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 3.9946166351437573*${_u_distance} variable lattice_constant_converted equal 3.9946166351437573*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 29.081248069394533*${_u_distance} variable xmax_converted equal 29.081248069394533*1 variable ymin_converted equal -58.16649075542421*${_u_distance} variable ymin_converted equal -58.16649075542421*1 variable ymax_converted equal 58.16649075542421*${_u_distance} variable ymax_converted equal 58.16649075542421*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.9946166351437573*${_u_distance} variable zmax_converted equal 3.9946166351437573*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.99461663514376 Lattice spacing in x,y,z = 3.99462 3.99462 3.99462 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 29.0812480693945 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 29.0812480693945 -58.1664907554242 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 29.0812480693945 -58.1664907554242 58.1664907554242 ${zmin_converted} ${zmax_converted} units box region whole block 0 29.0812480693945 -58.1664907554242 58.1664907554242 0 ${zmax_converted} units box region whole block 0 29.0812480693945 -58.1664907554242 58.1664907554242 0 3.99461663514376 units box create_box 2 whole Created orthogonal box = (0 -58.1665 0) to (29.0812 58.1665 3.99462) 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 58.1664907554242 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -2 0 orient y 2 7 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 7 -2 0 orient y 2 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.93833 4.93833 3.99462 create_atoms 1 region upper Created 426 atoms create_atoms CPU = 0.000187159 secs group upper type 1 426 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.276049450176233 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -58.1664907554242 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 2 0 orient y -2 7 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 7 2 0 orient y -2 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.93833 4.93833 3.99462 create_atoms 2 region lower Created 426 atoms create_atoms CPU = 7.29561e-05 secs group lower type 2 426 atoms in group lower displace_atoms lower move -3.276049450176233 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001 pair_coeff * * 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*3.99461663514376 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.99730831757188 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 8 31 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 834 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2722.4878 0 -2722.4878 511.52653 243 0 -2731.2818 0 -2731.2818 -4640.6785 Loop time of 2.75062 on 1 procs for 243 steps with 834 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 = -2722.48782164 -2731.28177173 -2731.28177173 Force two-norm initial, final = 10.1864 6.92514e-06 Force max component initial, final = 3.38894 1.44367e-06 Final line search alpha, max atom move = 1 1.44367e-06 Iterations, force evaluations = 243 475 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7215 | 2.7215 | 2.7215 | 0.0 | 98.94 Neigh | 0.001914 | 0.001914 | 0.001914 | 0.0 | 0.07 Comm | 0.017571 | 0.017571 | 0.017571 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009602 | | | 0.35 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6291 ave 6291 max 6291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108340 ave 108340 max 108340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108340 Ave neighs/atom = 129.904 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press Volume 243 0 -2731.2818 0 -2731.2818 -4640.6785 13514.221 252 0 -2731.3902 0 -2731.3902 -1706.5961 13412.816 Loop time of 0.294087 on 1 procs for 9 steps with 834 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -2731.28177173 -2731.39021998 -2731.39021998 Force two-norm initial, final = 40.0829 0.0657487 Force max component initial, final = 29.8461 0.0462055 Final line search alpha, max atom move = 1.75282e-06 8.09901e-08 Iterations, force evaluations = 9 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28735 | 0.28735 | 0.28735 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015945 | 0.0015945 | 0.0015945 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005147 | | | 1.75 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6346 ave 6346 max 6346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109520 ave 109520 max 109520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109520 Ave neighs/atom = 131.319 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 -6.30324000329931e-20 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.093 | 5.093 | 5.093 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2731.3902 0 -2731.3902 -1706.5961 Loop time of 1.19209e-06 on 1 procs for 0 steps with 834 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: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6361 ave 6361 max 6361 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109660 ave 109660 max 109660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109660 Ave neighs/atom = 131.487 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) = 5.093 | 5.093 | 5.093 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 -2731.3902 -2731.3902 28.966666 116.33298 3.9803256 -1706.5961 -1706.5961 -3.1665523 -5122.1212 5.4995588 2.5581094 447.77126 Loop time of 1.90735e-06 on 1 procs for 0 steps with 834 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 | | 1.907e-06 | | |100.00 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6361 ave 6361 max 6361 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54830 ave 54830 max 54830 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109660 ave 109660 max 109660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109660 Ave neighs/atom = 131.487 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_031.8908/numatoms.out 834 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2731.39021997704-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2731.39021997704-834*${isolated_atom_energy} variable adjusted_pe_metal equal -2731.39021997704-834*-6.30324000329931e-20 print "${adjusted_pe_metal} eV" file output/dump_031.8908/energy.out -2731.39021997704 eV print "${mindist_metal} Angstroms" file output/dump_031.8908/mindistance.out 2.55810939741312 Angstroms write_dump all cfg output/dump_031.8908/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_031.8908/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03