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 59.939988824120476*${_u_distance} variable xmax_converted equal 59.939988824120476*1 variable ymin_converted equal -59.94402082409592*${_u_distance} variable ymin_converted equal -59.94402082409592*1 variable ymax_converted equal 59.94402082409592*${_u_distance} variable ymax_converted equal 59.94402082409592*1 variable zmin_converted equal 0.0*${_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 59.9399888241205 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.9399888241205 -59.9440208240959 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.9399888241205 -59.9440208240959 59.9440208240959 ${zmin_converted} ${zmax_converted} units box region whole block 0 59.9399888241205 -59.9440208240959 59.9440208240959 0 ${zmax_converted} units box region whole block 0 59.9399888241205 -59.9440208240959 59.9440208240959 0 4.03199997544289 units box create_box 2 whole Created orthogonal box = (0 -59.944 0) to (59.94 59.944 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 59.9440208240959 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -5 0 orient y 5 14 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 14 -5 0 orient y 5 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.15321 5.15321 4.032 create_atoms 1 region upper Created 885 atoms create_atoms CPU = 0.000360012 secs group upper type 1 885 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.689730936293327 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -59.9440208240959 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 5 0 orient y -5 14 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 14 5 0 orient y -5 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.15321 5.15321 4.032 create_atoms 2 region lower Created 885 atoms create_atoms CPU = 0.000211954 secs group lower type 2 885 atoms in group lower displace_atoms lower move -6.689730936293327 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 14 28 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 22 atoms, new total = 1748 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 = 14 28 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) = 5.979 | 5.979 | 5.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5834.4556 0 -5834.4556 344.24342 319 0 -5856.3109 0 -5856.3109 -4639.5239 Loop time of 4.1624 on 1 procs for 319 steps with 1748 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5834.45563048 -5856.31086682 -5856.31086682 Force two-norm initial, final = 23.8708 7.24674e-07 Force max component initial, final = 4.75604 1.35814e-07 Final line search alpha, max atom move = 1 1.35814e-07 Iterations, force evaluations = 319 618 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0844 | 4.0844 | 4.0844 | 0.0 | 98.13 Neigh | 0.012681 | 0.012681 | 0.012681 | 0.0 | 0.30 Comm | 0.042008 | 0.042008 | 0.042008 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02333 | | | 0.56 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11945 ave 11945 max 11945 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: 306094 ave 306094 max 306094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306094 Ave neighs/atom = 175.111 Neighbor list builds = 2 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) = 5.979 | 5.979 | 5.979 Mbytes Step Temp E_pair E_mol TotEng Press Volume 319 0 -5856.3109 0 -5856.3109 -4639.5239 28974.306 1319 0 -5856.4936 0 -5856.4936 -830.23692 28834.425 Loop time of 14.1883 on 1 procs for 1000 steps with 1748 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 = -5856.31086682 -5856.49359287 -5856.49359309 Force two-norm initial, final = 106.72 0.0896791 Force max component initial, final = 78.3785 0.0873349 Final line search alpha, max atom move = 0.0495937 0.00433126 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.67 | 13.67 | 13.67 | 0.0 | 96.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11382 | 0.11382 | 0.11382 | 0.0 | 0.80 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4043 | | | 2.85 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11242 ave 11242 max 11242 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: 305876 ave 305876 max 305876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305876 Ave neighs/atom = 174.986 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 = 14 28 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) = 6.108 | 6.108 | 6.108 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5856.4936 0 -5856.4936 -830.23692 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1748 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: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11252 ave 11252 max 11252 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: 306018 ave 306018 max 306018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306018 Ave neighs/atom = 175.068 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) = 6.108 | 6.108 | 6.108 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 -5856.4936 -5856.4936 59.775113 119.88804 4.023602 -830.23692 -830.23692 4.8393912 -2495.8078 0.25761502 2.5671204 1034.266 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1748 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: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11252 ave 11252 max 11252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153009 ave 153009 max 153009 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 306018 ave 306018 max 306018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306018 Ave neighs/atom = 175.068 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.3076/numatoms.out 1748 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5856.49359309257-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5856.49359309257-1748*${isolated_atom_energy} variable adjusted_pe_metal equal -5856.49359309257-1748*0 print "${adjusted_pe_metal} eV" file output/dump_039.3076/energy.out -5856.49359309257 eV print "${mindist_metal} Angstroms" file output/dump_039.3076/mindistance.out 2.56712036426324 Angstroms write_dump all cfg output/dump_039.3076/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_039.3076/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:18