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 -73.396374 0) to (36.698187 73.396374 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3604094 5.3604094 3.8900001 Created 712 atoms using lattice units in orthogonal box = (0 -73.396374 0) to (36.698187 73.396374 3.8900001) create_atoms CPU = 0.000 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3604094 5.3604094 3.8900001 Created 714 atoms using lattice units in orthogonal box = (0 -73.396374 0) to (36.698187 73.396374 3.8900001) create_atoms CPU = 0.000 seconds 714 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 = 9 33 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 0 atoms, new total = 1426 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 = 9 33 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) = 7.9 | 7.9 | 7.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5020.6825 0 -5020.6825 91431.802 38 0 -5529.0809 0 -5529.0809 9860.824 Loop time of 0.487506 on 1 procs for 38 steps with 1426 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 = -5020.68252582203 -5529.07547629689 -5529.08089669715 Force two-norm initial, final = 749.19885 0.29534947 Force max component initial, final = 283.9429 0.070143217 Final line search alpha, max atom move = 1 0.070143217 Iterations, force evaluations = 38 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47966 | 0.47966 | 0.47966 | 0.0 | 98.39 Neigh | 0.0031537 | 0.0031537 | 0.0031537 | 0.0 | 0.65 Comm | 0.0030826 | 0.0030826 | 0.0030826 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001609 | | | 0.33 Nlocal: 1426 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12794 ave 12794 max 12794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142034 ave 142034 max 142034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142034 Ave neighs/atom = 99.603086 Neighbor list builds = 1 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.9 | 7.9 | 7.9 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -5529.0809 0 -5529.0809 9860.824 20955.538 44 0 -5529.5937 0 -5529.5937 -162.84759 21060.089 Loop time of 0.0596512 on 1 procs for 6 steps with 1426 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 = -5529.08089669715 -5529.59296684451 -5529.59373791482 Force two-norm initial, final = 238.87132 5.5428687 Force max component initial, final = 193.11911 4.3514624 Final line search alpha, max atom move = 0.00011801976 0.00051355857 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.058091 | 0.058091 | 0.058091 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035756 | 0.00035756 | 0.00035756 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001202 | | | 2.02 Nlocal: 1426 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12794 ave 12794 max 12794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142012 ave 142012 max 142012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142012 Ave neighs/atom = 99.587658 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 = 9 34 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) = 7.532 | 7.532 | 7.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5529.5937 0 -5529.5937 -162.84759 Loop time of 5.71e-07 on 1 procs for 0 steps with 1426 atoms 350.3% 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 | | 5.71e-07 | | |100.00 Nlocal: 1426 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12794 ave 12794 max 12794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141950 ave 141950 max 141950 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 = 141950 Ave neighs/atom = 99.54418 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) = 7.532 | 7.532 | 7.532 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 -5529.5937 -5529.5937 36.654953 147.55207 3.8938771 -162.84759 -162.84759 -244.13365 86.964572 -331.37369 2.5000254 472.57452 Loop time of 5.11e-07 on 1 procs for 0 steps with 1426 atoms 195.7% 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 | | 5.11e-07 | | |100.00 Nlocal: 1426 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12794 ave 12794 max 12794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141950 ave 141950 max 141950 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 283900 ave 283900 max 283900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283900 Ave neighs/atom = 199.08836 Neighbor list builds = 0 Dangerous builds = 0 1426 -5529.59373791481 eV 2.50002544338461 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00