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 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 9.018036446469582*${_u_distance} variable xmax_converted equal 9.018036446469582*1 variable ymin_converted equal -45.09421522085148*${_u_distance} variable ymin_converted equal -45.09421522085148*1 variable ymax_converted equal 45.09421522085148*${_u_distance} variable ymax_converted equal 45.09421522085148*1 variable zmin_converted equal 0.0*${_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 9.01803644646958 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01803644646958 -45.0942152208515 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01803644646958 -45.0942152208515 45.0942152208515 ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01803644646958 -45.0942152208515 45.0942152208515 0 ${zmax_converted} units box region whole block 0 9.01803644646958 -45.0942152208515 45.0942152208515 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -45.0942 0) to (9.01804 45.0942 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 45.0942152208515 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.41082 5.41082 4.03299 create_atoms 1 region upper Created 102 atoms create_atoms CPU = 0.000146151 secs group upper type 1 102 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.0062305898749053 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.0942152208515 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.41082 5.41082 4.03299 create_atoms 2 region lower Created 102 atoms create_atoms CPU = 3.60012e-05 secs group lower type 2 102 atoms in group lower displace_atoms lower move -1.0062305898749053 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_002 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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 = 2 14 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 8 atoms, new total = 196 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 = 2 14 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) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -560.57977 0 -560.57977 -185.51843 376 0 -567.70846 0 -567.70846 -10471.141 Loop time of 2.68779 on 1 procs for 376 steps with 196 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -560.579767701 -567.708462044 -567.708462044 Force two-norm initial, final = 9.79619 3.77362e-06 Force max component initial, final = 3.00809 5.88044e-07 Final line search alpha, max atom move = 1 5.88044e-07 Iterations, force evaluations = 376 742 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6411 | 2.6411 | 2.6411 | 0.0 | 98.26 Neigh | 0.00278 | 0.00278 | 0.00278 | 0.0 | 0.10 Comm | 0.035517 | 0.035517 | 0.035517 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00844 | | | 0.31 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8176 ave 8176 max 8176 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: 128672 ave 128672 max 128672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128672 Ave neighs/atom = 656.49 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) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press Volume 376 0 -567.70846 0 -567.70846 -10471.141 3280.1205 1376 0 -567.79871 0 -567.79871 -3039.7449 3246.3823 Loop time of 7.20698 on 1 procs for 1000 steps with 196 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 = -567.708462044 -567.798707427 -567.798707433 Force two-norm initial, final = 24.517 0.00225639 Force max component initial, final = 18.167 0.00141501 Final line search alpha, max atom move = 1 0.00141501 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9049 | 6.9049 | 6.9049 | 0.0 | 95.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.083484 | 0.083484 | 0.083484 | 0.0 | 1.16 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2185 | | | 3.03 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8024 ave 8024 max 8024 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: 127476 ave 127476 max 127476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127476 Ave neighs/atom = 650.388 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 2 14 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) = 5.073 | 5.073 | 5.073 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -567.79871 0 -567.79871 -3039.7449 Loop time of 9.53674e-07 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8053 ave 8053 max 8053 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: 128520 ave 128520 max 128520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128520 Ave neighs/atom = 655.714 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) = 5.073 | 5.073 | 5.073 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 -567.79871 -567.79871 8.9699151 90.18843 4.01292 -3039.7449 -3039.7449 -0.69462088 -9119.2044 0.6643193 2.5255189 142.15788 Loop time of 1.19209e-06 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8053 ave 8053 max 8053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64260 ave 64260 max 64260 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128520 ave 128520 max 128520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128520 Ave neighs/atom = 655.714 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_053.1301/numatoms.out 196 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -567.798707432614-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -567.798707432614-196*${isolated_atom_energy} variable adjusted_pe_metal equal -567.798707432614-196*0 print "${adjusted_pe_metal} eV" file output/dump_053.1301/energy.out -567.798707432614 eV print "${mindist_metal} Angstroms" file output/dump_053.1301/mindistance.out 2.52551893629596 Angstroms write_dump all cfg output/dump_053.1301/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_053.1301/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09