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 -54.511103 0.0000000) to (22.254064 54.511103 7.7090341) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3409755 4.7242956 5.1393560 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -54.511103 0.0000000) to (22.254064 54.511103 7.7090341) create_atoms CPU = 0.004 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3409755 4.7242956 5.1393560 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -54.511103 0.0000000) to (22.254064 54.511103 7.7090341) create_atoms CPU = 0.003 seconds 602 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 = 8 35 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 0 atoms, new total = 1202 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 = 8 35 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7766.8758 0 -7766.8758 78864.575 64 0 -8153.0462 0 -8153.0462 11374.864 Loop time of 1.4319 on 1 procs for 64 steps with 1202 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 = -7766.87575762867 -8153.03884445535 -8153.04621880162 Force two-norm initial, final = 480.33312 0.40422387 Force max component initial, final = 113.16022 0.065813065 Final line search alpha, max atom move = 1.0000000 0.065813065 Iterations, force evaluations = 64 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3887 | 1.3887 | 1.3887 | 0.0 | 96.99 Neigh | 0.014353 | 0.014353 | 0.014353 | 0.0 | 1.00 Comm | 0.012431 | 0.012431 | 0.012431 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01638 | | | 1.14 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4086.00 ave 4086 max 4086 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: 70428.0 ave 70428 max 70428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70428 Ave neighs/atom = 58.592346 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 = 8 35 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -8153.0462 0 -8153.0462 11374.864 18703.56 70 0 -8153.602 0 -8153.602 -6.5903014 18775.826 Loop time of 0.105488 on 1 procs for 6 steps with 1202 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 = -8153.04621880162 -8153.60174924236 -8153.60196732821 Force two-norm initial, final = 269.56794 0.75998964 Force max component initial, final = 245.02919 0.14526470 Final line search alpha, max atom move = 0.00019088694 2.7729134e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1009 | 0.1009 | 0.1009 | 0.0 | 95.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081034 | 0.00081034 | 0.00081034 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003777 | | | 3.58 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4357.00 ave 4357 max 4357 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: 70260.0 ave 70260 max 70260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70260 Ave neighs/atom = 58.452579 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 = 8 36 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) = 4.712 | 4.712 | 4.712 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8153.602 0 -8153.602 -6.5903014 Loop time of 7.267e-06 on 1 procs for 0 steps with 1202 atoms 178.9% 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 | | 7.267e-06 | | |100.00 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4357.00 ave 4357 max 4357 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: 70196.0 ave 70196 max 70196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70196 Ave neighs/atom = 58.399334 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 = 8 36 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) = 4.712 | 4.712 | 4.712 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 -8153.602 -8153.602 22.258922 109.53945 7.7005971 -6.5903014 -6.5903014 -11.880473 -2.4588353 -5.4315963 2.4506981 917.46538 Loop time of 7.217e-06 on 1 procs for 0 steps with 1202 atoms 235.6% 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 | | 7.217e-06 | | |100.00 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4357.00 ave 4357 max 4357 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35098.0 ave 35098 max 35098 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70196.0 ave 70196 max 70196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70196 Ave neighs/atom = 58.399334 Neighbor list builds = 0 Dangerous builds = 0 1202 -8153.60196732821 eV 2.45069814442096 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42