1359 0 -8862.1359 165336.8 95 0 -11861.76 0 -11861.76 -4963.5812 Loop time of 4.59513 on 1 procs for 95 steps with 3478 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 = -8862.13586624852 -11861.750674805 -11861.7604512498 Force two-norm initial, final = 3939.6127 0.25446241 Force max component initial, final = 749.62949 0.013642644 Final line search alpha, max atom move = 1.0000000 0.013642644 Iterations, force evaluations = 95 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3634 | 4.3634 | 4.3634 | 0.0 | 94.96 Neigh | 0.18673 | 0.18673 | 0.18673 | 0.0 | 4.06 Comm | 0.018561 | 0.018561 | 0.018561 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02644 | | | 0.58 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11415.0 ave 11415 max 11415 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: 610816.0 ave 610816 max 610816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610816 Ave neighs/atom = 175.62277 Neighbor list builds = 5 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 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.388 | 7.388 | 7.388 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -11861.76 0 -11861.76 -4963.5812 42214.434 99 0 -11862.059 0 -11862.059 31.147403 42065.779 Loop time of 0.203961 on 1 procs for 4 steps with 3478 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 = -11861.7604512499 -11862.0577499482 -11862.0585692439 Force two-norm initial, final = 234.90051 1.4849994 Force max component initial, final = 178.01429 0.98657308 Final line search alpha, max atom move = 0.00017742301 0.00017504076 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19981 | 0.19981 | 0.19981 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061655 | 0.00061655 | 0.00061655 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003539 | | | 1.74 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11584.0 ave 11584 max 11584 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: 610948.0 ave 610948 max 610948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610948 Ave neighs/atom = 175.66072 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 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.526 | 7.526 | 7.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11862.059 0 -11862.059 31.147403 Loop time of 2.072e-06 on 1 procs for 0 steps with 3478 atoms 193.1% 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 | | 2.072e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11584.0 ave 11584 max 11584 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: 611616.0 ave 611616 max 611616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 611616 Ave neighs/atom = 175.85279 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 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.526 | 7.526 | 7.526 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 -11862.059 -11862.059 53.820875 87.68053 8.914049 31.147403 31.147403 34.445775 37.464661 21.531775 2.3702343 1494.8581 Loop time of 2.545e-06 on 1 procs for 0 steps with 3478 atoms 235.8% 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 | | 2.545e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11584.0 ave 11584 max 11584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 305808.0 ave 305808 max 305808 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 611616.0 ave 611616 max 611616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 611616 Ave neighs/atom = 175.85279 Neighbor list builds = 0 Dangerous builds = 0 3478 -11862.0585692439 eV 2.37023425893048 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05