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 -47.936722 0.0000000) to (23.968361 47.936722 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1324760 4.1324760 3.1472000 Created 232 atoms using lattice units in orthogonal box = (0.0000000 -47.936722 0.0000000) to (23.968361 47.936722 3.1472000) create_atoms CPU = 0.002 seconds 232 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1324760 4.1324760 3.1472000 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -47.936722 0.0000000) to (23.968361 47.936722 3.1472000) create_atoms CPU = 0.001 seconds 234 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 31 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 = 466 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 31 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 -3004.8083 0 -3004.8083 105282.75 103 0 -3157.9439 0 -3157.9439 23002.556 Loop time of 1.15064 on 1 procs for 103 steps with 466 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 = -3004.80831497692 -3157.94093450063 -3157.94389199405 Force two-norm initial, final = 257.37749 0.25643869 Force max component initial, final = 84.647483 0.070933751 Final line search alpha, max atom move = 1.0000000 0.070933751 Iterations, force evaluations = 103 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1175 | 1.1175 | 1.1175 | 0.0 | 97.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017998 | 0.017998 | 0.017998 | 0.0 | 1.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01517 | | | 1.32 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3539.00 ave 3539 max 3539 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: 27332.0 ave 27332 max 27332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27332 Ave neighs/atom = 58.652361 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 = 8 31 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 : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -3157.9439 0 -3157.9439 23002.556 7232.043 113 0 -3158.7785 0 -3158.7785 -196.47648 7287.4424 Loop time of 0.0650256 on 1 procs for 10 steps with 466 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 = -3157.94389199405 -3158.77820930091 -3158.77850458786 Force two-norm initial, final = 213.00842 1.8394137 Force max component initial, final = 195.76499 0.95098282 Final line search alpha, max atom move = 0.00041493234 0.00039459353 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060933 | 0.060933 | 0.060933 | 0.0 | 93.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087014 | 0.00087014 | 0.00087014 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003223 | | | 4.96 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3332.00 ave 3332 max 3332 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: 27484.0 ave 27484 max 27484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27484 Ave neighs/atom = 58.978541 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 31 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) = 4.588 | 4.588 | 4.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3158.7785 0 -3158.7785 -196.47648 Loop time of 6.775e-06 on 1 procs for 0 steps with 466 atoms 236.2% 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 | | 6.775e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3351.00 ave 3351 max 3351 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: 27188.0 ave 27188 max 27188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27188 Ave neighs/atom = 58.343348 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 31 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) = 4.588 | 4.588 | 4.588 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 -3158.7785 -3158.7785 23.964222 96.753858 3.1429937 -196.47648 -196.47648 -209.04168 -177.59876 -202.78899 2.449983 284.37504 Loop time of 7.477e-06 on 1 procs for 0 steps with 466 atoms 227.4% 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 | | 7.477e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3351.00 ave 3351 max 3351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13594.0 ave 13594 max 13594 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27188.0 ave 27188 max 27188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27188 Ave neighs/atom = 58.343348 Neighbor list builds = 0 Dangerous builds = 0 466 -3158.77850458786 eV 2.44998295466952 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