LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 75.01792258793812*${_u_distance} variable xmax_converted equal 75.01792258793812*1 variable ymin_converted equal -75.0219555764417*${_u_distance} variable ymin_converted equal -75.0219555764417*1 variable ymax_converted equal 75.0219555764417*${_u_distance} variable ymax_converted equal 75.0219555764417*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032988503575325*${_u_distance} variable zmax_converted equal 4.032988503575325*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03298850357533 Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 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 75.0179225879381 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 75.0179225879381 -75.0219555764417 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 75.0179225879381 -75.0219555764417 75.0219555764417 ${zmin_converted} ${zmax_converted} units box region whole block 0 75.0179225879381 -75.0219555764417 75.0219555764417 0 ${zmax_converted} units box region whole block 0 75.0179225879381 -75.0219555764417 75.0219555764417 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -75.022 0) to (75.0179 75.022 4.03299) 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 75.0219555764417 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.63718 5.63718 4.03299 create_atoms 1 region upper Created 1386 atoms create_atoms CPU = 0.000352859 secs group upper type 1 1386 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.370483856982224 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -75.0219555764417 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.63718 5.63718 4.03299 create_atoms 2 region lower Created 1386 atoms create_atoms CPU = 0.000245094 secs group lower type 2 1386 atoms in group lower displace_atoms lower move -8.370483856982224 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.03298850357533 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01649425178767 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 11 22 1 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 2738 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 11 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 19.94 | 19.94 | 19.94 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7905.4908 0 -7905.4908 413.08651 590 0 -7975.7316 0 -7975.7316 -6514.8408 Loop time of 40.5452 on 1 procs for 590 steps with 2738 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 = -7905.49076202 -7975.73164522 -7975.73164522 Force two-norm initial, final = 31.2266 6.09546e-05 Force max component initial, final = 5.69102 4.88271e-06 Final line search alpha, max atom move = 1 4.88271e-06 Iterations, force evaluations = 590 1154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.26 | 40.26 | 40.26 | 0.0 | 99.30 Neigh | 0.054452 | 0.054452 | 0.054452 | 0.0 | 0.13 Comm | 0.17246 | 0.17246 | 0.17246 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05873 | | | 0.14 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 32590 ave 32590 max 32590 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: 1.81746e+06 ave 1.81746e+06 max 1.81746e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1817460 Ave neighs/atom = 663.791 Neighbor list builds = 2 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) = 19.94 | 19.94 | 19.94 Mbytes Step Temp E_pair E_mol TotEng Press Volume 590 0 -7975.7316 0 -7975.7316 -6514.8408 45395.248 1590 0 -7976.0362 0 -7976.0362 -2814.7828 45165.417 Loop time of 72.798 on 1 procs for 1000 steps with 2738 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 = -7975.73164522 -7976.03613736 -7976.03624374 Force two-norm initial, final = 161.814 0.149591 Force max component initial, final = 121.577 0.121379 Final line search alpha, max atom move = 0.0673789 0.00817835 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 71.744 | 71.744 | 71.744 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.28794 | 0.28794 | 0.28794 | 0.0 | 0.40 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.7659 | | | 1.05 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 32622 ave 32622 max 32622 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: 1.80607e+06 ave 1.80607e+06 max 1.80607e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1806068 Ave neighs/atom = 659.63 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 18.83 | 18.83 | 18.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7976.0362 0 -7976.0362 -2814.7828 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2738 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: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 32622 ave 32622 max 32622 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: 1.81227e+06 ave 1.81227e+06 max 1.81227e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1812268 Ave neighs/atom = 661.895 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:52) Per MPI rank memory allocation (min/avg/max) = 18.83 | 18.83 | 18.83 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 -7976.0362 -7976.0362 74.970131 150.04391 4.0151279 -2814.7828 -2814.7828 -2.8655491 -8445.7695 4.2866582 2.5348168 667.07513 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2738 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 | | 2.146e-06 | | |100.00 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 32622 ave 32622 max 32622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 906134 ave 906134 max 906134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.81227e+06 ave 1.81227e+06 max 1.81227e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1812268 Ave neighs/atom = 661.895 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_072.5077/numatoms.out 2738 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7976.03624374124-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7976.03624374124-2738*${isolated_atom_energy} variable adjusted_pe_metal equal -7976.03624374124-2738*0 print "${adjusted_pe_metal} eV" file output/dump_072.5077/energy.out -7976.03624374124 eV print "${mindist_metal} Angstroms" file output/dump_072.5077/mindistance.out 2.53481676752264 Angstroms write_dump all cfg output/dump_072.5077/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_072.5077/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:53