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 -40.796766 0.0000000) to (28.845178 40.796766 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5968256 6.0885436 4.9836877 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -40.796766 0.0000000) to (28.845178 40.796766 4.9836877) create_atoms CPU = 0.001 seconds 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5968256 6.0885436 4.9836877 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -40.796766 0.0000000) to (28.845178 40.796766 4.9836877) create_atoms CPU = 0.001 seconds 538 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 = 7 19 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 = 1064 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 = 7 19 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) = 7.773 | 7.773 | 7.773 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4681.6693 0 -4681.6693 10901.669 65 0 -4712.7929 0 -4712.7929 -9188.2955 Loop time of 2.18093 on 1 procs for 65 steps with 1064 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4681.66933536555 -4712.78850222956 -4712.79287936967 Force two-norm initial, final = 56.824535 0.23196297 Force max component initial, final = 17.756475 0.045765635 Final line search alpha, max atom move = 1.0000000 0.045765635 Iterations, force evaluations = 65 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1516 | 2.1516 | 2.1516 | 0.0 | 98.66 Neigh | 0.012855 | 0.012855 | 0.012855 | 0.0 | 0.59 Comm | 0.009845 | 0.009845 | 0.009845 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006612 | | | 0.30 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8960.00 ave 8960 max 8960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134460.0 ave 134460 max 134460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134460 Ave neighs/atom = 126.37218 Neighbor list builds = 2 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.773 | 7.773 | 7.773 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -4712.7929 0 -4712.7929 -9188.2955 11729.508 71 0 -4713.032 0 -4713.032 -1162.0474 11677.307 Loop time of 0.168295 on 1 procs for 6 steps with 1064 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4712.79287936966 -4713.03191883248 -4713.03201466317 Force two-norm initial, final = 111.53324 0.27571656 Force max component initial, final = 104.70876 0.045053620 Final line search alpha, max atom move = 0.00044741650 2.0157733e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16535 | 0.16535 | 0.16535 | 0.0 | 98.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056383 | 0.00056383 | 0.00056383 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002378 | | | 1.41 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8885.00 ave 8885 max 8885 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134714.0 ave 134714 max 134714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134714 Ave neighs/atom = 126.61090 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 = 7 19 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) = 7.404 | 7.404 | 7.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4713.032 0 -4713.032 -1162.0474 Loop time of 1.873e-06 on 1 procs for 0 steps with 1064 atoms 160.2% 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 | | 1.873e-06 | | |100.00 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8914.00 ave 8914 max 8914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135496.0 ave 135496 max 135496 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 = 135496 Ave neighs/atom = 127.34586 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) = 7.404 | 7.404 | 7.404 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 -4713.032 -4713.032 28.712567 81.593532 4.9844235 -1162.0474 -1162.0474 4.3593236 -3487.9463 -2.5551237 2.3197097 554.47951 Loop time of 1.832e-06 on 1 procs for 0 steps with 1064 atoms 218.3% 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 | | 1.832e-06 | | |100.00 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8914.00 ave 8914 max 8914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135496.0 ave 135496 max 135496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270992.0 ave 270992 max 270992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270992 Ave neighs/atom = 254.69173 Neighbor list builds = 0 Dangerous builds = 0 1064 -4713.03201466317 eV 2.31970968680354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02