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 23.562447865063845*${_u_distance} variable xmax_converted equal 23.562447865063845*1 variable ymin_converted equal -47.128936656599045*${_u_distance} variable ymin_converted equal -47.128936656599045*1 variable ymax_converted equal 47.128936656599045*${_u_distance} variable ymax_converted equal 47.128936656599045*1 variable zmin_converted equal 0.0*${_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 23.5624478650638 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 23.5624478650638 -47.128936656599 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 23.5624478650638 -47.128936656599 47.128936656599 ${zmin_converted} ${zmax_converted} units box region whole block 0 23.5624478650638 -47.128936656599 47.128936656599 0 ${zmax_converted} units box region whole block 0 23.5624478650638 -47.128936656599 47.128936656599 0 4.04092647135258 units box create_box 2 whole Created orthogonal box = (0 -47.1289 0) to (23.5624 47.1289 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 47.128936656599 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -3 0 orient y 3 5 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 5 -3 0 orient y 3 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.54411 5.54411 4.04093 create_atoms 1 region upper Created 274 atoms create_atoms CPU = 0.000225067 secs group upper type 1 274 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.623928352680385 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -47.128936656599 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 3 0 orient y -3 5 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 5 3 0 orient y -3 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.54411 5.54411 4.04093 create_atoms 2 region lower Created 274 atoms create_atoms CPU = 9.67979e-05 secs group lower type 2 274 atoms in group lower displace_atoms lower move -2.623928352680385 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 5 19 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 12 atoms, new total = 536 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 = 5 19 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) = 4.926 | 4.926 | 4.926 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2075.6123 0 -2075.6123 1618.3084 259 0 -2085.2502 0 -2085.2502 -3926.4518 Loop time of 1.98175 on 1 procs for 259 steps with 536 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 = -2075.61226115 -2085.25015896 -2085.25015896 Force two-norm initial, final = 17.8184 1.74826e-05 Force max component initial, final = 5.27641 4.77368e-06 Final line search alpha, max atom move = 1 4.77368e-06 Iterations, force evaluations = 259 516 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9504 | 1.9504 | 1.9504 | 0.0 | 98.42 Neigh | 0.0022931 | 0.0022931 | 0.0022931 | 0.0 | 0.12 Comm | 0.020758 | 0.020758 | 0.020758 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008339 | | | 0.42 Nlocal: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6627 ave 6627 max 6627 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: 131072 ave 131072 max 131072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131072 Ave neighs/atom = 244.537 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) = 4.926 | 4.926 | 4.926 Mbytes Step Temp E_pair E_mol TotEng Press Volume 259 0 -2085.2502 0 -2085.2502 -3926.4518 8974.6804 1259 0 -2085.2895 0 -2085.2895 -757.72062 8940.0051 Loop time of 8.04941 on 1 procs for 1000 steps with 536 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 = -2085.25015896 -2085.2895023 -2085.28950231 Force two-norm initial, final = 28.4497 0.0104804 Force max component initial, final = 20.9665 0.00931509 Final line search alpha, max atom move = 0.365466 0.00340435 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7587 | 7.7587 | 7.7587 | 0.0 | 96.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.072 | 0.072 | 0.072 | 0.0 | 0.89 Output | 7.2956e-05 | 7.2956e-05 | 7.2956e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2186 | | | 2.72 Nlocal: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6551 ave 6551 max 6551 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: 130600 ave 130600 max 130600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130600 Ave neighs/atom = 243.657 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 = 5 19 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2085.2895 0 -2085.2895 -757.72062 Loop time of 1.19209e-06 on 1 procs for 0 steps with 536 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: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6584 ave 6584 max 6584 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: 131012 ave 131012 max 131012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131012 Ave neighs/atom = 244.425 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) = 5.064 | 5.064 | 5.064 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 -2085.2895 -2085.2895 23.52749 94.257873 4.0312945 -757.72062 -757.72062 0.27831217 -2275.1056 1.6654174 2.5169217 428.83685 Loop time of 9.53674e-07 on 1 procs for 0 steps with 536 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: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6584 ave 6584 max 6584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65506 ave 65506 max 65506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 131012 ave 131012 max 131012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131012 Ave neighs/atom = 244.425 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_061.9275/numatoms.out 536 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2085.28950230816-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2085.28950230816-536*${isolated_atom_energy} variable adjusted_pe_metal equal -2085.28950230816-536*0 print "${adjusted_pe_metal} eV" file output/dump_061.9275/energy.out -2085.28950230816 eV print "${mindist_metal} Angstroms" file output/dump_061.9275/mindistance.out 2.51692174043352 Angstroms write_dump all cfg output/dump_061.9275/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_061.9275/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:10