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 37.339147468554316*${_u_distance} variable xmax_converted equal 37.339147468554316*1 variable ymin_converted equal -74.68234493628609*${_u_distance} variable ymin_converted equal -74.68234493628609*1 variable ymax_converted equal 74.68234493628609*${_u_distance} variable ymax_converted equal 74.68234493628609*1 variable zmin_converted equal 0.0*${_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 37.3391474685543 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391474685543 -74.6823449362861 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391474685543 -74.6823449362861 74.6823449362861 ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391474685543 -74.6823449362861 74.6823449362861 0 ${zmax_converted} units box region whole block 0 37.3391474685543 -74.6823449362861 74.6823449362861 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -74.6823 0) to (37.3391 74.6823 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 74.6823449362861 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.83212 4.83212 4.05 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000235796 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.148795005781799 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.6823449362861 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.83212 4.83212 4.05 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.000110149 secs group lower type 2 682 atoms in group lower displace_atoms lower move -4.148795005781799 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 11 43 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 = 1352 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 = 11 43 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) = 13.16 | 13.16 | 13.16 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4501.7952 0 -4501.7952 2146.88 323 0 -4520.1243 0 -4520.1243 -1675.3383 Loop time of 14.365 on 1 procs for 323 steps with 1352 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 = -4501.79516054 -4520.12431846 -4520.12431846 Force two-norm initial, final = 25.9811 1.17084e-05 Force max component initial, final = 6.71872 2.25702e-06 Final line search alpha, max atom move = 1 2.25702e-06 Iterations, force evaluations = 323 641 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.313 | 14.313 | 14.313 | 0.0 | 99.64 Neigh | 0.002913 | 0.002913 | 0.002913 | 0.0 | 0.02 Comm | 0.029285 | 0.029285 | 0.029285 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01936 | | | 0.13 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7756 ave 7756 max 7756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53318 ave 53318 max 53318 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106636 ave 106636 max 106636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106636 Ave neighs/atom = 78.8728 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) = 13.18 | 13.18 | 13.18 Mbytes Step Temp E_pair E_mol TotEng Press Volume 323 0 -4520.1243 0 -4520.1243 -1675.3383 22587.454 877 0 -4520.1513 0 -4520.1513 -175.64777 22543.252 Loop time of 26.2958 on 1 procs for 554 steps with 1352 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 = -4520.12431846 -4520.15129972 -4520.15129972 Force two-norm initial, final = 33.9435 0.000997552 Force max component initial, final = 28.6345 0.000818454 Final line search alpha, max atom move = 1 0.000818454 Iterations, force evaluations = 554 1107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.078 | 26.078 | 26.078 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.04779 | 0.04779 | 0.04779 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1704 | | | 0.65 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7747 ave 7747 max 7747 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53182 ave 53182 max 53182 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106364 ave 106364 max 106364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106364 Ave neighs/atom = 78.6716 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 = 11 43 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) = 12.05 | 12.05 | 12.05 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4520.1513 0 -4520.1513 -175.64777 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7753 ave 7753 max 7753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53308 ave 53308 max 53308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106616 ave 106616 max 106616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106616 Ave neighs/atom = 78.858 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) = 12.05 | 12.05 | 12.05 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 -4520.1513 -4520.1513 37.331386 149.36469 4.042914 -175.64777 -175.64777 0.058156419 -527.02176 0.020303459 2.3843412 517.28678 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7753 ave 7753 max 7753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53308 ave 53308 max 53308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106616 ave 106616 max 106616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106616 Ave neighs/atom = 78.858 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.0576/numatoms.out 1352 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4520.15129971526-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4520.15129971526-1352*${isolated_atom_energy} variable adjusted_pe_metal equal -4520.15129971526-1352*0 print "${adjusted_pe_metal} eV" file output/dump_025.0576/energy.out -4520.15129971526 eV print "${mindist_metal} Angstroms" file output/dump_025.0576/mindistance.out 2.38434117037448 Angstroms write_dump all cfg output/dump_025.0576/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_025.0576/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:40