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 21.809913039359213*${_u_distance} variable xmax_converted equal 21.809913039359213*1 variable ymin_converted equal -43.62387607789588*${_u_distance} variable ymin_converted equal -43.62387607789588*1 variable ymax_converted equal 43.62387607789588*${_u_distance} variable ymax_converted equal 43.62387607789588*1 variable zmin_converted equal 0.0*${_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 21.8099130393592 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.8099130393592 -43.6238760778959 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.8099130393592 -43.6238760778959 43.6238760778959 ${zmin_converted} ${zmax_converted} units box region whole block 0 21.8099130393592 -43.6238760778959 43.6238760778959 0 ${zmax_converted} units box region whole block 0 21.8099130393592 -43.6238760778959 43.6238760778959 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -43.6239 0) to (21.8099 43.6239 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 43.6238760778959 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.26446 5.26446 4.05 create_atoms 1 region upper Created 234 atoms create_atoms CPU = 0.000175953 secs group upper type 1 234 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.4233241632105265 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -43.6238760778959 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.26446 5.26446 4.05 create_atoms 2 region lower Created 234 atoms create_atoms CPU = 5.60284e-05 secs group lower type 2 234 atoms in group lower displace_atoms lower move -2.4233241632105265 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 7 25 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 10 atoms, new total = 458 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 = 7 25 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) = 10.9 | 10.9 | 10.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1515.2109 0 -1515.2109 3972.9305 252 0 -1528.0042 0 -1528.0042 -5034.8432 Loop time of 3.84471 on 1 procs for 252 steps with 458 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1515.21094811 -1528.00415448 -1528.00415448 Force two-norm initial, final = 21.984 4.61466e-06 Force max component initial, final = 6.28948 5.54373e-07 Final line search alpha, max atom move = 1 5.54373e-07 Iterations, force evaluations = 252 496 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8254 | 3.8254 | 3.8254 | 0.0 | 99.50 Neigh | 0.002388 | 0.002388 | 0.002388 | 0.0 | 0.06 Comm | 0.01037 | 0.01037 | 0.01037 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006558 | | | 0.17 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3458 ave 3458 max 3458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18236 ave 18236 max 18236 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36472 ave 36472 max 36472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36472 Ave neighs/atom = 79.6332 Neighbor list builds = 2 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) = 10.91 | 10.91 | 10.91 Mbytes Step Temp E_pair E_mol TotEng Press Volume 252 0 -1528.0042 0 -1528.0042 -5034.8432 7706.6053 1252 0 -1528.0763 0 -1528.0763 -634.9883 7661.4659 Loop time of 15.424 on 1 procs for 1000 steps with 458 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 = -1528.00415448 -1528.07634088 -1528.07634089 Force two-norm initial, final = 33.4971 0.00353523 Force max component initial, final = 26.0276 0.00195681 Final line search alpha, max atom move = 0.34288 0.000670951 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.258 | 15.258 | 15.258 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.038369 | 0.038369 | 0.038369 | 0.0 | 0.25 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1276 | | | 0.83 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3480 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18006 ave 18006 max 18006 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36012 ave 36012 max 36012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36012 Ave neighs/atom = 78.6288 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 = 7 25 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) = 9.795 | 9.795 | 9.795 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1528.0763 0 -1528.0763 -634.9883 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3482 ave 3482 max 3482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18614 ave 18614 max 18614 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37228 ave 37228 max 37228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37228 Ave neighs/atom = 81.2838 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) = 9.795 | 9.795 | 9.795 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 -1528.0763 -1528.0763 21.770639 87.247752 4.0335408 -634.9883 -634.9883 0.40847475 -1905.6739 0.30056431 2.4578951 387.2089 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3482 ave 3482 max 3482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18614 ave 18614 max 18614 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37228 ave 37228 max 37228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37228 Ave neighs/atom = 81.2838 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_043.6028/numatoms.out 458 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1528.07634088597-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1528.07634088597-458*${isolated_atom_energy} variable adjusted_pe_metal equal -1528.07634088597-458*0 print "${adjusted_pe_metal} eV" file output/dump_043.6028/energy.out -1528.07634088597 eV print "${mindist_metal} Angstroms" file output/dump_043.6028/mindistance.out 2.45789508999343 Angstroms write_dump all cfg output/dump_043.6028/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_043.6028/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:19