LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 41.52215799566417*${_u_distance} variable xmax_converted equal 41.52215799566417*1 variable ymin_converted equal -41.52619098416775*${_u_distance} variable ymin_converted equal -41.52619098416775*1 variable ymax_converted equal 41.52619098416775*${_u_distance} variable ymax_converted equal 41.52619098416775*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032988503575325*${_u_distance} variable zmax_converted equal 4.032988503575325*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03298850357533 Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 41.5221579956642 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 41.5221579956642 -41.5261909841677 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 41.5221579956642 -41.5261909841677 41.5261909841677 ${zmin_converted} ${zmax_converted} units box region whole block 0 41.5221579956642 -41.5261909841677 41.5261909841677 0 ${zmax_converted} units box region whole block 0 41.5221579956642 -41.5261909841677 41.5261909841677 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -41.5262 0) to (41.5222 41.5262 4.03299) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 41.5261909841677 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -5 0 orient y 5 9 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 9 -5 0 orient y 5 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48406 5.48406 4.03299 create_atoms 1 region upper Created 426 atoms create_atoms CPU = 0.000203133 secs group upper type 1 426 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.63303356344415 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -41.5261909841677 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 5 0 orient y -5 9 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 9 5 0 orient y -5 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48406 5.48406 4.03299 create_atoms 2 region lower Created 426 atoms create_atoms CPU = 8.29697e-05 secs group lower type 2 426 atoms in group lower displace_atoms lower move -4.63303356344415 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) pair_coeff * * Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*4.03298850357533 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01649425178767 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 7 13 1 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 834 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 7 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.633 | 6.633 | 6.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2378.7428 0 -2378.7428 2763.6704 476 0 -2416.2586 0 -2416.2586 -7989.0404 Loop time of 10.097 on 1 procs for 476 steps with 834 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 = -2378.74279397 -2416.25859378 -2416.25859378 Force two-norm initial, final = 29.9532 1.1427e-05 Force max component initial, final = 6.85297 1.52139e-06 Final line search alpha, max atom move = 1 1.52139e-06 Iterations, force evaluations = 476 925 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.9983 | 9.9983 | 9.9983 | 0.0 | 99.02 Neigh | 0.023385 | 0.023385 | 0.023385 | 0.0 | 0.23 Comm | 0.058428 | 0.058428 | 0.058428 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01691 | | | 0.17 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13910 ave 13910 max 13910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 546552 ave 546552 max 546552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 546552 Ave neighs/atom = 655.338 Neighbor list builds = 3 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 6.633 | 6.633 | 6.633 Mbytes Step Temp E_pair E_mol TotEng Press Volume 476 0 -2416.2586 0 -2416.2586 -7989.0404 13907.818 1476 0 -2416.4935 0 -2416.4935 -3033.178 13812.237 Loop time of 22.8397 on 1 procs for 1000 steps with 834 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2416.25859378 -2416.49353319 -2416.49354084 Force two-norm initial, final = 76.6715 0.241783 Force max component initial, final = 65.7916 0.155084 Final line search alpha, max atom move = 0.00807463 0.00125225 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.397 | 22.397 | 22.397 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1239 | 0.1239 | 0.1239 | 0.0 | 0.54 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3183 | | | 1.39 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13918 ave 13918 max 13918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 546072 ave 546072 max 546072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 546072 Ave neighs/atom = 654.763 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal 0.0 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 6 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 6.771 | 6.771 | 6.771 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2416.4935 0 -2416.4935 -3033.178 Loop time of 9.53674e-07 on 1 procs for 0 steps with 834 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13958 ave 13958 max 13958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 546972 ave 546972 max 546972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 546972 Ave neighs/atom = 655.842 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom 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 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:52) Per MPI rank memory allocation (min/avg/max) = 6.771 | 6.771 | 6.771 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 -2416.4935 -2416.4935 41.142987 83.052382 4.0421844 -3033.178 -3033.178 17.825014 -9124.9211 7.5622478 2.5272002 573.58625 Loop time of 9.53674e-07 on 1 procs for 0 steps with 834 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13958 ave 13958 max 13958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 273486 ave 273486 max 273486 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 546972 ave 546972 max 546972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 546972 Ave neighs/atom = 655.842 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_058.1092/numatoms.out 834 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2416.49354084163-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2416.49354084163-834*${isolated_atom_energy} variable adjusted_pe_metal equal -2416.49354084163-834*0 print "${adjusted_pe_metal} eV" file output/dump_058.1092/energy.out -2416.49354084163 eV print "${mindist_metal} Angstroms" file output/dump_058.1092/mindistance.out 2.52720019494085 Angstroms write_dump all cfg output/dump_058.1092/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_058.1092/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:33