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 4.032082714140415*${_u_distance} variable lattice_constant_converted equal 4.032082714140415*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 60.61549446378711*${_u_distance} variable xmax_converted equal 60.61549446378711*1 variable ymin_converted equal -60.61952654650125*${_u_distance} variable ymin_converted equal -60.61952654650125*1 variable ymax_converted equal 60.61952654650125*${_u_distance} variable ymax_converted equal 60.61952654650125*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082714140415*${_u_distance} variable zmax_converted equal 4.032082714140415*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03208271414042 Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 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 60.6154944637871 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.6154944637871 -60.6195265465012 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.6154944637871 -60.6195265465012 60.6195265465012 ${zmin_converted} ${zmax_converted} units box region whole block 0 60.6154944637871 -60.6195265465012 60.6195265465012 0 ${zmax_converted} units box region whole block 0 60.6154944637871 -60.6195265465012 60.6195265465012 0 4.03208271414042 units box create_box 2 whole Created orthogonal box = (0 -60.6195 0) to (60.6155 60.6195 4.03208) 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 60.6195265465012 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 lattice fcc 4.03208271414042 orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.29136 4.29136 4.03208 create_atoms 1 region upper Created 906 atoms create_atoms CPU = 0.000324011 secs group upper type 1 906 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.764983370267808 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -60.6195265465012 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 lattice fcc 4.03208271414042 orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.29136 4.29136 4.03208 create_atoms 2 region lower Created 906 atoms create_atoms CPU = 0.00018096 secs group lower type 2 906 atoms in group lower displace_atoms lower move -6.764983370267808 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_ErcolessiAdams_1994_Al__MO_324507536345_002 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.03208271414042 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604135707021 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 17 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1784 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 17 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.564 | 5.564 | 5.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5964.921 0 -5964.921 -101.78183 228 0 -5981.7066 0 -5981.7066 -7986.3132 Loop time of 2.84003 on 1 procs for 228 steps with 1784 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 = -5964.92095012 -5981.70660688 -5981.70660688 Force two-norm initial, final = 15.049 4.66781e-06 Force max component initial, final = 3.97302 9.62951e-07 Final line search alpha, max atom move = 1 9.62951e-07 Iterations, force evaluations = 228 447 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7906 | 2.7906 | 2.7906 | 0.0 | 98.26 Neigh | 0.0036709 | 0.0036709 | 0.0036709 | 0.0 | 0.13 Comm | 0.027789 | 0.027789 | 0.027789 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01793 | | | 0.63 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10651 ave 10651 max 10651 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: 187944 ave 187944 max 187944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187944 Ave neighs/atom = 105.35 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) = 5.564 | 5.564 | 5.564 Mbytes Step Temp E_pair E_mol TotEng Press Volume 228 0 -5981.7066 0 -5981.7066 -7986.3132 29631.635 1228 0 -5982.0795 0 -5982.0795 -2770.947 29432.325 Loop time of 12.7057 on 1 procs for 1000 steps with 1784 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 = -5981.70660688 -5982.07950708 -5982.07950708 Force two-norm initial, final = 154.253 0.0159048 Force max component initial, final = 115.075 0.0127245 Final line search alpha, max atom move = 0.846633 0.010773 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.184 | 12.184 | 12.184 | 0.0 | 95.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11475 | 0.11475 | 0.11475 | 0.0 | 0.90 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4071 | | | 3.20 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10650 ave 10650 max 10650 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: 189896 ave 189896 max 189896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189896 Ave neighs/atom = 106.444 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 16 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 5.7 | 5.7 | 5.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5982.0795 0 -5982.0795 -2770.947 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10660 ave 10660 max 10660 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: 201296 ave 201296 max 201296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201296 Ave neighs/atom = 112.834 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) = 5.7 | 5.7 | 5.7 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 -5982.0795 -5982.0795 60.363513 121.23905 4.0216802 -2770.947 -2770.947 -0.68979326 -8311.6455 -0.50580295 2.5914198 344.69486 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10660 ave 10660 max 10660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100648 ave 100648 max 100648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201296 ave 201296 max 201296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201296 Ave neighs/atom = 112.834 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_007.6281/numatoms.out 1784 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5982.07950708268-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5982.07950708268-1784*${isolated_atom_energy} variable adjusted_pe_metal equal -5982.07950708268-1784*0 print "${adjusted_pe_metal} eV" file output/dump_007.6281/energy.out -5982.07950708268 eV print "${mindist_metal} Angstroms" file output/dump_007.6281/mindistance.out 2.59141983574997 Angstroms write_dump all cfg output/dump_007.6281/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_007.6281/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15