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 -36.702343 0.0000000) to (18.351172 36.702343 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3179227 4.3179227 3.1472000 Created 136 atoms using lattice units in orthogonal box = (0.0000000 -36.702343 0.0000000) to (18.351172 36.702343 3.1472000) create_atoms CPU = 0.002 seconds 136 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3179227 4.3179227 3.1472000 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -36.702343 0.0000000) to (18.351172 36.702343 3.1472000) create_atoms CPU = 0.001 seconds 138 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 = 6 24 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 = 274 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 = 6 24 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) = 4.401 | 4.401 | 4.401 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1620.437 0 -1620.437 142953.57 47 0 -1853.4077 0 -1853.4077 32781.353 Loop time of 0.278555 on 1 procs for 47 steps with 274 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 = -1620.43695125991 -1853.40585373894 -1853.40766731776 Force two-norm initial, final = 455.74270 0.15422950 Force max component initial, final = 222.02593 0.024103533 Final line search alpha, max atom move = 1.0000000 0.024103533 Iterations, force evaluations = 47 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27088 | 0.27088 | 0.27088 | 0.0 | 97.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043942 | 0.0043942 | 0.0043942 | 0.0 | 1.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003279 | | | 1.18 Nlocal: 274.000 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2406.00 ave 2406 max 2406 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: 16180.0 ave 16180 max 16180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16180 Ave neighs/atom = 59.051095 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 = 6 24 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.401 | 4.401 | 4.401 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1853.4077 0 -1853.4077 32781.353 4239.4735 62 0 -1854.4722 0 -1854.4722 156.99043 4283.9291 Loop time of 0.0597612 on 1 procs for 15 steps with 274 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 = -1853.40766731776 -1854.47164449536 -1854.47221997429 Force two-norm initial, final = 180.07804 2.5354640 Force max component initial, final = 167.72136 2.0575784 Final line search alpha, max atom move = 0.0014815679 0.0030484421 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05271 | 0.05271 | 0.05271 | 0.0 | 88.20 Neigh | 0.0031745 | 0.0031745 | 0.0031745 | 0.0 | 5.31 Comm | 0.00092018 | 0.00092018 | 0.00092018 | 0.0 | 1.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002957 | | | 4.95 Nlocal: 274.000 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2406.00 ave 2406 max 2406 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: 16004.0 ave 16004 max 16004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16004 Ave neighs/atom = 58.408759 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 6 24 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) = 4.539 | 4.539 | 4.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1854.4722 0 -1854.4722 156.99043 Loop time of 6.315e-06 on 1 procs for 0 steps with 274 atoms 190.0% 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 | | 6.315e-06 | | |100.00 Nlocal: 274.000 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2406.00 ave 2406 max 2406 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: 16008.0 ave 16008 max 16008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16008 Ave neighs/atom = 58.423358 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 = 6 24 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) = 4.539 | 4.539 | 4.539 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 -1854.4722 -1854.4722 18.308918 74.44859 3.1428462 156.99043 156.99043 767.75624 -258.00106 -38.783903 2.4360296 227.50942 Loop time of 7.237e-06 on 1 procs for 0 steps with 274 atoms 221.1% 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 | | 7.237e-06 | | |100.00 Nlocal: 274.000 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2406.00 ave 2406 max 2406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8004.00 ave 8004 max 8004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16008.0 ave 16008 max 16008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16008 Ave neighs/atom = 58.423358 Neighbor list builds = 0 Dangerous builds = 0 274 -1854.47221997429 eV 2.43602963354208 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