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 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 59.797516958973546*${_u_distance} variable xmax_converted equal 59.797516958973546*1 variable ymin_converted equal -59.80156695786043*${_u_distance} variable ymin_converted equal -59.80156695786043*1 variable ymax_converted equal 59.80156695786043*${_u_distance} variable ymax_converted equal 59.80156695786043*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 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 59.7975169589735 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7975169589735 -59.8015669578604 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7975169589735 -59.8015669578604 59.8015669578604 ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7975169589735 -59.8015669578604 59.8015669578604 0 ${zmax_converted} units box region whole block 0 59.7975169589735 -59.8015669578604 59.8015669578604 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -59.8016 0) to (59.7975 59.8016 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 59.8015669578604 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48601 5.48601 4.05 create_atoms 1 region upper Created 874 atoms create_atoms CPU = 0.000258923 secs group upper type 1 874 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.64417037710503 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -59.8015669578604 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48601 5.48601 4.05 create_atoms 2 region lower Created 874 atoms create_atoms CPU = 0.000151873 secs group lower type 2 874 atoms in group lower displace_atoms lower move -6.64417037710503 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_721930391003_000-files/b'AlU-library.meam' Al U ./SM_721930391003_000-files/b'AlU.meam' Al Al 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*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 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 = 18 35 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 26 atoms, new total = 1722 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 = 18 35 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) = 13.82 | 13.82 | 13.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5731.338 0 -5731.338 3520.5368 479 0 -5765.525 0 -5765.525 -4292.8863 Loop time of 16.5091 on 1 procs for 479 steps with 1722 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 = -5731.33796784 -5765.52502424 -5765.52502424 Force two-norm initial, final = 46.0937 2.66893e-05 Force max component initial, final = 9.96528 6.32028e-06 Final line search alpha, max atom move = 1 6.32028e-06 Iterations, force evaluations = 479 950 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.419 | 16.419 | 16.419 | 0.0 | 99.45 Neigh | 0.004914 | 0.004914 | 0.004914 | 0.0 | 0.03 Comm | 0.049731 | 0.049731 | 0.049731 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0354 | | | 0.21 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8922 ave 8922 max 8922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67568 ave 67568 max 67568 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 135136 ave 135136 max 135136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135136 Ave neighs/atom = 78.4762 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) = 13.84 | 13.84 | 13.84 Mbytes Step Temp E_pair E_mol TotEng Press Volume 479 0 -5765.525 0 -5765.525 -4292.8863 28965.472 1479 0 -5765.7001 0 -5765.7001 -762.3947 28829.324 Loop time of 34.3382 on 1 procs for 1000 steps with 1722 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 = -5765.52502424 -5765.70006644 -5765.70006654 Force two-norm initial, final = 103.071 0.0500377 Force max component initial, final = 76.7833 0.0425818 Final line search alpha, max atom move = 0.0694097 0.00295559 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.933 | 33.933 | 33.933 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.084566 | 0.084566 | 0.084566 | 0.0 | 0.25 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3209 | | | 0.93 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7742 ave 7742 max 7742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67398 ave 67398 max 67398 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134796 ave 134796 max 134796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134796 Ave neighs/atom = 78.2787 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 = 18 35 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) = 12.72 | 12.72 | 12.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5765.7001 0 -5765.7001 -762.3947 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1722 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: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7750 ave 7750 max 7750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68186 ave 68186 max 68186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136372 ave 136372 max 136372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136372 Ave neighs/atom = 79.194 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) = 12.72 | 12.72 | 12.72 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 -5765.7001 -5765.7001 59.699173 119.60313 4.0376027 -762.3947 -762.3947 -2.3625705 -2284.554 -0.2674945 2.5253672 1029.3935 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1722 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 | | 1.192e-06 | | |100.00 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7750 ave 7750 max 7750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68186 ave 68186 max 68186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136372 ave 136372 max 136372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136372 Ave neighs/atom = 79.194 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.6015/numatoms.out 1722 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5765.70006654497-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5765.70006654497-1722*${isolated_atom_energy} variable adjusted_pe_metal equal -5765.70006654497-1722*0 print "${adjusted_pe_metal} eV" file output/dump_056.6015/energy.out -5765.70006654497 eV print "${mindist_metal} Angstroms" file output/dump_056.6015/mindistance.out 2.52536719497645 Angstroms write_dump all cfg output/dump_056.6015/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_056.6015/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:50