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 -40.487671 0.0000000) to (28.629106 40.487671 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0728408 5.5210460 4.9836877 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -40.487671 0.0000000) to (28.629106 40.487671 4.9836877) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0728408 5.5210460 4.9836877 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.487671 0.0000000) to (28.629106 40.487671 4.9836877) create_atoms CPU = 0.001 seconds 532 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 4 atoms, new total = 1056 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) = 7.760 | 7.760 | 7.760 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3930.4538 0 -3930.4538 174548.98 78 0 -4674.3481 0 -4674.3481 5920.3954 Loop time of 3.05747 on 1 procs for 78 steps with 1056 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 = -3930.45376805051 -4674.34442758504 -4674.34811606128 Force two-norm initial, final = 1132.1717 0.20088043 Force max component initial, final = 219.32425 0.018188435 Final line search alpha, max atom move = 1.0000000 0.018188435 Iterations, force evaluations = 78 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0174 | 3.0174 | 3.0174 | 0.0 | 98.69 Neigh | 0.014352 | 0.014352 | 0.014352 | 0.0 | 0.47 Comm | 0.015124 | 0.015124 | 0.015124 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01057 | | | 0.35 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8352.00 ave 8352 max 8352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134956.0 ave 134956 max 134956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134956 Ave neighs/atom = 127.79924 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.760 | 7.760 | 7.760 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -4674.3481 0 -4674.3481 5920.3954 11553.442 82 0 -4674.4616 0 -4674.4616 51.643832 11590.275 Loop time of 0.15766 on 1 procs for 4 steps with 1056 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 = -4674.34811606128 -4674.46150222291 -4674.46156445819 Force two-norm initial, final = 84.432594 0.89472046 Force max component initial, final = 72.709091 0.84325738 Final line search alpha, max atom move = 0.00071552844 0.00060337464 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15485 | 0.15485 | 0.15485 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049115 | 0.00049115 | 0.00049115 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002322 | | | 1.47 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8313.00 ave 8313 max 8313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135136.0 ave 135136 max 135136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135136 Ave neighs/atom = 127.96970 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) = 7.391 | 7.391 | 7.391 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4674.4616 0 -4674.4616 51.643832 Loop time of 2.419e-06 on 1 procs for 0 steps with 1056 atoms 165.4% 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 | | 2.419e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8313.00 ave 8313 max 8313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134448.0 ave 134448 max 134448 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 = 134448 Ave neighs/atom = 127.31818 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) = 7.391 | 7.391 | 7.391 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 -4674.4616 -4674.4616 28.70472 81.060374 4.9811751 51.643832 51.643832 14.463486 116.68972 23.77829 2.3286403 680.74885 Loop time of 2.282e-06 on 1 procs for 0 steps with 1056 atoms 262.9% 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 | | 2.282e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8313.00 ave 8313 max 8313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134448.0 ave 134448 max 134448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 268896.0 ave 268896 max 268896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268896 Ave neighs/atom = 254.63636 Neighbor list builds = 0 Dangerous builds = 0 1056 -4674.46156445819 eV 2.32864034632367 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03