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 4.040926471352577*${_u_distance} variable lattice_constant_converted equal 4.040926471352577*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 62.73204847601899*${_u_distance} variable xmax_converted equal 62.73204847601899*1 variable ymin_converted equal -62.73608940249034*${_u_distance} variable ymin_converted equal -62.73608940249034*1 variable ymax_converted equal 62.73608940249034*${_u_distance} variable ymax_converted equal 62.73608940249034*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.040926471352577*${_u_distance} variable zmax_converted equal 4.040926471352577*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04092647135258 Lattice spacing in x,y,z = 4.04093 4.04093 4.04093 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 62.732048476019 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 62.732048476019 -62.7360894024903 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 62.732048476019 -62.7360894024903 62.7360894024903 ${zmin_converted} ${zmax_converted} units box region whole block 0 62.732048476019 -62.7360894024903 62.7360894024903 0 ${zmax_converted} units box region whole block 0 62.732048476019 -62.7360894024903 62.7360894024903 0 4.04092647135258 units box create_box 2 whole Created orthogonal box = (0 -62.7361 0) to (62.732 62.7361 4.04093) 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 62.7360894024903 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.94568 4.94568 4.04093 create_atoms 1 region upper Created 966 atoms create_atoms CPU = 0.000355005 secs group upper type 1 966 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.985878613317011 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -62.7360894024903 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.94568 4.94568 4.04093 create_atoms 2 region lower Created 966 atoms create_atoms CPU = 0.000224113 secs group lower type 2 966 atoms in group lower displace_atoms lower move -6.985878613317011 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_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*4.04092647135258 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02046323567629 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 13 26 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1904 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 13 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.31 | 10.31 | 10.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7400.76 0 -7400.76 -637.4465 368 0 -7416.8331 0 -7416.8331 -4738.9898 Loop time of 8.59767 on 1 procs for 368 steps with 1904 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7400.76000299 -7416.83305946 -7416.83305946 Force two-norm initial, final = 17.3031 5.84801e-08 Force max component initial, final = 3.64621 1.76845e-08 Final line search alpha, max atom move = 1 1.76845e-08 Iterations, force evaluations = 368 726 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.4951 | 8.4951 | 8.4951 | 0.0 | 98.81 Neigh | 0.0081592 | 0.0081592 | 0.0081592 | 0.0 | 0.09 Comm | 0.065103 | 0.065103 | 0.065103 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02933 | | | 0.34 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15520 ave 15520 max 15520 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: 466828 ave 466828 max 466828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466828 Ave neighs/atom = 245.183 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) = 10.31 | 10.31 | 10.31 Mbytes Step Temp E_pair E_mol TotEng Press Volume 368 0 -7416.8331 0 -7416.8331 -4738.9898 31806.645 1368 0 -7417.0255 0 -7417.0255 -1026.8984 31660.932 Loop time of 24.8293 on 1 procs for 1000 steps with 1904 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 = -7416.83305946 -7417.02547177 -7417.02547182 Force two-norm initial, final = 116.967 0.0233739 Force max component initial, final = 87.4835 0.0210058 Final line search alpha, max atom move = 0.125956 0.0026458 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.159 | 24.159 | 24.159 | 0.0 | 97.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.16093 | 0.16093 | 0.16093 | 0.0 | 0.65 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5096 | | | 2.05 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15532 ave 15532 max 15532 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: 467800 ave 467800 max 467800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 467800 Ave neighs/atom = 245.693 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 13 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 9.819 | 9.819 | 9.819 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7417.0255 0 -7417.0255 -1026.8984 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1904 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: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15532 ave 15532 max 15532 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: 468144 ave 468144 max 468144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468144 Ave neighs/atom = 245.874 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) = 9.819 | 9.819 | 9.819 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 -7417.0255 -7417.0255 62.620026 125.47218 4.0296099 -1026.8984 -1026.8984 -1.0610825 -3079.4292 -0.20498384 2.5178701 1121.286 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1904 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: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15532 ave 15532 max 15532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 234072 ave 234072 max 234072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 468144 ave 468144 max 468144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468144 Ave neighs/atom = 245.874 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_029.8628/numatoms.out 1904 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7417.02547182291-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7417.02547182291-1904*${isolated_atom_energy} variable adjusted_pe_metal equal -7417.02547182291-1904*0 print "${adjusted_pe_metal} eV" file output/dump_029.8628/energy.out -7417.02547182291 eV print "${mindist_metal} Angstroms" file output/dump_029.8628/mindistance.out 2.51787008572648 Angstroms write_dump all cfg output/dump_029.8628/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_029.8628/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:33