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 -39.873026 0.0000000) to (6.1037460 39.873026 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1037460 4.9836877 5.7546669 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -39.873026 0.0000000) to (6.1037460 39.873026 8.6320004) create_atoms CPU = 0.001 seconds 198 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1037460 4.9836877 5.7546669 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -39.873026 0.0000000) to (6.1037460 39.873026 8.6320004) create_atoms CPU = 0.000 seconds 198 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 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 12 atoms, new total = 384 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 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) = 7.315 | 7.315 | 7.315 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1704.9588 0 -1704.9588 -164.24207 1 0 -1704.9596 0 -1704.9596 -165.2209 Loop time of 0.022693 on 1 procs for 1 steps with 384 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1704.95883032216 -1704.95883032216 -1704.95962643874 Force two-norm initial, final = 0.13647018 0.042133808 Force max component initial, final = 0.035080286 0.010973384 Final line search alpha, max atom move = 1.0000000 0.010973384 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022401 | 0.022401 | 0.022401 | 0.0 | 98.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015111 | 0.00015111 | 0.00015111 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001414 | | | 0.62 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5460.00 ave 5460 max 5460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47616.0 ave 47616 max 47616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47616 Ave neighs/atom = 124.00000 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 : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.315 | 7.315 | 7.315 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -1704.9596 0 -1704.9596 -165.2209 4201.6231 2 0 -1704.9596 0 -1704.9596 -80.666516 4201.4337 Loop time of 0.0314792 on 1 procs for 1 steps with 384 atoms 73.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1704.95962643874 -1704.95962643874 -1704.95963248883 Force two-norm initial, final = 0.37325322 0.051319641 Force max component initial, final = 0.28997780 0.024778863 Final line search alpha, max atom move = 0.0034485398 8.5450896e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030713 | 0.030713 | 0.030713 | 0.0 | 97.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013286 | 0.00013286 | 0.00013286 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006332 | | | 2.01 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5460.00 ave 5460 max 5460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47616.0 ave 47616 max 47616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47616 Ave neighs/atom = 124.00000 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 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) = 6.947 | 6.947 | 6.947 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1704.9596 0 -1704.9596 -80.666516 Loop time of 1.1468e-05 on 1 procs for 0 steps with 384 atoms 104.6% 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 | | 1.147e-05 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5460.00 ave 5460 max 5460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47616.0 ave 47616 max 47616 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 = 47616 Ave neighs/atom = 124.00000 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) = 6.947 | 6.947 | 6.947 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 -1704.9596 -1704.9596 6.103624 79.746052 8.6317839 -80.666516 -80.666516 9.4489931 -245.46564 -5.9829023 2.4917806 0.00023222517 Loop time of 2.473e-06 on 1 procs for 0 steps with 384 atoms 161.7% 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 | | 2.473e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5460.00 ave 5460 max 5460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47616.0 ave 47616 max 47616 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95232.0 ave 95232 max 95232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95232 Ave neighs/atom = 248.00000 Neighbor list builds = 0 Dangerous builds = 0 384 -1704.95963248883 eV 2.49178060960802 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00