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 4.031999975442886*${_u_distance} variable lattice_constant_converted equal 4.031999975442886*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 9.015826030367776*${_u_distance} variable xmax_converted equal 9.015826030367776*1 variable ymin_converted equal -45.08316215181433*${_u_distance} variable ymin_converted equal -45.08316215181433*1 variable ymax_converted equal 45.08316215181433*${_u_distance} variable ymax_converted equal 45.08316215181433*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031999975442886*${_u_distance} variable zmax_converted equal 4.031999975442886*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03199997544289 Lattice spacing in x,y,z = 4.032 4.032 4.032 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 9.01582603036778 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01582603036778 -45.0831621518143 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01582603036778 -45.0831621518143 45.0831621518143 ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01582603036778 -45.0831621518143 45.0831621518143 0 ${zmax_converted} units box region whole block 0 9.01582603036778 -45.0831621518143 45.0831621518143 0 4.03199997544289 units box create_box 2 whole Created orthogonal box = (0 -45.0832 0) to (9.01583 45.0832 4.032) 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 45.0831621518143 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.4095 5.4095 4.032 create_atoms 1 region upper Created 102 atoms create_atoms CPU = 0.000144005 secs group upper type 1 102 atoms in group upper mass 1 26.981538*${_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 -45.0831621518143 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.4095 5.4095 4.032 create_atoms 2 region lower Created 102 atoms create_atoms CPU = 3.50475e-05 secs group lower type 2 102 atoms in group lower displace_atoms lower move -1.0062305898749053 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_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*4.03199997544289 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01599998772144 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 3 21 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 8.875 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 3 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -653.28218 0 -653.28218 -2743.1692 209 0 -655.9564 0 -655.9564 -9570.4052 Loop time of 0.281915 on 1 procs for 209 steps with 196 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -653.282183906 -655.956400277 -655.956400277 Force two-norm initial, final = 7.12679 1.56038e-06 Force max component initial, final = 2.84928 1.90545e-07 Final line search alpha, max atom move = 1 1.90545e-07 Iterations, force evaluations = 209 413 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27292 | 0.27292 | 0.27292 | 0.0 | 96.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0068195 | 0.0068195 | 0.0068195 | 0.0 | 2.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00218 | | | 0.77 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3500 ave 3500 max 3500 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: 33852 ave 33852 max 33852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33852 Ave neighs/atom = 172.714 Neighbor list builds = 0 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) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 209 0 -655.9564 0 -655.9564 -9570.4052 3277.7091 1209 0 -656.04794 0 -656.04794 -1704.4689 3244.5631 Loop time of 1.70643 on 1 procs for 1000 steps with 196 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -655.956400277 -656.047941379 -656.04794138 Force two-norm initial, final = 25.1312 0.000890205 Force max component initial, final = 18.2667 0.000599948 Final line search alpha, max atom move = 0.68995 0.000413935 Iterations, force evaluations = 1000 1994 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5732 | 1.5732 | 1.5732 | 0.0 | 92.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.035093 | 0.035093 | 0.035093 | 0.0 | 2.06 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09815 | | | 5.75 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3567 ave 3567 max 3567 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: 34112 ave 34112 max 34112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34112 Ave neighs/atom = 174.041 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 3 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 4.578 | 4.578 | 4.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -656.04794 0 -656.04794 -1704.4689 Loop time of 1.90735e-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 | | 1.907e-06 | | |100.00 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3615 ave 3615 max 3615 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: 34176 ave 34176 max 34176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34176 Ave neighs/atom = 174.367 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) = 4.578 | 4.578 | 4.578 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 -656.04794 -656.04794 8.9845804 90.166324 4.0051064 -1704.4689 -1704.4689 0.13354135 -5113.2459 -0.29428059 2.594722 155.16739 Loop time of 1.90735e-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 | | 1.907e-06 | | |100.00 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3615 ave 3615 max 3615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17088 ave 17088 max 17088 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34176 ave 34176 max 34176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34176 Ave neighs/atom = 174.367 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -656.047941379905-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -656.047941379905-196*${isolated_atom_energy} variable adjusted_pe_metal equal -656.047941379905-196*0 print "${adjusted_pe_metal} eV" file output/dump_053.1301/energy.out -656.047941379905 eV print "${mindist_metal} Angstroms" file output/dump_053.1301/mindistance.out 2.59472197372521 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: 0:00:02