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 61.15031369531198*${_u_distance} variable xmax_converted equal 61.15031369531198*1 variable ymin_converted equal -61.154354621783334*${_u_distance} variable ymin_converted equal -61.154354621783334*1 variable ymax_converted equal 61.154354621783334*${_u_distance} variable ymax_converted equal 61.154354621783334*1 variable zmin_converted equal 0.0*${_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 61.150313695312 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.150313695312 -61.1543546217833 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.150313695312 -61.1543546217833 61.1543546217833 ${zmin_converted} ${zmax_converted} units box region whole block 0 61.150313695312 -61.1543546217833 61.1543546217833 0 ${zmax_converted} units box region whole block 0 61.150313695312 -61.1543546217833 61.1543546217833 0 4.04092647135258 units box create_box 2 whole Created orthogonal box = (0 -61.1544 0) to (61.1503 61.1544 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 61.1543546217833 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -2 0 orient y 2 15 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 15 -2 0 orient y 2 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.53954 4.53954 4.04093 create_atoms 1 region upper Created 918 atoms create_atoms CPU = 0.000229836 secs group upper type 1 918 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.8097356776897 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.1543546217833 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 2 0 orient y -2 15 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 15 2 0 orient y -2 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.53954 4.53954 4.04093 create_atoms 2 region lower Created 918 atoms create_atoms CPU = 0.000123024 secs group lower type 2 918 atoms in group lower displace_atoms lower move -6.8097356776897 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 25 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 26 atoms, new total = 1810 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 25 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) = 10.28 | 10.28 | 10.28 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7037.5169 0 -7037.5169 -439.60813 312 0 -7051.4012 0 -7051.4012 -4572.6388 Loop time of 7.44793 on 1 procs for 312 steps with 1810 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 = -7037.51694162 -7051.40120376 -7051.40120376 Force two-norm initial, final = 15.3179 3.4784e-06 Force max component initial, final = 3.63327 9.78185e-07 Final line search alpha, max atom move = 1 9.78185e-07 Iterations, force evaluations = 312 619 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3577 | 7.3577 | 7.3577 | 0.0 | 98.79 Neigh | 0.011184 | 0.011184 | 0.011184 | 0.0 | 0.15 Comm | 0.053968 | 0.053968 | 0.053968 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02511 | | | 0.34 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14942 ave 14942 max 14942 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: 444732 ave 444732 max 444732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444732 Ave neighs/atom = 245.708 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) = 10.28 | 10.28 | 10.28 Mbytes Step Temp E_pair E_mol TotEng Press Volume 312 0 -7051.4012 0 -7051.4012 -4572.6388 30222.962 1312 0 -7051.5544 0 -7051.5544 -1166.2673 30096.378 Loop time of 23.1406 on 1 procs for 1000 steps with 1810 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 = -7051.40120376 -7051.55435135 -7051.55435135 Force two-norm initial, final = 101.672 0.000872887 Force max component initial, final = 76.4108 0.000828036 Final line search alpha, max atom move = 1 0.000828036 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.507 | 22.507 | 22.507 | 0.0 | 97.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15223 | 0.15223 | 0.15223 | 0.0 | 0.66 Output | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4818 | | | 2.08 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14942 ave 14942 max 14942 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: 444676 ave 444676 max 444676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444676 Ave neighs/atom = 245.677 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 25 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) = 9.796 | 9.796 | 9.796 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7051.5544 0 -7051.5544 -1166.2673 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1810 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 | | 1.192e-06 | | |100.00 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14960 ave 14960 max 14960 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: 444960 ave 444960 max 444960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444960 Ave neighs/atom = 245.834 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) = 9.796 | 9.796 | 9.796 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 -7051.5544 -7051.5544 61.051333 122.30871 4.0305258 -1166.2673 -1166.2673 -5.2646841e-05 -3498.7578 -0.043966913 2.5036313 1027.5589 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1810 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 | | 1.192e-06 | | |100.00 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14960 ave 14960 max 14960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 222480 ave 222480 max 222480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 444960 ave 444960 max 444960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444960 Ave neighs/atom = 245.834 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_015.1893/numatoms.out 1810 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7051.55435134869-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7051.55435134869-1810*${isolated_atom_energy} variable adjusted_pe_metal equal -7051.55435134869-1810*0 print "${adjusted_pe_metal} eV" file output/dump_015.1893/energy.out -7051.55435134869 eV print "${mindist_metal} Angstroms" file output/dump_015.1893/mindistance.out 2.50363131940261 Angstroms write_dump all cfg output/dump_015.1893/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_015.1893/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:30