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 -43.160002 0.0000000) to (6.1037460 43.160002 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1037460 5.7546669 4.9836877 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -43.160002 0.0000000) to (6.1037460 43.160002 4.9836877) create_atoms CPU = 0.001 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1037460 5.7546669 4.9836877 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.160002 0.0000000) to (6.1037460 43.160002 4.9836877) create_atoms CPU = 0.001 seconds 122 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 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 = 240 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 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) = 7.124 | 7.124 | 7.124 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1020.4257 0 -1020.4257 94475.961 140 0 -1062.1901 0 -1062.1901 6099.2159 Loop time of 1.45818 on 1 procs for 140 steps with 240 atoms 96.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1020.42573219212 -1062.18911101065 -1062.19006054869 Force two-norm initial, final = 153.54981 0.10934758 Force max component initial, final = 55.635249 0.024034970 Final line search alpha, max atom move = 1.0000000 0.024034970 Iterations, force evaluations = 140 273 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4242 | 1.4242 | 1.4242 | 0.0 | 97.67 Neigh | 0.0017115 | 0.0017115 | 0.0017115 | 0.0 | 0.12 Comm | 0.013438 | 0.013438 | 0.013438 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01885 | | | 1.29 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5081.00 ave 5081 max 5081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30488.0 ave 30488 max 30488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30488 Ave neighs/atom = 127.03333 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 : 140 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.124 | 7.124 | 7.124 Mbytes Step Temp E_pair E_mol TotEng Press Volume 140 0 -1062.1901 0 -1062.1901 6099.2159 2625.7824 143 0 -1062.2116 0 -1062.2116 157.89256 2634.2366 Loop time of 0.0260751 on 1 procs for 3 steps with 240 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 = -1062.19006054869 -1062.21098637321 -1062.21160342909 Force two-norm initial, final = 18.528836 0.48725063 Force max component initial, final = 15.382480 0.37838228 Final line search alpha, max atom move = 0.00065402601 0.00024747186 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.025159 | 0.025159 | 0.025159 | 0.0 | 96.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018814 | 0.00018814 | 0.00018814 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007275 | | | 2.79 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4953.00 ave 4953 max 4953 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30442.0 ave 30442 max 30442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30442 Ave neighs/atom = 126.84167 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 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) = 6.753 | 6.753 | 6.753 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1062.2116 0 -1062.2116 157.89256 Loop time of 2.02e-06 on 1 procs for 0 steps with 240 atoms 198.0% 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 | | 2.02e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4935.00 ave 4935 max 4935 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30400.0 ave 30400 max 30400 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 = 30400 Ave neighs/atom = 126.66667 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) = 6.753 | 6.753 | 6.753 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 -1062.2116 -1062.2116 6.1178168 86.364049 4.9856905 157.89256 157.89256 230.66749 139.73533 103.27487 2.3702142 154.44209 Loop time of 2.15e-06 on 1 procs for 0 steps with 240 atoms 232.6% 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 | | 2.15e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4935.00 ave 4935 max 4935 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30400.0 ave 30400 max 30400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60800.0 ave 60800 max 60800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60800 Ave neighs/atom = 253.33333 Neighbor list builds = 0 Dangerous builds = 0 240 -1062.21160342909 eV 2.37021421735263 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01