LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -47.959142 0) to (16.956117 47.959142 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2469905 5.0483307 5.5012908 Created 304 atoms using lattice units in orthogonal box = (0 -47.959142 0) to (16.956117 47.959142 5.5012908) create_atoms CPU = 0.000 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2469905 5.0483307 5.5012908 Created 306 atoms using lattice units in orthogonal box = (0 -47.959142 0) to (16.956117 47.959142 5.5012908) create_atoms CPU = 0.000 seconds 306 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 = 4 22 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 4 atoms, new total = 606 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:187) 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 = 4 22 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) = 7.187 | 7.187 | 7.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1826.3201 0 -1826.3201 154707.43 89 0 -2346.9723 0 -2346.9723 1735.5967 Loop time of 0.548539 on 1 procs for 89 steps with 606 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1826.32009009723 -2346.96998541372 -2346.97226232284 Force two-norm initial, final = 842.49652 0.18594481 Force max component initial, final = 205.90882 0.045422262 Final line search alpha, max atom move = 1 0.045422262 Iterations, force evaluations = 89 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54057 | 0.54057 | 0.54057 | 0.0 | 98.55 Neigh | 0.0029149 | 0.0029149 | 0.0029149 | 0.0 | 0.53 Comm | 0.0033773 | 0.0033773 | 0.0033773 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001678 | | | 0.31 Nlocal: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5616 ave 5616 max 5616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60202 ave 60202 max 60202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60202 Ave neighs/atom = 99.343234 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.188 | 7.188 | 7.188 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -2346.9723 0 -2346.9723 1735.5967 8947.3085 94 0 -2347.015 0 -2347.015 -32.13217 8955.1275 Loop time of 0.0266925 on 1 procs for 5 steps with 606 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2346.97226232283 -2347.01500951438 -2347.01502235123 Force two-norm initial, final = 24.93121 0.41343267 Force max component initial, final = 24.524628 0.24621871 Final line search alpha, max atom move = 0.0042077334 0.0010360227 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026019 | 0.026019 | 0.026019 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015523 | 0.00015523 | 0.00015523 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005178 | | | 1.94 Nlocal: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5646 ave 5646 max 5646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60208 ave 60208 max 60208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60208 Ave neighs/atom = 99.353135 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 = 4 22 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) = 6.819 | 6.819 | 6.819 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2347.015 0 -2347.015 -32.13217 Loop time of 6.61e-07 on 1 procs for 0 steps with 606 atoms 302.6% 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 | | 6.61e-07 | | |100.00 Nlocal: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5658 ave 5658 max 5658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60186 ave 60186 max 60186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60186 Ave neighs/atom = 99.316832 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.819 | 6.819 | 6.819 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 -2347.015 -2347.015 16.937124 96.274531 5.4918756 -32.13217 -32.13217 -17.931317 -44.215002 -34.250191 2.5390865 504.77747 Loop time of 4.81e-07 on 1 procs for 0 steps with 606 atoms 415.8% 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 | | 4.81e-07 | | |100.00 Nlocal: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5658 ave 5658 max 5658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60186 ave 60186 max 60186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120372 ave 120372 max 120372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120372 Ave neighs/atom = 198.63366 Neighbor list builds = 0 Dangerous builds = 0 606 -2347.01502235123 eV 2.5390865033569 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00