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 # Using KIM Simulator Model : Sim_LAMMPS_ADP_StarikovKolotovaKuksin_2017_UMo__SM_682749584055_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.1491000 3.1491000 3.1491000 Created orthogonal box = (0.0000000 -40.081500 0.0000000) to (9.4473001 40.081500 4.4535000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2485001 4.4535000 4.4535000 Created 108 atoms using lattice units in orthogonal box = (0.0000000 -40.081500 0.0000000) to (9.4473001 40.081500 4.4535000) create_atoms CPU = 0.001 seconds 108 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2485001 4.4535000 4.4535000 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -40.081500 0.0000000) to (9.4473001 40.081500 4.4535000) create_atoms CPU = 0.000 seconds 110 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 = 8.196997 ghost atom cutoff = 8.196997 binsize = 4.0984985, bins = 3 20 2 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 2 atoms, new total = 216 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/SM_682749584055_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 = 8.196997 ghost atom cutoff = 8.196997 binsize = 4.0984985, bins = 3 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.993 | 6.993 | 6.993 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1460.9869 0 -1460.9869 16484.376 36 0 -1477.4024 0 -1477.4024 13571.197 Loop time of 0.150098 on 1 procs for 36 steps with 216 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 = -1460.98685554109 -1477.40110176308 -1477.40244307955 Force two-norm initial, final = 21.990143 0.37471956 Force max component initial, final = 7.8869308 0.11733595 Final line search alpha, max atom move = 0.18245071 0.021408027 Iterations, force evaluations = 36 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14614 | 0.14614 | 0.14614 | 0.0 | 97.36 Neigh | 0.00095735 | 0.00095735 | 0.00095735 | 0.0 | 0.64 Comm | 0.0018535 | 0.0018535 | 0.0018535 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001152 | | | 0.77 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2970.00 ave 2970 max 2970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17526.0 ave 17526 max 17526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17526 Ave neighs/atom = 81.138889 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.993 | 6.993 | 6.993 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1477.4024 0 -1477.4024 13571.197 3372.742 43 0 -1477.5523 0 -1477.5523 -62.226825 3388.0839 Loop time of 0.0211727 on 1 procs for 7 steps with 216 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1477.40244307955 -1477.5522306213 -1477.55226835231 Force two-norm initial, final = 62.134772 0.51425858 Force max component initial, final = 59.250654 0.17006609 Final line search alpha, max atom move = 0.0014398739 0.00024487374 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0198 | 0.0198 | 0.0198 | 0.0 | 93.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023961 | 0.00023961 | 0.00023961 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001133 | | | 5.35 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2972.00 ave 2972 max 2972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17754.0 ave 17754 max 17754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17754 Ave neighs/atom = 82.194444 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 = 8.196997 ghost atom cutoff = 8.196997 binsize = 4.0984985, bins = 3 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.624 | 6.624 | 6.624 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1477.5523 0 -1477.5523 -62.226825 Loop time of 1.693e-06 on 1 procs for 0 steps with 216 atoms 118.1% 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 | | 1.693e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2981.00 ave 2981 max 2981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17680.0 ave 17680 max 17680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17680 Ave neighs/atom = 81.851852 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.624 | 6.624 | 6.624 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 -1477.5523 -1477.5523 9.4402644 80.636087 4.4508254 -62.226825 -62.226825 -80.361934 -77.737324 -28.581217 2.47 134.98706 Loop time of 1.781e-06 on 1 procs for 0 steps with 216 atoms 168.4% 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 | | 1.781e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2981.00 ave 2981 max 2981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17680.0 ave 17680 max 17680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35360.0 ave 35360 max 35360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35360 Ave neighs/atom = 163.70370 Neighbor list builds = 0 Dangerous builds = 0 216 -1477.55226835231 eV 2.46999995867648 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00