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 -57.171091 0) to (20.213033 57.171091 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.240416 6.3523435 5.5012908 Created 432 atoms using lattice units in orthogonal box = (0 -57.171091 0) to (20.213033 57.171091 5.5012908) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.240416 6.3523435 5.5012908 Created 434 atoms using lattice units in orthogonal box = (0 -57.171091 0) to (20.213033 57.171091 5.5012908) create_atoms CPU = 0.000 seconds 434 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 = 866 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 = 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) = 7.314 | 7.314 | 7.314 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2875.0353 0 -2875.0353 127782.47 83 0 -3355.0124 0 -3355.0124 13722.631 Loop time of 0.728348 on 1 procs for 83 steps with 866 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 = -2875.03528894445 -3355.00912546552 -3355.01241192421 Force two-norm initial, final = 767.88112 0.22852648 Force max component initial, final = 278.92625 0.047261891 Final line search alpha, max atom move = 1 0.047261891 Iterations, force evaluations = 83 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7199 | 0.7199 | 0.7199 | 0.0 | 98.84 Neigh | 0.0021543 | 0.0021543 | 0.0021543 | 0.0 | 0.30 Comm | 0.0041324 | 0.0041324 | 0.0041324 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002166 | | | 0.30 Nlocal: 866 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7137 ave 7137 max 7137 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86246 ave 86246 max 86246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86246 Ave neighs/atom = 99.591224 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.314 | 7.314 | 7.314 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -3355.0124 0 -3355.0124 13722.631 12714.596 90 0 -3355.5293 0 -3355.5293 -106.84551 12801.619 Loop time of 0.0416973 on 1 procs for 7 steps with 866 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 = -3355.01241192421 -3355.52872923865 -3355.52926787429 Force two-norm initial, final = 198.13045 2.8185067 Force max component initial, final = 156.07244 2.4638552 Final line search alpha, max atom move = 0.00017701661 0.00043614328 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040724 | 0.040724 | 0.040724 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021073 | 0.00021073 | 0.00021073 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007621 | | | 1.83 Nlocal: 866 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6943 ave 6943 max 6943 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86234 ave 86234 max 86234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86234 Ave neighs/atom = 99.577367 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 = 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) = 6.944 | 6.944 | 6.944 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3355.5293 0 -3355.5293 -106.84551 Loop time of 6.21e-07 on 1 procs for 0 steps with 866 atoms 161.0% 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 | | 6.21e-07 | | |100.00 Nlocal: 866 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6956 ave 6956 max 6956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86164 ave 86164 max 86164 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 = 86164 Ave neighs/atom = 99.496536 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) = 6.944 | 6.944 | 6.944 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 -3355.5293 -3355.5293 20.237678 115.04583 5.4983619 -106.84551 -106.84551 -308.73782 110.27904 -122.07774 2.5481583 559.55899 Loop time of 6.71e-07 on 1 procs for 0 steps with 866 atoms 298.1% 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 | | 6.71e-07 | | |100.00 Nlocal: 866 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6956 ave 6956 max 6956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86164 ave 86164 max 86164 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 172328 ave 172328 max 172328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172328 Ave neighs/atom = 198.99307 Neighbor list builds = 0 Dangerous builds = 0 866 -3355.52926787429 eV 2.54815829103671 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00