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 -39.399511 0.0000000) to (7.8799022 39.399511 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7279413 4.7279413 3.5239994 Created 100 atoms using lattice units in orthogonal box = (0.0000000 -39.399511 0.0000000) to (7.8799022 39.399511 3.5239994) create_atoms CPU = 0.001 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7279413 4.7279413 3.5239994 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.399511 0.0000000) to (7.8799022 39.399511 3.5239994) create_atoms CPU = 0.000 seconds 102 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 = 2 18 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 2 atoms, new total = 200 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 = 2 18 1 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) = 7.048 | 7.048 | 7.048 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -832.90388 0 -832.90388 115333.17 16 0 -883.36399 0 -883.36399 13676.947 Loop time of 0.111193 on 1 procs for 16 steps with 200 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 = -832.903884384345 -883.363471850541 -883.36399428724 Force two-norm initial, final = 215.18180 0.073253008 Force max component initial, final = 76.076538 0.015140854 Final line search alpha, max atom move = 1.0000000 0.015140854 Iterations, force evaluations = 16 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1096 | 0.1096 | 0.1096 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010929 | 0.0010929 | 0.0010929 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004999 | | | 0.45 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5071.00 ave 5071 max 5071 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24992.0 ave 24992 max 24992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24992 Ave neighs/atom = 124.96000 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 : 16 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.048 | 7.048 | 7.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 16 0 -883.36399 0 -883.36399 13676.947 2188.152 27 0 -883.52709 0 -883.52709 194.8163 2204.0106 Loop time of 0.0523763 on 1 procs for 11 steps with 200 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 = -883.36399428724 -883.527016288696 -883.52709342247 Force two-norm initial, final = 39.467064 0.60338667 Force max component initial, final = 36.721762 0.36870081 Final line search alpha, max atom move = 0.0017886991 0.00065949481 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.050096 | 0.050096 | 0.050096 | 0.0 | 95.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048103 | 0.00048103 | 0.00048103 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001799 | | | 3.43 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5071.00 ave 5071 max 5071 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25072.0 ave 25072 max 25072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25072 Ave neighs/atom = 125.36000 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 = 2 18 1 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) = 6.680 | 6.680 | 6.680 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -883.52709 0 -883.52709 194.8163 Loop time of 2.207e-06 on 1 procs for 0 steps with 200 atoms 135.9% 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 | | 2.207e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5071.00 ave 5071 max 5071 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24920.0 ave 24920 max 24920 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 = 24920 Ave neighs/atom = 124.60000 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) = 6.680 | 6.680 | 6.680 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 -883.52709 -883.52709 7.8715347 79.558363 3.5193984 194.8163 194.8163 267.73759 96.835741 219.87555 2.2546432 117.98209 Loop time of 1.977e-06 on 1 procs for 0 steps with 200 atoms 151.7% 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 | | 1.977e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5071.00 ave 5071 max 5071 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24920.0 ave 24920 max 24920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49840.0 ave 49840 max 49840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49840 Ave neighs/atom = 249.20000 Neighbor list builds = 0 Dangerous builds = 0 200 -883.52709342247 eV 2.25464318932725 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00