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 57.987163529230024*${_u_distance} variable xmax_converted equal 57.987163529230024*1 variable ymin_converted equal -57.99121352840748*${_u_distance} variable ymin_converted equal -57.99121352840748*1 variable ymax_converted equal 57.99121352840748*${_u_distance} variable ymax_converted equal 57.99121352840748*1 variable zmin_converted equal 0.0*${_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 57.98716352923 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.98716352923 -57.9912135284075 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.98716352923 -57.9912135284075 57.9912135284075 ${zmin_converted} ${zmax_converted} units box region whole block 0 57.98716352923 -57.9912135284075 57.9912135284075 0 ${zmax_converted} units box region whole block 0 57.98716352923 -57.9912135284075 57.9912135284075 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -57.9912 0) to (57.9872 57.9912 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 57.9912135284075 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -6 0 orient y 6 13 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 13 -6 0 orient y 6 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.37442 5.37442 4.05 create_atoms 1 region upper Created 821 atoms create_atoms CPU = 0.000276089 secs group upper type 1 821 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.443019478474359 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -57.9912135284075 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 6 0 orient y -6 13 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 13 6 0 orient y -6 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.37442 5.37442 4.05 create_atoms 2 region lower Created 821 atoms create_atoms CPU = 0.000145912 secs group lower type 2 821 atoms in group lower displace_atoms lower move -6.443019478474359 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 34 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 22 atoms, new total = 1620 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 34 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) = 13.61 | 13.61 | 13.61 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5392.9653 0 -5392.9653 -148.38473 297 0 -5411.4369 0 -5411.4369 -5333.4375 Loop time of 19.1106 on 1 procs for 297 steps with 1620 atoms 88.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5392.96527873 -5411.43686716 -5411.43686716 Force two-norm initial, final = 17.5678 1.03756e-05 Force max component initial, final = 3.76477 2.52086e-06 Final line search alpha, max atom move = 1 2.52086e-06 Iterations, force evaluations = 297 586 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.054 | 19.054 | 19.054 | 0.0 | 99.71 Neigh | 0.004704 | 0.004704 | 0.004704 | 0.0 | 0.02 Comm | 0.02974 | 0.02974 | 0.02974 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02192 | | | 0.11 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8477 ave 8477 max 8477 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63871 ave 63871 max 63871 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127742 ave 127742 max 127742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127742 Ave neighs/atom = 78.8531 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) = 13.64 | 13.64 | 13.64 Mbytes Step Temp E_pair E_mol TotEng Press Volume 297 0 -5411.4369 0 -5411.4369 -5333.4375 27238.237 1297 0 -5411.6618 0 -5411.6618 -1116.8507 27086.091 Loop time of 71.4539 on 1 procs for 1000 steps with 1620 atoms 80.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5411.43686716 -5411.66180541 -5411.66180542 Force two-norm initial, final = 113.26 0.00716759 Force max component initial, final = 80.7883 0.00511237 Final line search alpha, max atom move = 0.245256 0.00125384 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.958 | 70.958 | 70.958 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.093982 | 0.093982 | 0.093982 | 0.0 | 0.13 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4017 | | | 0.56 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8468 ave 8468 max 8468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63830 ave 63830 max 63830 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127660 ave 127660 max 127660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127660 Ave neighs/atom = 78.8025 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 34 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) = 12.54 | 12.54 | 12.54 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5411.6618 0 -5411.6618 -1116.8507 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1620 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: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8481 ave 8481 max 8481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64905 ave 64905 max 64905 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129810 ave 129810 max 129810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129810 Ave neighs/atom = 80.1296 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) = 12.54 | 12.54 | 12.54 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 -5411.6618 -5411.6618 57.834614 115.98243 4.0379999 -1116.8507 -1116.8507 0.3016076 -3350.9088 0.055089088 2.413491 1043.8175 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1620 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: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8481 ave 8481 max 8481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64905 ave 64905 max 64905 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129810 ave 129810 max 129810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129810 Ave neighs/atom = 80.1296 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_049.5503/numatoms.out 1620 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5411.66180541663-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5411.66180541663-1620*${isolated_atom_energy} variable adjusted_pe_metal equal -5411.66180541663-1620*0 print "${adjusted_pe_metal} eV" file output/dump_049.5503/energy.out -5411.66180541663 eV print "${mindist_metal} Angstroms" file output/dump_049.5503/mindistance.out 2.41349102504172 Angstroms write_dump all cfg output/dump_049.5503/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_049.5503/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:30