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 -35.941407 0.0000000) to (17.968942 35.941407 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1466788 4.1466788 3.5239994 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -35.941407 0.0000000) to (17.968942 35.941407 3.5239994) create_atoms CPU = 0.002 seconds 210 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1466788 4.1466788 3.5239994 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -35.941407 0.0000000) to (17.968942 35.941407 3.5239994) create_atoms CPU = 0.001 seconds 210 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 17 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 8 atoms, new total = 412 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 17 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) = 7.115 | 7.115 | 7.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1804.7268 0 -1804.7268 17342.911 34 0 -1819.5729 0 -1819.5729 -4579.5285 Loop time of 1.08254 on 1 procs for 34 steps with 412 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1804.72678617106 -1819.57153437743 -1819.57290605752 Force two-norm initial, final = 43.123452 0.12865824 Force max component initial, final = 12.289743 0.018048004 Final line search alpha, max atom move = 1.0000000 0.018048004 Iterations, force evaluations = 34 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0681 | 1.0681 | 1.0681 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0090719 | 0.0090719 | 0.0090719 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005404 | | | 0.50 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6240.00 ave 6240 max 6240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51028.0 ave 51028 max 51028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51028 Ave neighs/atom = 123.85437 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.115 | 7.115 | 7.115 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -1819.5729 0 -1819.5729 -4579.5285 4551.8024 36 0 -1819.5849 0 -1819.5849 -781.59713 4542.3644 Loop time of 0.0687045 on 1 procs for 2 steps with 412 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1819.57290605752 -1819.58459180453 -1819.5849225099 Force two-norm initial, final = 16.508578 1.1595695 Force max component initial, final = 13.096541 1.1456701 Final line search alpha, max atom move = 0.00042708326 0.00048929654 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066802 | 0.066802 | 0.066802 | 0.0 | 97.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050039 | 0.00050039 | 0.00050039 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001402 | | | 2.04 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6180.00 ave 6180 max 6180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51558.0 ave 51558 max 51558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51558 Ave neighs/atom = 125.14078 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 17 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) = 6.746 | 6.746 | 6.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1819.5849 0 -1819.5849 -781.59713 Loop time of 6.515e-06 on 1 procs for 0 steps with 412 atoms 168.8% 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 | | 6.515e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6180.00 ave 6180 max 6180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51618.0 ave 51618 max 51618 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 = 51618 Ave neighs/atom = 125.28641 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) = 6.746 | 6.746 | 6.746 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 -1819.5849 -1819.5849 17.945979 71.882815 3.5211922 -781.59713 -781.59713 -41.357081 -2707.2116 403.77729 2.3066163 190.90988 Loop time of 7.557e-06 on 1 procs for 0 steps with 412 atoms 251.4% 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 | | 7.557e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6180.00 ave 6180 max 6180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51618.0 ave 51618 max 51618 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103236.0 ave 103236 max 103236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103236 Ave neighs/atom = 250.57282 Neighbor list builds = 0 Dangerous builds = 0 412 -1819.5849225099 eV 2.30661630214056 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01