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 83.09903546397308*${_u_distance} variable xmax_converted equal 83.09903546397308*1 variable ymin_converted equal -83.10308546315053*${_u_distance} variable ymin_converted equal -83.10308546315053*1 variable ymax_converted equal 83.10308546315053*${_u_distance} variable ymax_converted equal 83.10308546315053*1 variable zmin_converted equal 0.0*${_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 83.0990354639731 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0990354639731 -83.1030854631505 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0990354639731 -83.1030854631505 83.1030854631505 ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0990354639731 -83.1030854631505 83.1030854631505 0 ${zmax_converted} units box region whole block 0 83.0990354639731 -83.1030854631505 83.1030854631505 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -83.1031 0) to (83.099 83.1031 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 83.1030854631505 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72416 5.72416 4.05 create_atoms 1 region upper Created 1686 atoms create_atoms CPU = 0.000396967 secs group upper type 1 1686 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 9.233228037907434 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -83.1030854631505 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72416 5.72416 4.05 create_atoms 2 region lower Created 1686 atoms create_atoms CPU = 0.000289917 secs group lower type 2 1686 atoms in group lower displace_atoms lower move -9.233228037907434 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 24 48 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 38 atoms, new total = 3334 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 = 24 48 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) = 26.6 | 26.6 | 26.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11121.12 0 -11121.12 -422.36016 285 0 -11162.062 0 -11162.062 -6492.1588 Loop time of 24.0088 on 1 procs for 285 steps with 3334 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 = -11121.1195833 -11162.0623122 -11162.0623122 Force two-norm initial, final = 18.9749 1.46914e-05 Force max component initial, final = 3.51763 1.08725e-06 Final line search alpha, max atom move = 1 1.08725e-06 Iterations, force evaluations = 285 547 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.933 | 23.933 | 23.933 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.043148 | 0.043148 | 0.043148 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03264 | | | 0.14 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15581 ave 15581 max 15581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129186 ave 129186 max 129186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258372 ave 258372 max 258372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258372 Ave neighs/atom = 77.4961 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) = 26.66 | 26.66 | 26.66 Mbytes Step Temp E_pair E_mol TotEng Press Volume 285 0 -11162.062 0 -11162.062 -6492.1588 55936.857 874 0 -11162.573 0 -11162.573 -2060.9399 55610.806 Loop time of 54.0649 on 1 procs for 589 steps with 3334 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 = -11162.0623122 -11162.5732573 -11162.5732573 Force two-norm initial, final = 245.274 0.00339798 Force max component initial, final = 179.654 0.00335884 Final line search alpha, max atom move = 1 0.00335884 Iterations, force evaluations = 589 1175 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53.663 | 53.663 | 53.663 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.087727 | 0.087727 | 0.087727 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3139 | | | 0.58 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15616 ave 15616 max 15616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131812 ave 131812 max 131812 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 263624 ave 263624 max 263624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263624 Ave neighs/atom = 79.0714 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 = 24 48 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) = 24.5 | 24.5 | 24.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11162.573 0 -11162.573 -2060.9399 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15640 ave 15640 max 15640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135386 ave 135386 max 135386 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270772 ave 270772 max 270772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270772 Ave neighs/atom = 81.2154 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) = 24.5 | 24.5 | 24.5 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 -11162.573 -11162.573 82.896657 166.20617 4.0362219 -2060.9399 -2060.9399 -0.0057195977 -6182.7176 -0.096440763 2.5550676 347.64514 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15640 ave 15640 max 15640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135386 ave 135386 max 135386 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270772 ave 270772 max 270772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270772 Ave neighs/atom = 81.2154 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_086.0501/numatoms.out 3334 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11162.5732572778-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11162.5732572778-3334*${isolated_atom_energy} variable adjusted_pe_metal equal -11162.5732572778-3334*0 print "${adjusted_pe_metal} eV" file output/dump_086.0501/energy.out -11162.5732572778 eV print "${mindist_metal} Angstroms" file output/dump_086.0501/mindistance.out 2.55506763967881 Angstroms write_dump all cfg output/dump_086.0501/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_086.0501/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:18