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 3.987558534741402*${_u_distance} variable lattice_constant_converted equal 3.987558534741402*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 32.14872469351288*${_u_distance} variable xmax_converted equal 32.14872469351288*1 variable ymin_converted equal -64.30143694556051*${_u_distance} variable ymin_converted equal -64.30143694556051*1 variable ymax_converted equal 64.30143694556051*${_u_distance} variable ymax_converted equal 64.30143694556051*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.987558534741402*${_u_distance} variable zmax_converted equal 3.987558534741402*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.9875585347414 Lattice spacing in x,y,z = 3.98756 3.98756 3.98756 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 32.1487246935129 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 32.1487246935129 -64.3014369455605 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 32.1487246935129 -64.3014369455605 64.3014369455605 ${zmin_converted} ${zmax_converted} units box region whole block 0 32.1487246935129 -64.3014369455605 64.3014369455605 0 ${zmax_converted} units box region whole block 0 32.1487246935129 -64.3014369455605 64.3014369455605 0 3.9875585347414 units box create_box 2 whole Created orthogonal box = (0 -64.3014 0) to (32.1487 64.3014 3.98756) 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 64.3014369455605 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -4 0 orient y 4 7 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 7 -4 0 orient y 4 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.44055 5.44055 3.98756 create_atoms 1 region upper Created 522 atoms create_atoms CPU = 0.000313997 secs group upper type 1 522 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.628015986734347 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -64.3014369455605 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 4 0 orient y -4 7 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 7 4 0 orient y -4 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.44055 5.44055 3.98756 create_atoms 2 region lower Created 522 atoms create_atoms CPU = 0.000159025 secs group lower type 2 522 atoms in group lower displace_atoms lower move -3.628015986734347 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000 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*3.9875585347414 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.9937792673707 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 33 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1032 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3471.3585 0 -3471.3585 2033.3777 321 0 -3486.1768 0 -3486.1768 -3642.8751 Loop time of 1.9273 on 1 procs for 321 steps with 1032 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3471.35845338 -3486.1767955 -3486.1767955 Force two-norm initial, final = 21.7146 7.08101e-06 Force max component initial, final = 5.12055 1.59088e-06 Final line search alpha, max atom move = 1 1.59088e-06 Iterations, force evaluations = 321 634 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8837 | 1.8837 | 1.8837 | 0.0 | 97.74 Neigh | 0.0025518 | 0.0025518 | 0.0025518 | 0.0 | 0.13 Comm | 0.026417 | 0.026417 | 0.026417 | 0.0 | 1.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0146 | | | 0.76 Nlocal: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653 ave 7653 max 7653 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: 142540 ave 142540 max 142540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142540 Ave neighs/atom = 138.12 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) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press Volume 321 0 -3486.1768 0 -3486.1768 -3642.8751 16486.235 1321 0 -3486.2377 0 -3486.2377 -664.78311 16432.721 Loop time of 6.3216 on 1 procs for 1000 steps with 1032 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3486.1767955 -3486.2376977 -3486.23769792 Force two-norm initial, final = 49.1166 0.0668857 Force max component initial, final = 38.9812 0.0600952 Final line search alpha, max atom move = 0.043458 0.00261162 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9748 | 5.9748 | 5.9748 | 0.0 | 94.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.078168 | 0.078168 | 0.078168 | 0.0 | 1.24 Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2685 | | | 4.25 Nlocal: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653 ave 7653 max 7653 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: 142176 ave 142176 max 142176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142176 Ave neighs/atom = 137.767 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 -1.81000000000002 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.172 | 5.172 | 5.172 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3486.2377 0 -3486.2377 -664.78311 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1032 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: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653 ave 7653 max 7653 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: 142384 ave 142384 max 142384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142384 Ave neighs/atom = 137.969 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) = 5.172 | 5.172 | 5.172 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 -3486.2377 -3486.2377 32.064698 128.60287 3.9850307 -664.78311 -664.78311 5.8439144 -2001.0097 0.81644793 2.5264984 443.59984 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1032 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: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653 ave 7653 max 7653 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71192 ave 71192 max 71192 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 142384 ave 142384 max 142384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142384 Ave neighs/atom = 137.969 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_059.4898/numatoms.out 1032 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3486.23769792346-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3486.23769792346-1032*${isolated_atom_energy} variable adjusted_pe_metal equal -3486.23769792346-1032*-1.81000000000002 print "${adjusted_pe_metal} eV" file output/dump_059.4898/energy.out -1618.31769792344 eV print "${mindist_metal} Angstroms" file output/dump_059.4898/mindistance.out 2.52649840270409 Angstroms write_dump all cfg output/dump_059.4898/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_059.4898/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:08