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 4.049999177455902*${_u_distance} variable lattice_constant_converted equal 4.049999177455902*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 56.264386730123896*${_u_distance} variable xmax_converted equal 56.264386730123896*1 variable ymin_converted equal -56.26843672930135*${_u_distance} variable ymin_converted equal -56.26843672930135*1 variable ymax_converted equal 56.26843672930135*${_u_distance} variable ymax_converted equal 56.26843672930135*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049999177455902*${_u_distance} variable zmax_converted equal 4.049999177455902*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0499991774559 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 56.2643867301239 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.2643867301239 -56.2684367293013 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.2643867301239 -56.2684367293013 56.2684367293013 ${zmin_converted} ${zmax_converted} units box region whole block 0 56.2643867301239 -56.2684367293013 56.2684367293013 0 ${zmax_converted} units box region whole block 0 56.2643867301239 -56.2684367293013 56.2684367293013 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -56.2684 0) to (56.2644 56.2684 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 56.2684367293013 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -7 0 orient y 7 12 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 12 -7 0 orient y 7 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.53898 5.53898 4.05 create_atoms 1 region upper Created 774 atoms create_atoms CPU = 0.000349045 secs group upper type 1 774 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.251599795252412 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -56.2684367293013 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 7 0 orient y -7 12 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 12 7 0 orient y -7 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.53898 5.53898 4.05 create_atoms 2 region lower Created 774 atoms create_atoms CPU = 0.000230074 secs group lower type 2 774 atoms in group lower displace_atoms lower move -6.251599795252412 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_656517352485_000-files/b'library.meam' Al Si Mg Cu Fe ./SM_656517352485_000-files/b'AlSiMgCuFe.meam' Al Al Reading potential file ./SM_656517352485_000-files/b'library.meam' with DATE: 2012-06-29 Reading potential file ./SM_656517352485_000-files/b'AlSiMgCuFe.meam' with DATE: 2012-06-29 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*4.0499991774559 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499958872795 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 = 17 33 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 24 atoms, new total = 1524 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 = 17 33 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) = 13.42 | 13.42 | 13.42 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5067.4028 0 -5067.4028 261.33898 213 0 -5092.0729 0 -5092.0729 -6387.6412 Loop time of 10.4956 on 1 procs for 213 steps with 1524 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 = -5067.40277759 -5092.07292556 -5092.07292556 Force two-norm initial, final = 22.3987 1.53876e-05 Force max component initial, final = 5.17945 1.96157e-06 Final line search alpha, max atom move = 1 1.96157e-06 Iterations, force evaluations = 213 418 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.458 | 10.458 | 10.458 | 0.0 | 99.64 Neigh | 0.0042038 | 0.0042038 | 0.0042038 | 0.0 | 0.04 Comm | 0.020118 | 0.020118 | 0.020118 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01375 | | | 0.13 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8007 ave 8007 max 8007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60058 ave 60058 max 60058 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120116 ave 120116 max 120116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120116 Ave neighs/atom = 78.8163 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) = 13.44 | 13.44 | 13.44 Mbytes Step Temp E_pair E_mol TotEng Press Volume 213 0 -5092.0729 0 -5092.0729 -6387.6412 25643.858 1213 0 -5092.3932 0 -5092.3932 -1210.5199 25468.266 Loop time of 50.5827 on 1 procs for 1000 steps with 1524 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 = -5092.07292556 -5092.39315209 -5092.39315209 Force two-norm initial, final = 131.27 0.00247872 Force max component initial, final = 94.2657 0.00116005 Final line search alpha, max atom move = 0.284531 0.00033007 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 50.211 | 50.211 | 50.211 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.079066 | 0.079066 | 0.079066 | 0.0 | 0.16 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2925 | | | 0.58 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7020 ave 7020 max 7020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59822 ave 59822 max 59822 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119644 ave 119644 max 119644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119644 Ave neighs/atom = 78.5066 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 = 17 33 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) = 12.34 | 12.34 | 12.34 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5092.3932 0 -5092.3932 -1210.5199 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1524 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 | | 1.192e-06 | | |100.00 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7024 ave 7024 max 7024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61334 ave 61334 max 61334 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122668 ave 122668 max 122668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122668 Ave neighs/atom = 80.4908 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) = 12.34 | 12.34 | 12.34 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 -5092.3932 -5092.3932 56.086583 112.53687 4.0350186 -1210.5199 -1210.5199 0.072746712 -3631.6832 0.05076397 2.4784196 905.85605 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1524 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 | | 1.907e-06 | | |100.00 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7024 ave 7024 max 7024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61334 ave 61334 max 61334 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122668 ave 122668 max 122668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122668 Ave neighs/atom = 80.4908 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_060.5129/numatoms.out 1524 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5092.39315209204-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5092.39315209204-1524*${isolated_atom_energy} variable adjusted_pe_metal equal -5092.39315209204-1524*0 print "${adjusted_pe_metal} eV" file output/dump_060.5129/energy.out -5092.39315209204 eV print "${mindist_metal} Angstroms" file output/dump_060.5129/mindistance.out 2.47841959263452 Angstroms write_dump all cfg output/dump_060.5129/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_060.5129/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:01