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 4.050010219216347*${_u_distance} variable lattice_constant_converted equal 4.050010219216347*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 30.843958905981847*${_u_distance} variable xmax_converted equal 30.843958905981847*1 variable ymin_converted equal -61.69196782218291*${_u_distance} variable ymin_converted equal -61.69196782218291*1 variable ymax_converted equal 61.69196782218291*${_u_distance} variable ymax_converted equal 61.69196782218291*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050010219216347*${_u_distance} variable zmax_converted equal 4.050010219216347*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05001021921635 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 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 30.8439589059818 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8439589059818 -61.6919678221829 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8439589059818 -61.6919678221829 61.6919678221829 ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8439589059818 -61.6919678221829 61.6919678221829 0 ${zmax_converted} units box region whole block 0 30.8439589059818 -61.6919678221829 61.6919678221829 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -61.692 0) to (30.844 61.692 4.05001) 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 61.6919678221829 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.31792 5.31792 4.05001 create_atoms 1 region upper Created 466 atoms create_atoms CPU = 0.000304937 secs group upper type 1 466 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.4270978976387587 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.6919678221829 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.31792 5.31792 4.05001 create_atoms 2 region lower Created 466 atoms create_atoms CPU = 0.000149012 secs group lower type 2 466 atoms in group lower displace_atoms lower move -3.4270978976387587 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_005 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*4.05001021921635 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500510960818 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 9 33 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 916 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3087.9066 0 -3087.9066 -299.97918 481 0 -3095.1693 0 -3095.1693 -5502.786 Loop time of 2.25031 on 1 procs for 481 steps with 916 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 = -3087.90661616 -3095.16926964 -3095.16926964 Force two-norm initial, final = 13.1553 1.32792e-05 Force max component initial, final = 3.36753 3.07097e-06 Final line search alpha, max atom move = 1 3.07097e-06 Iterations, force evaluations = 481 959 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1892 | 2.1892 | 2.1892 | 0.0 | 97.28 Neigh | 0.0020719 | 0.0020719 | 0.0020719 | 0.0 | 0.09 Comm | 0.03824 | 0.03824 | 0.03824 | 0.0 | 1.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02084 | | | 0.93 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6577 ave 6577 max 6577 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: 99320 ave 99320 max 99320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99320 Ave neighs/atom = 108.428 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) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press Volume 481 0 -3095.1693 0 -3095.1693 -5502.786 15412.918 1481 0 -3095.3252 0 -3095.3252 -734.35809 15315.167 Loop time of 4.51976 on 1 procs for 1000 steps with 916 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 = -3095.16926964 -3095.32522037 -3095.32522058 Force two-norm initial, final = 70.2207 0.0443963 Force max component initial, final = 50.9853 0.034051 Final line search alpha, max atom move = 0.0399214 0.00135936 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2356 | 4.2356 | 4.2356 | 0.0 | 93.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.063946 | 0.063946 | 0.063946 | 0.0 | 1.41 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2202 | | | 4.87 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6412 ave 6412 max 6412 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: 99784 ave 99784 max 99784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99784 Ave neighs/atom = 108.934 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.121 | 5.121 | 5.121 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3095.3252 0 -3095.3252 -734.35809 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 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: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6434 ave 6434 max 6434 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: 104184 ave 104184 max 104184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104184 Ave neighs/atom = 113.738 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) = 5.121 | 5.121 | 5.121 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 -3095.3252 -3095.3252 30.736889 123.38394 4.0383431 -734.35809 -734.35809 3.5498405 -2207.0254 0.40128303 2.5520064 526.80877 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 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: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6434 ave 6434 max 6434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52092 ave 52092 max 52092 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 104184 ave 104184 max 104184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104184 Ave neighs/atom = 113.738 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_046.3972/numatoms.out 916 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3095.32522058057-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3095.32522058057-916*${isolated_atom_energy} variable adjusted_pe_metal equal -3095.32522058057-916*0 print "${adjusted_pe_metal} eV" file output/dump_046.3972/energy.out -3095.32522058057 eV print "${mindist_metal} Angstroms" file output/dump_046.3972/mindistance.out 2.5520063660599 Angstroms write_dump all cfg output/dump_046.3972/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_046.3972/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06