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 4.050000011920929*${_u_distance} variable lattice_constant_converted equal 4.050000011920929*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 42.28324148554588*${_u_distance} variable xmax_converted equal 42.28324148554588*1 variable ymin_converted equal -42.2872914855578*${_u_distance} variable ymin_converted equal -42.2872914855578*1 variable ymax_converted equal 42.2872914855578*${_u_distance} variable ymax_converted equal 42.2872914855578*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050000011920929*${_u_distance} variable zmax_converted equal 4.050000011920929*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000001192093 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 42.2832414855459 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2832414855459 -42.2872914855578 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2832414855459 -42.2872914855578 42.2872914855578 ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2832414855459 -42.2872914855578 42.2872914855578 0 ${zmax_converted} units box region whole block 0 42.2832414855459 -42.2872914855578 42.2872914855578 0 4.05000001192093 units box create_box 2 whole Created orthogonal box = (0 -42.2873 0) to (42.2832 42.2873 4.05) 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 42.2872914855578 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 lattice fcc 4.05000001192093 orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.04296 5.04296 4.05 create_atoms 1 region upper Created 437 atoms create_atoms CPU = 0.00018692 secs group upper type 1 437 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.698137929009748 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.2872914855578 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 lattice fcc 4.05000001192093 orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.04296 5.04296 4.05 create_atoms 2 region lower Created 437 atoms create_atoms CPU = 7.51019e-05 secs group lower type 2 437 atoms in group lower displace_atoms lower move -4.698137929009748 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_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*4.05000001192093 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500000596046 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 10 20 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 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 17 atoms, new total = 857 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 10 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.968 | 4.968 | 4.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2858.3169 0 -2858.3169 -3083.5165 196 0 -2867.2395 0 -2867.2395 -6001.236 Loop time of 1.09322 on 1 procs for 196 steps with 857 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 = -2858.31688468 -2867.23946024 -2867.23946024 Force two-norm initial, final = 8.7338 6.75686e-06 Force max component initial, final = 2.14932 9.77079e-07 Final line search alpha, max atom move = 1 9.77079e-07 Iterations, force evaluations = 196 383 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0742 | 1.0742 | 1.0742 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012014 | 0.012014 | 0.012014 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00703 | | | 0.64 Nlocal: 857 ave 857 max 857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6418 ave 6418 max 6418 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: 147730 ave 147730 max 147730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147730 Ave neighs/atom = 172.38 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) = 4.969 | 4.969 | 4.969 Mbytes Step Temp E_pair E_mol TotEng Press Volume 196 0 -2867.2395 0 -2867.2395 -6001.236 14483.154 1196 0 -2867.3933 0 -2867.3933 -1181.9853 14393.186 Loop time of 7.62776 on 1 procs for 1000 steps with 857 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2867.23946024 -2867.39333833 -2867.39333833 Force two-norm initial, final = 69.4378 0.00583053 Force max component initial, final = 50.5407 0.00474768 Final line search alpha, max atom move = 0.37317 0.00177169 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3194 | 7.3194 | 7.3194 | 0.0 | 95.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.069503 | 0.069503 | 0.069503 | 0.0 | 0.91 Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2388 | | | 3.13 Nlocal: 857 ave 857 max 857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6501 ave 6501 max 6501 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: 147526 ave 147526 max 147526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147526 Ave neighs/atom = 172.142 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 -0.00607941459516994 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 10 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 5.107 | 5.107 | 5.107 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2867.3933 0 -2867.3933 -1181.9853 Loop time of 9.53674e-07 on 1 procs for 0 steps with 857 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: 857 ave 857 max 857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6534 ave 6534 max 6534 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: 147764 ave 147764 max 147764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147764 Ave neighs/atom = 172.42 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) = 5.107 | 5.107 | 5.107 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 -2867.3933 -2867.3933 42.16677 84.574583 4.0359591 -1181.9853 -1181.9853 0.057780132 -3546.5402 0.52665507 2.5613556 764.59267 Loop time of 1.90735e-06 on 1 procs for 0 steps with 857 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: 857 ave 857 max 857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6534 ave 6534 max 6534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73882 ave 73882 max 73882 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 147764 ave 147764 max 147764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147764 Ave neighs/atom = 172.42 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_033.3985/numatoms.out 857 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2867.39333833401-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2867.39333833401-857*${isolated_atom_energy} variable adjusted_pe_metal equal -2867.39333833401-857*-0.00607941459516994 print "${adjusted_pe_metal} eV" file output/dump_033.3985/energy.out -2862.18328002595 eV print "${mindist_metal} Angstroms" file output/dump_033.3985/mindistance.out 2.56135563839671 Angstroms write_dump all cfg output/dump_033.3985/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_033.3985/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:08