LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) 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 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 83.09902950192091*${_u_distance} variable xmax_converted equal 83.09902950192091*1 variable ymin_converted equal -83.1030795008078*${_u_distance} variable ymin_converted equal -83.1030795008078*1 variable ymax_converted equal 83.1030795008078*${_u_distance} variable ymax_converted equal 83.1030795008078*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 83.0990295019209 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0990295019209 -83.1030795008078 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0990295019209 -83.1030795008078 83.1030795008078 ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0990295019209 -83.1030795008078 83.1030795008078 0 ${zmax_converted} units box region whole block 0 83.0990295019209 -83.1030795008078 83.1030795008078 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -83.1031 0) to (83.099 83.1031 4.05) 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 83.1030795008078 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72416 5.72416 4.05 create_atoms 1 region upper Created 1686 atoms create_atoms CPU = 0.000416994 secs group upper type 1 1686 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 9.233228037907434 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -83.1030795008078 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72416 5.72416 4.05 create_atoms 2 region lower Created 1686 atoms create_atoms CPU = 0.00028491 secs group lower type 2 1686 atoms in group lower displace_atoms lower move -9.233228037907434 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_721930391003_000-files/b'AlU-library.meam' Al U ./SM_721930391003_000-files/b'AlU.meam' 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*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 24 48 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 38 atoms, new total = 3334 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 24 48 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 26.6 | 26.6 | 26.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11135.058 0 -11135.058 2147.2125 454 0 -11184.217 0 -11184.217 -5222.137 Loop time of 26.6387 on 1 procs for 454 steps with 3334 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 = -11135.0578828 -11184.2170216 -11184.2170216 Force two-norm initial, final = 46.2571 4.72244e-05 Force max component initial, final = 9.19361 3.06705e-06 Final line search alpha, max atom move = 1 3.06705e-06 Iterations, force evaluations = 454 901 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.5 | 26.5 | 26.5 | 0.0 | 99.48 Neigh | 0.007226 | 0.007226 | 0.007226 | 0.0 | 0.03 Comm | 0.076805 | 0.076805 | 0.076805 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05496 | | | 0.21 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15588 ave 15588 max 15588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131702 ave 131702 max 131702 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 263404 ave 263404 max 263404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263404 Ave neighs/atom = 79.0054 Neighbor list builds = 1 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) = 26.66 | 26.66 | 26.66 Mbytes Step Temp E_pair E_mol TotEng Press Volume 454 0 -11184.217 0 -11184.217 -5222.137 55936.845 1454 0 -11184.485 0 -11184.485 -2361.0977 55723.274 Loop time of 63.2188 on 1 procs for 1000 steps with 3334 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -11184.2170216 -11184.4854287 -11184.4854287 Force two-norm initial, final = 162.688 0.00606993 Force max component initial, final = 141.216 0.00374436 Final line search alpha, max atom move = 0.74255 0.00278037 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 62.52 | 62.52 | 62.52 | 0.0 | 98.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15236 | 0.15236 | 0.15236 | 0.0 | 0.24 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5469 | | | 0.87 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15601 ave 15601 max 15601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131806 ave 131806 max 131806 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 263612 ave 263612 max 263612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263612 Ave neighs/atom = 79.0678 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:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 24 48 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 24.43 | 24.43 | 24.43 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11184.485 0 -11184.485 -2361.0977 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15619 ave 15619 max 15619 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132448 ave 132448 max 132448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 264896 ave 264896 max 264896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264896 Ave neighs/atom = 79.4529 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:55) Per MPI rank memory allocation (min/avg/max) = 24.43 | 24.43 | 24.43 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 -11184.485 -11184.485 83.092236 166.20616 4.0348655 -2361.0977 -2361.0977 -0.081239158 -7083.1047 -0.10725691 2.6116517 368.16428 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15619 ave 15619 max 15619 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132448 ave 132448 max 132448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 264896 ave 264896 max 264896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264896 Ave neighs/atom = 79.4529 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_086.0501/numatoms.out 3334 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11184.4854286855-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11184.4854286855-3334*${isolated_atom_energy} variable adjusted_pe_metal equal -11184.4854286855-3334*0 print "${adjusted_pe_metal} eV" file output/dump_086.0501/energy.out -11184.4854286855 eV print "${mindist_metal} Angstroms" file output/dump_086.0501/mindistance.out 2.61165167162934 Angstroms write_dump all cfg output/dump_086.0501/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_086.0501/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:30