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 25.932647894750986*${_u_distance} variable xmax_converted equal 25.932647894750986*1 variable ymin_converted equal -51.869345788679425*${_u_distance} variable ymin_converted equal -51.869345788679425*1 variable ymax_converted equal 51.869345788679425*${_u_distance} variable ymax_converted equal 51.869345788679425*1 variable zmin_converted equal 0.0*${_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 25.932647894751 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.932647894751 -51.8693457886794 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.932647894751 -51.8693457886794 51.8693457886794 ${zmin_converted} ${zmax_converted} units box region whole block 0 25.932647894751 -51.8693457886794 51.8693457886794 0 ${zmax_converted} units box region whole block 0 25.932647894751 -51.8693457886794 51.8693457886794 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -51.8693 0) to (25.9326 51.8693 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 51.8693457886794 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -4 0 orient y 4 5 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 5 -4 0 orient y 4 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69253 5.69253 4.05 create_atoms 1 region upper Created 330 atoms create_atoms CPU = 0.000193834 secs group upper type 1 330 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.881405906844782 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -51.8693457886794 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 4 0 orient y -4 5 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 5 4 0 orient y -4 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69253 5.69253 4.05 create_atoms 2 region lower Created 330 atoms create_atoms CPU = 7.9155e-05 secs group lower type 2 330 atoms in group lower displace_atoms lower move -2.881405906844782 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 8 30 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 12 atoms, new total = 648 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 = 8 30 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) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2154.4675 0 -2154.4675 293.92708 249 0 -2166.0172 0 -2166.0172 -6775.6836 Loop time of 4.33837 on 1 procs for 249 steps with 648 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2154.46748022 -2166.01717782 -2166.01717782 Force two-norm initial, final = 15.1815 1.8167e-06 Force max component initial, final = 3.62389 3.61763e-07 Final line search alpha, max atom move = 1 3.61763e-07 Iterations, force evaluations = 249 489 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3203 | 4.3203 | 4.3203 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010698 | 0.010698 | 0.010698 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007402 | | | 0.17 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4426 ave 4426 max 4426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25116 ave 25116 max 25116 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50232 ave 50232 max 50232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50232 Ave neighs/atom = 77.5185 Neighbor list builds = 0 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) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 249 0 -2166.0172 0 -2166.0172 -6775.6836 10895.385 1249 0 -2166.1435 0 -2166.1435 -1772.7978 10823.573 Loop time of 17.732 on 1 procs for 1000 steps with 648 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 = -2166.01717782 -2166.14353925 -2166.14353925 Force two-norm initial, final = 53.8914 0.00212345 Force max component initial, final = 38.383 0.00127956 Final line search alpha, max atom move = 0.565421 0.000723492 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.56 | 17.56 | 17.56 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.039842 | 0.039842 | 0.039842 | 0.0 | 0.22 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1323 | | | 0.75 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4282 ave 4282 max 4282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25540 ave 25540 max 25540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51080 ave 51080 max 51080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51080 Ave neighs/atom = 78.8272 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 = 8 30 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) = 10.22 | 10.22 | 10.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2166.1435 0 -2166.1435 -1772.7978 Loop time of 9.53674e-07 on 1 procs for 0 steps with 648 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: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4334 ave 4334 max 4334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26414 ave 26414 max 26414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52828 ave 52828 max 52828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52828 Ave neighs/atom = 81.5247 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) = 10.22 | 10.22 | 10.22 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 -2166.1435 -2166.1435 25.847916 103.73869 4.0364942 -1772.7978 -1772.7978 -0.09711749 -5318.1075 -0.18877764 2.3165698 219.83157 Loop time of 9.53674e-07 on 1 procs for 0 steps with 648 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: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4334 ave 4334 max 4334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26414 ave 26414 max 26414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52828 ave 52828 max 52828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52828 Ave neighs/atom = 81.5247 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_077.3196/numatoms.out 648 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2166.14353925291-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2166.14353925291-648*${isolated_atom_energy} variable adjusted_pe_metal equal -2166.14353925291-648*0 print "${adjusted_pe_metal} eV" file output/dump_077.3196/energy.out -2166.14353925291 eV print "${mindist_metal} Angstroms" file output/dump_077.3196/mindistance.out 2.31656982964246 Angstroms write_dump all cfg output/dump_077.3196/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_077.3196/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:22