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 68.84998601675034*${_u_distance} variable xmax_converted equal 68.84998601675034*1 variable ymin_converted equal -68.85403601592779*${_u_distance} variable ymin_converted equal -68.85403601592779*1 variable ymax_converted equal 68.85403601592779*${_u_distance} variable ymax_converted equal 68.85403601592779*1 variable zmin_converted equal 0.0*${_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 68.8499860167503 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8499860167503 -68.8540360159278 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8499860167503 -68.8540360159278 68.8540360159278 ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8499860167503 -68.8540360159278 68.8540360159278 0 ${zmax_converted} units box region whole block 0 68.8499860167503 -68.8540360159278 68.8540360159278 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -68.854 0) to (68.85 68.854 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 68.8540360159278 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.47941 5.47941 4.05 create_atoms 1 region upper Created 1158 atoms create_atoms CPU = 0.000325918 secs group upper type 1 1158 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.65 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -68.8540360159278 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.47941 5.47941 4.05 create_atoms 2 region lower Created 1158 atoms create_atoms CPU = 0.000228882 secs group lower type 2 1158 atoms in group lower displace_atoms lower move -7.65 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 20 40 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 34 atoms, new total = 2282 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 = 20 40 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) = 14.92 | 14.92 | 14.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7598.7659 0 -7598.7659 -293.88444 264 0 -7626.4673 0 -7626.4673 -7028.9673 Loop time of 20.2738 on 1 procs for 264 steps with 2282 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7598.76591436 -7626.46726797 -7626.46726797 Force two-norm initial, final = 18.4759 2.21607e-05 Force max component initial, final = 3.25446 2.93934e-06 Final line search alpha, max atom move = 1 2.93934e-06 Iterations, force evaluations = 264 520 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.206 | 20.206 | 20.206 | 0.0 | 99.67 Neigh | 0.0064919 | 0.0064919 | 0.0064919 | 0.0 | 0.03 Comm | 0.035826 | 0.035826 | 0.035826 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02554 | | | 0.13 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11268 ave 11268 max 11268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89186 ave 89186 max 89186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 178372 ave 178372 max 178372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178372 Ave neighs/atom = 78.1648 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) = 14.95 | 14.95 | 14.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 264 0 -7626.4673 0 -7626.4673 -7028.9673 38398.847 1264 0 -7626.8791 0 -7626.8791 -2237.8419 38154.56 Loop time of 78.6549 on 1 procs for 1000 steps with 2282 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 = -7626.46726797 -7626.8791427 -7626.87914272 Force two-norm initial, final = 182.096 0.0257227 Force max component initial, final = 129.317 0.0229715 Final line search alpha, max atom move = 0.0405803 0.000932189 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 78.064 | 78.064 | 78.064 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12399 | 0.12399 | 0.12399 | 0.0 | 0.16 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4665 | | | 0.59 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11271 ave 11271 max 11271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89702 ave 89702 max 89702 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179404 ave 179404 max 179404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179404 Ave neighs/atom = 78.617 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 = 20 40 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) = 13.87 | 13.87 | 13.87 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7626.8791 0 -7626.8791 -2237.8419 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2282 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: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11282 ave 11282 max 11282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91750 ave 91750 max 91750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 183500 ave 183500 max 183500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183500 Ave neighs/atom = 80.4119 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) = 13.87 | 13.87 | 13.87 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 -7626.8791 -7626.8791 68.635971 137.70807 4.0367818 -2237.8419 -2237.8419 0.96161421 -6714.5679 0.080617722 2.4408188 1263.6861 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2282 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: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11282 ave 11282 max 11282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91750 ave 91750 max 91750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 183500 ave 183500 max 183500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183500 Ave neighs/atom = 80.4119 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.1450/numatoms.out 2282 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7626.87914272415-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7626.87914272415-2282*${isolated_atom_energy} variable adjusted_pe_metal equal -7626.87914272415-2282*0 print "${adjusted_pe_metal} eV" file output/dump_056.1450/energy.out -7626.87914272415 eV print "${mindist_metal} Angstroms" file output/dump_056.1450/mindistance.out 2.44081881657927 Angstroms write_dump all cfg output/dump_056.1450/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_056.1450/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:39