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 -55.590635 0.0000000) to (32.095268 55.590635 5.4511103) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9377336 4.9889032 5.4511103 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -55.590635 0.0000000) to (32.095268 55.590635 5.4511103) create_atoms CPU = 0.002 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9377336 4.9889032 5.4511103 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -55.590635 0.0000000) to (32.095268 55.590635 5.4511103) create_atoms CPU = 0.002 seconds 626 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 = 11 36 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 1 atoms, new total = 1247 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 = 11 36 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7761.5519 0 -7761.5519 94923.776 84 0 -8460.3972 0 -8460.3972 3430.1408 Loop time of 0.850465 on 1 procs for 84 steps with 1247 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7761.55185314353 -8460.38930171535 -8460.39716920916 Force two-norm initial, final = 716.75658 0.44968718 Force max component initial, final = 147.15136 0.082358237 Final line search alpha, max atom move = 1.0000000 0.082358237 Iterations, force evaluations = 84 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82839 | 0.82839 | 0.82839 | 0.0 | 97.40 Neigh | 0.0061118 | 0.0061118 | 0.0061118 | 0.0 | 0.72 Comm | 0.007446 | 0.007446 | 0.007446 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008519 | | | 1.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5180.00 ave 5180 max 5180 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: 72956.0 ave 72956 max 72956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72956 Ave neighs/atom = 58.505213 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 = 11 36 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -8460.3972 0 -8460.3972 3430.1408 19451.702 87 0 -8460.4831 0 -8460.4831 141.50353 19475.062 Loop time of 0.0334127 on 1 procs for 3 steps with 1247 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8460.39716920916 -8460.48281186959 -8460.4830652756 Force two-norm initial, final = 94.054303 3.3358091 Force max component initial, final = 71.854947 2.8787279 Final line search alpha, max atom move = 0.00029839533 0.00085899898 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.03175 | 0.03175 | 0.03175 | 0.0 | 95.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025793 | 0.00025793 | 0.00025793 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001404 | | | 4.20 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188.00 ave 5188 max 5188 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: 72906.0 ave 72906 max 72906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72906 Ave neighs/atom = 58.465116 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 = 11 36 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) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8460.4831 0 -8460.4831 141.50353 Loop time of 1.898e-06 on 1 procs for 0 steps with 1247 atoms 158.1% 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 | | 1.898e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188.00 ave 5188 max 5188 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: 72880.0 ave 72880 max 72880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72880 Ave neighs/atom = 58.444266 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 = 11 36 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) = 4.777 | 4.777 | 4.777 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 -8460.4831 -8460.4831 32.058196 111.27809 5.4592139 141.50353 141.50353 101.70509 85.625931 237.17957 2.4855986 786.13683 Loop time of 2.17e-06 on 1 procs for 0 steps with 1247 atoms 230.4% 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 | | 2.17e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188.00 ave 5188 max 5188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36440.0 ave 36440 max 36440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72880.0 ave 72880 max 72880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72880 Ave neighs/atom = 58.444266 Neighbor list builds = 0 Dangerous builds = 0 1247 -8460.4830652756 eV 2.48559864493915 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