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 -33.602900 0.0000000) to (19.400644 33.602900 5.4511103) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1054325 4.7161965 5.4511103 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -33.602900 0.0000000) to (19.400644 33.602900 5.4511103) create_atoms CPU = 0.001 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1054325 4.7161965 5.4511103 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -33.602900 0.0000000) to (19.400644 33.602900 5.4511103) create_atoms CPU = 0.000 seconds 230 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 = 7 22 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 kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 457 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 = 7 22 2 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) = 4.451 | 4.451 | 4.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2831.1307 0 -2831.1307 101486.81 72 0 -3091.6853 0 -3091.6853 19760.861 Loop time of 0.300206 on 1 procs for 72 steps with 457 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2831.13071735493 -3091.68249585869 -3091.68529515675 Force two-norm initial, final = 446.79941 0.23574676 Force max component initial, final = 164.02611 0.031717669 Final line search alpha, max atom move = 1.0000000 0.031717669 Iterations, force evaluations = 72 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29398 | 0.29398 | 0.29398 | 0.0 | 97.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0031302 | 0.0031302 | 0.0031302 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003093 | | | 1.03 Nlocal: 457.000 ave 457 max 457 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2496.00 ave 2496 max 2496 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: 26844.0 ave 26844 max 26844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26844 Ave neighs/atom = 58.739606 Neighbor list builds = 0 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 = 7 22 2 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 : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.451 | 4.451 | 4.451 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -3091.6853 0 -3091.6853 19760.861 7107.3526 79 0 -3092.1697 0 -3092.1697 -384.45343 7153.5556 Loop time of 0.0211025 on 1 procs for 7 steps with 457 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3091.68529515675 -3092.16883208253 -3092.16972677432 Force two-norm initial, final = 169.47061 3.7098943 Force max component initial, final = 143.01439 3.3280871 Final line search alpha, max atom move = 0.00017748097 0.00059067211 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019897 | 0.019897 | 0.019897 | 0.0 | 94.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002054 | 0.0002054 | 0.0002054 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001 | | | 4.74 Nlocal: 457.000 ave 457 max 457 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2462.00 ave 2462 max 2462 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: 27074.0 ave 27074 max 27074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27074 Ave neighs/atom = 59.242888 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 = 7 22 2 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) = 4.589 | 4.589 | 4.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3092.1697 0 -3092.1697 -384.45343 Loop time of 1.826e-06 on 1 procs for 0 steps with 457 atoms 164.3% 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 | | 1.826e-06 | | |100.00 Nlocal: 457.000 ave 457 max 457 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2454.00 ave 2454 max 2454 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: 26852.0 ave 26852 max 26852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26852 Ave neighs/atom = 58.757112 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 = 7 22 2 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) = 4.589 | 4.589 | 4.589 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 -3092.1697 -3092.1697 19.368811 67.608536 5.4628272 -384.45343 -384.45343 -744.16614 -90.962005 -318.23215 2.4206987 411.97317 Loop time of 2.163e-06 on 1 procs for 0 steps with 457 atoms 184.9% 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 | | 2.163e-06 | | |100.00 Nlocal: 457.000 ave 457 max 457 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2454.00 ave 2454 max 2454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13426.0 ave 13426 max 13426 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26852.0 ave 26852 max 26852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26852 Ave neighs/atom = 58.757112 Neighbor list builds = 0 Dangerous builds = 0 457 -3092.16972677432 eV 2.42069868914372 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42