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 Lattice spacing in x,y,z = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -49.562155 0.0000000) to (30.350497 49.562155 7.7090341) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8952415 4.7963376 5.1393560 Created 742 atoms using lattice units in orthogonal box = (0.0000000 -49.562155 0.0000000) to (30.350497 49.562155 7.7090341) create_atoms CPU = 0.005 seconds 742 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8952415 4.7963376 5.1393560 Created 748 atoms using lattice units in orthogonal box = (0.0000000 -49.562155 0.0000000) to (30.350497 49.562155 7.7090341) create_atoms CPU = 0.004 seconds 748 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 32 3 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 kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1488 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/MO_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.636 | 4.636 | 4.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8197.0825 0 -8197.0825 110776.58 98 0 -10091.284 0 -10091.284 4471.3058 Loop time of 2.65805 on 1 procs for 98 steps with 1488 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 = -8197.08247917336 -10091.275636916 -10091.2838693286 Force two-norm initial, final = 1433.8334 0.41020537 Force max component initial, final = 248.85905 0.056579961 Final line search alpha, max atom move = 1.0000000 0.056579961 Iterations, force evaluations = 98 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5904 | 2.5904 | 2.5904 | 0.0 | 97.46 Neigh | 0.017411 | 0.017411 | 0.017411 | 0.0 | 0.66 Comm | 0.020807 | 0.020807 | 0.020807 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02941 | | | 1.11 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4801.00 ave 4801 max 4801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87168.0 ave 87168 max 87168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87168 Ave neighs/atom = 58.580645 Neighbor list builds = 1 Dangerous builds = 0 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.636 | 4.636 | 4.636 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -10091.284 0 -10091.284 4471.3058 23192.414 104 0 -10092.054 0 -10092.054 -75.032114 23227.092 Loop time of 0.112994 on 1 procs for 6 steps with 1488 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 = -10091.2838693286 -10092.0535364084 -10092.0541660906 Force two-norm initial, final = 273.31909 2.1124590 Force max component initial, final = 261.51669 1.2050214 Final line search alpha, max atom move = 0.00015735024 0.00018961041 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10825 | 0.10825 | 0.10825 | 0.0 | 95.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088425 | 0.00088425 | 0.00088425 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003862 | | | 3.42 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4808.00 ave 4808 max 4808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87094.0 ave 87094 max 87094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87094 Ave neighs/atom = 58.530914 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/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 attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10092.054 0 -10092.054 -75.032114 Loop time of 5.983e-06 on 1 procs for 0 steps with 1488 atoms 183.9% 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 | | 5.983e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4808.00 ave 4808 max 4808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87038.0 ave 87038 max 87038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87038 Ave neighs/atom = 58.493280 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/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 attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 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 -10092.054 -10092.054 30.263325 99.634891 7.7031215 -75.032114 -75.032114 -76.557361 -65.481825 -83.057157 2.4161226 1216.3016 Loop time of 6.886e-06 on 1 procs for 0 steps with 1488 atoms 275.9% 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 | | 6.886e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4808.00 ave 4808 max 4808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43519.0 ave 43519 max 43519 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87038.0 ave 87038 max 87038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87038 Ave neighs/atom = 58.493280 Neighbor list builds = 0 Dangerous builds = 0 1488 -10092.0541660906 eV 2.41612261106562 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42