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 52.80552496887478*${_u_distance} variable xmax_converted equal 52.80552496887478*1 variable ymin_converted equal -52.80957496776166*${_u_distance} variable ymin_converted equal -52.80957496776166*1 variable ymax_converted equal 52.80957496776166*${_u_distance} variable ymax_converted equal 52.80957496776166*1 variable zmin_converted equal 0.0*${_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 52.8055249688748 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.8055249688748 -52.8095749677617 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.8055249688748 -52.8095749677617 52.8095749677617 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.8055249688748 -52.8095749677617 52.8095749677617 0 ${zmax_converted} units box region whole block 0 52.8055249688748 -52.8095749677617 52.8095749677617 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -52.8096 0) to (52.8055 52.8096 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 52.8095749677617 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.34869 4.34869 4.05 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000281096 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.867282164682384 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -52.8095749677617 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.34869 4.34869 4.05 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.020149 secs group lower type 2 682 atoms in group lower displace_atoms lower move -5.867282164682384 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 16 31 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 24 atoms, new total = 1340 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 = 16 31 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) = 13.05 | 13.05 | 13.05 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4452.929 0 -4452.929 4018.4058 244 0 -4489.3366 0 -4489.3366 -6785.8278 Loop time of 6.72813 on 1 procs for 244 steps with 1340 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4452.92899265 -4489.33659974 -4489.33659974 Force two-norm initial, final = 33.8768 1.63884e-05 Force max component initial, final = 6.87559 1.93045e-06 Final line search alpha, max atom move = 1 1.93045e-06 Iterations, force evaluations = 244 480 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.692 | 6.692 | 6.692 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020722 | 0.020722 | 0.020722 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01539 | | | 0.23 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7268 ave 7268 max 7268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51902 ave 51902 max 51902 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103804 ave 103804 max 103804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103804 Ave neighs/atom = 77.4657 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) = 13.07 | 13.07 | 13.07 Mbytes Step Temp E_pair E_mol TotEng Press Volume 244 0 -4489.3366 0 -4489.3366 -6785.8278 22587.956 1244 0 -4489.5206 0 -4489.5206 -2718.3485 22462.488 Loop time of 30.1145 on 1 procs for 1000 steps with 1340 atoms 94.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4489.33659974 -4489.52056707 -4489.52056707 Force two-norm initial, final = 92.1637 0.00134155 Force max component initial, final = 68.334 0.000589794 Final line search alpha, max atom move = 0.823054 0.000485432 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.705 | 29.705 | 29.705 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.080873 | 0.080873 | 0.080873 | 0.0 | 0.27 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3285 | | | 1.09 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7289 ave 7289 max 7289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52880 ave 52880 max 52880 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105760 ave 105760 max 105760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105760 Ave neighs/atom = 78.9254 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 = 16 31 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) = 11.95 | 11.95 | 11.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4489.5206 0 -4489.5206 -2718.3485 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1340 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: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7289 ave 7289 max 7289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53024 ave 53024 max 53024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106048 ave 106048 max 106048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106048 Ave neighs/atom = 79.1403 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) = 11.95 | 11.95 | 11.95 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 -4489.5206 -4489.5206 52.689274 105.61915 4.0363886 -2718.3485 -2718.3485 0.039252845 -8155.1268 0.041926705 2.6113732 214.06883 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1340 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: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7289 ave 7289 max 7289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53024 ave 53024 max 53024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106048 ave 106048 max 106048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106048 Ave neighs/atom = 79.1403 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_008.7974/numatoms.out 1340 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4489.52056706815-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4489.52056706815-1340*${isolated_atom_energy} variable adjusted_pe_metal equal -4489.52056706815-1340*0 print "${adjusted_pe_metal} eV" file output/dump_008.7974/energy.out -4489.52056706815 eV print "${mindist_metal} Angstroms" file output/dump_008.7974/mindistance.out 2.61137321953178 Angstroms write_dump all cfg output/dump_008.7974/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_008.7974/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:36