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 37.33914478960691*${_u_distance} variable xmax_converted equal 37.33914478960691*1 variable ymin_converted equal -74.68233957810071*${_u_distance} variable ymin_converted equal -74.68233957810071*1 variable ymax_converted equal 74.68233957810071*${_u_distance} variable ymax_converted equal 74.68233957810071*1 variable zmin_converted equal 0.0*${_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 37.3391447896069 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391447896069 -74.6823395781007 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391447896069 -74.6823395781007 74.6823395781007 ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391447896069 -74.6823395781007 74.6823395781007 0 ${zmax_converted} units box region whole block 0 37.3391447896069 -74.6823395781007 74.6823395781007 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -74.6823 0) to (37.3391 74.6823 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 74.6823395781007 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.83212 4.83212 4.05 create_atoms 1 region upper Created 681 atoms create_atoms CPU = 0.000221014 secs group upper type 1 681 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.148795005781799 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.6823395781007 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.83212 4.83212 4.05 create_atoms 2 region lower Created 681 atoms create_atoms CPU = 0.000110149 secs group lower type 2 681 atoms in group lower displace_atoms lower move -4.148795005781799 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 11 43 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 11 atoms, new total = 1351 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 = 11 43 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) = 13.16 | 13.16 | 13.16 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4494.1896 0 -4494.1896 5439.6156 435 0 -4526.0422 0 -4526.0422 -424.22524 Loop time of 11.9364 on 1 procs for 435 steps with 1351 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 = -4494.18963018 -4526.04221641 -4526.04221641 Force two-norm initial, final = 56.9443 2.28814e-05 Force max component initial, final = 14.6985 6.89193e-06 Final line search alpha, max atom move = 1 6.89193e-06 Iterations, force evaluations = 435 862 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.869 | 11.869 | 11.869 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.040087 | 0.040087 | 0.040087 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02678 | | | 0.22 Nlocal: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7775 ave 7775 max 7775 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52608 ave 52608 max 52608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105216 ave 105216 max 105216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105216 Ave neighs/atom = 77.8801 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) = 13.19 | 13.19 | 13.19 Mbytes Step Temp E_pair E_mol TotEng Press Volume 435 0 -4526.0422 0 -4526.0422 -424.22524 22587.449 1435 0 -4526.0451 0 -4526.0451 36.377482 22573.805 Loop time of 27.8273 on 1 procs for 1000 steps with 1351 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 = -4526.04221641 -4526.04507761 -4526.04507762 Force two-norm initial, final = 10.6435 0.00510216 Force max component initial, final = 9.36929 0.00429325 Final line search alpha, max atom move = 0.622731 0.00267354 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.447 | 27.447 | 27.447 | 0.0 | 98.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.08282 | 0.08282 | 0.08282 | 0.0 | 0.30 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2975 | | | 1.07 Nlocal: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7718 ave 7718 max 7718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53863 ave 53863 max 53863 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107726 ave 107726 max 107726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107726 Ave neighs/atom = 79.738 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 = 11 43 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) = 12.06 | 12.06 | 12.06 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4526.0451 0 -4526.0451 36.377482 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1351 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: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7727 ave 7727 max 7727 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53948 ave 53948 max 53948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107896 ave 107896 max 107896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107896 Ave neighs/atom = 79.8638 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) = 12.06 | 12.06 | 12.06 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 -4526.0451 -4526.0451 37.339666 149.36468 4.0474961 36.377482 36.377482 -0.30471815 109.48552 -0.048352579 2.5005292 559.79997 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1351 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: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7727 ave 7727 max 7727 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53948 ave 53948 max 53948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107896 ave 107896 max 107896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107896 Ave neighs/atom = 79.8638 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.0576/numatoms.out 1351 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4526.04507761637-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4526.04507761637-1351*${isolated_atom_energy} variable adjusted_pe_metal equal -4526.04507761637-1351*0 print "${adjusted_pe_metal} eV" file output/dump_025.0576/energy.out -4526.04507761637 eV print "${mindist_metal} Angstroms" file output/dump_025.0576/mindistance.out 2.50052921909068 Angstroms write_dump all cfg output/dump_025.0576/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_025.0576/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:39