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_MishinMehlPapaconstantopoulos_2005_Ni__SM_477692857359_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -39.824254 0.0000000) to (17.244408 39.824254 6.0968188) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7481359 4.9780317 6.0968188 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -39.824254 0.0000000) to (17.244408 39.824254 6.0968188) create_atoms CPU = 0.003 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7481359 4.9780317 6.0968188 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -39.824254 0.0000000) to (17.244408 39.824254 6.0968188) create_atoms CPU = 0.002 seconds 396 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXESXEsA/Ni.adp with DATE: 2011-06-20 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 = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 5 23 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 = 776 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_477692857359_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 = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 5 23 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) = 7.241 | 7.241 | 7.241 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3357.5036 0 -3357.5036 15512.932 44 0 -3432.7302 0 -3432.7302 27856.967 Loop time of 1.18478 on 1 procs for 44 steps with 776 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 = -3357.50363181018 -3432.72684497433 -3432.73021135567 Force two-norm initial, final = 34.191232 0.21112590 Force max component initial, final = 4.2836092 0.024372494 Final line search alpha, max atom move = 1.0000000 0.024372494 Iterations, force evaluations = 44 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1661 | 1.1661 | 1.1661 | 0.0 | 98.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0099862 | 0.0099862 | 0.0099862 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008714 | | | 0.74 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4778.00 ave 4778 max 4778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54952.0 ave 54952 max 54952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54952 Ave neighs/atom = 70.814433 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.241 | 7.241 | 7.241 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3432.7302 0 -3432.7302 27856.967 8373.9278 59 0 -3434.5876 0 -3434.5876 15.764433 8501.6949 Loop time of 0.257844 on 1 procs for 15 steps with 776 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 = -3432.73021135567 -3434.58498570929 -3434.58758893517 Force two-norm initial, final = 286.27497 0.79317749 Force max component initial, final = 255.23003 0.43047363 Final line search alpha, max atom move = 0.00017394849 7.4880237e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24177 | 0.24177 | 0.24177 | 0.0 | 93.77 Neigh | 0.0068573 | 0.0068573 | 0.0068573 | 0.0 | 2.66 Comm | 0.0021302 | 0.0021302 | 0.0021302 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007083 | | | 2.75 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4766.00 ave 4766 max 4766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54208.0 ave 54208 max 54208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54208 Ave neighs/atom = 69.855670 Neighbor list builds = 1 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 = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 5 23 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) = 6.872 | 6.872 | 6.872 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3434.5876 0 -3434.5876 15.764433 Loop time of 6.194e-06 on 1 procs for 0 steps with 776 atoms 177.6% 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 | | 6.194e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4766.00 ave 4766 max 4766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54200.0 ave 54200 max 54200 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 = 54200 Ave neighs/atom = 69.845361 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) = 6.872 | 6.872 | 6.872 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 -3434.5876 -3434.5876 17.253154 80.807785 6.0979495 15.764433 15.764433 -21.341992 -12.504135 81.139426 2.1445031 311.59107 Loop time of 8.089e-06 on 1 procs for 0 steps with 776 atoms 482.1% 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 | | 8.089e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4766.00 ave 4766 max 4766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54200.0 ave 54200 max 54200 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108400.0 ave 108400 max 108400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108400 Ave neighs/atom = 139.69072 Neighbor list builds = 0 Dangerous builds = 0 776 -3434.58758893517 eV 2.14450307796928 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01