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 -57.258213 0.0000000) to (20.243835 57.258213 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5210460 4.3377434 4.9836877 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.258213 0.0000000) to (20.243835 57.258213 4.9836877) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5210460 4.3377434 4.9836877 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.258213 0.0000000) to (20.243835 57.258213 4.9836877) create_atoms CPU = 0.001 seconds 530 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 = 5 26 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 0 atoms, new total = 1058 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 = 5 26 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) = 7.817 | 7.817 | 7.817 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4388.9446 0 -4388.9446 113676.26 77 0 -4684.4214 0 -4684.4214 9145.8768 Loop time of 2.89107 on 1 procs for 77 steps with 1058 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4388.94462844685 -4684.41684735151 -4684.42144032539 Force two-norm initial, final = 493.69568 0.24503786 Force max component initial, final = 133.46534 0.030040902 Final line search alpha, max atom move = 1.0000000 0.030040902 Iterations, force evaluations = 77 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8538 | 2.8538 | 2.8538 | 0.0 | 98.71 Neigh | 0.0083191 | 0.0083191 | 0.0083191 | 0.0 | 0.29 Comm | 0.017641 | 0.017641 | 0.017641 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01128 | | | 0.39 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9769.00 ave 9769 max 9769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133768.0 ave 133768 max 133768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133768 Ave neighs/atom = 126.43478 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 : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.817 | 7.817 | 7.817 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -4684.4214 0 -4684.4214 9145.8768 11553.442 83 0 -4684.6811 0 -4684.6811 -282.24715 11612.281 Loop time of 0.172875 on 1 procs for 6 steps with 1058 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 = -4684.42144032539 -4684.68027453785 -4684.68110181628 Force two-norm initial, final = 121.72878 4.3463458 Force max component initial, final = 98.905939 3.0840324 Final line search alpha, max atom move = 0.00017944348 0.00055340950 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1692 | 0.1692 | 0.1692 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064527 | 0.00064527 | 0.00064527 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00303 | | | 1.75 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9831.00 ave 9831 max 9831 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134144.0 ave 134144 max 134144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134144 Ave neighs/atom = 126.79017 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 = 5 26 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) = 7.449 | 7.449 | 7.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4684.6811 0 -4684.6811 -282.24715 Loop time of 2.506e-06 on 1 procs for 0 steps with 1058 atoms 199.5% 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 | | 2.506e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9831.00 ave 9831 max 9831 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133440.0 ave 133440 max 133440 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 = 133440 Ave neighs/atom = 126.12476 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) = 7.449 | 7.449 | 7.449 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 -4684.6811 -4684.6811 20.233017 115.12284 4.9853469 -282.24715 -282.24715 -419.87424 -1.2136056 -425.65361 2.341099 533.8916 Loop time of 2.479e-06 on 1 procs for 0 steps with 1058 atoms 322.7% 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 | | 2.479e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9831.00 ave 9831 max 9831 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133440.0 ave 133440 max 133440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 266880.0 ave 266880 max 266880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266880 Ave neighs/atom = 252.24953 Neighbor list builds = 0 Dangerous builds = 0 1058 -4684.68110181628 eV 2.34109895599626 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03