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_XuWangQian_2022_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -36.626000 0.0000000) to (25.896001 36.626000 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7546669 4.7473580 4.9836877 Created 440 atoms using lattice units in orthogonal box = (0.0000000 -36.626000 0.0000000) to (25.896001 36.626000 4.9836877) create_atoms CPU = 0.001 seconds 440 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7546669 4.7473580 4.9836877 Created 440 atoms using lattice units in orthogonal box = (0.0000000 -36.626000 0.0000000) to (25.896001 36.626000 4.9836877) create_atoms CPU = 0.001 seconds 440 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 17 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 16 atoms, new total = 864 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_559286646876_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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 17 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) = 7.691 | 7.691 | 7.691 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3769.3003 0 -3769.3003 36868.386 32 0 -3819.6794 0 -3819.6794 10417.948 Loop time of 0.963022 on 1 procs for 32 steps with 864 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3769.30031639079 -3819.67674689085 -3819.67941470637 Force two-norm initial, final = 82.036310 0.18043312 Force max component initial, final = 13.476301 0.014027146 Final line search alpha, max atom move = 1.0000000 0.014027146 Iterations, force evaluations = 32 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95431 | 0.95431 | 0.95431 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0050958 | 0.0050958 | 0.0050958 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003614 | | | 0.38 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7371.00 ave 7371 max 7371 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108024.0 ave 108024 max 108024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108024 Ave neighs/atom = 125.02778 Neighbor list builds = 0 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.691 | 7.691 | 7.691 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -3819.6794 0 -3819.6794 10417.948 9453.7261 35 0 -3819.7772 0 -3819.7772 2964.0207 9491.3074 Loop time of 0.0741981 on 1 procs for 3 steps with 864 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3819.67941470637 -3819.77718473558 -3819.77719839151 Force two-norm initial, final = 69.909155 0.20700274 Force max component initial, final = 50.381450 0.044381538 Final line search alpha, max atom move = 0.0018359764 8.1483458e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072907 | 0.072907 | 0.072907 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025951 | 0.00025951 | 0.00025951 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001032 | | | 1.39 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7326.00 ave 7326 max 7326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108640.0 ave 108640 max 108640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108640 Ave neighs/atom = 125.74074 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 17 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) = 7.322 | 7.322 | 7.322 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3819.7772 0 -3819.7772 2964.0207 Loop time of 1.957e-06 on 1 procs for 0 steps with 864 atoms 204.4% 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 | | 1.957e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7326.00 ave 7326 max 7326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108472.0 ave 108472 max 108472 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 = 108472 Ave neighs/atom = 125.54630 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) = 7.322 | 7.322 | 7.322 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 -3819.7772 -3819.7772 25.948405 73.252 4.9933946 2964.0207 2964.0207 -7.5069691 8905.4089 -5.839871 2.3598456 422.7693 Loop time of 1.88e-06 on 1 procs for 0 steps with 864 atoms 212.8% 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 | | 1.88e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7326.00 ave 7326 max 7326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108472.0 ave 108472 max 108472 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 216944.0 ave 216944 max 216944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216944 Ave neighs/atom = 251.09259 Neighbor list builds = 0 Dangerous builds = 0 864 -3819.77719839151 eV 2.35984555134927 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01