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 4.0499994456768045*${_u_distance} variable lattice_constant_converted equal 4.0499994456768045*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 38.20761835535468*${_u_distance} variable xmax_converted equal 38.20761835535468*1 variable ymin_converted equal -76.41928671015505*${_u_distance} variable ymin_converted equal -76.41928671015505*1 variable ymax_converted equal 76.41928671015505*${_u_distance} variable ymax_converted equal 76.41928671015505*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.0499994456768045*${_u_distance} variable zmax_converted equal 4.0499994456768045*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0499994456768 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 38.2076183553547 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 38.2076183553547 -76.419286710155 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 38.2076183553547 -76.419286710155 76.419286710155 ${zmin_converted} ${zmax_converted} units box region whole block 0 38.2076183553547 -76.419286710155 76.419286710155 0 ${zmax_converted} units box region whole block 0 38.2076183553547 -76.419286710155 76.419286710155 0 4.0499994456768 units box create_box 2 whole Created orthogonal box = (0 -76.4193 0) to (38.2076 76.4193 4.05) 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 76.419286710155 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -5 0 orient y 5 8 0 orient z 0 0 1 lattice fcc 4.0499994456768 orient x 8 -5 0 orient y 5 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.58089 5.58089 4.05 create_atoms 1 region upper Created 714 atoms create_atoms CPU = 0.000247002 secs group upper type 1 714 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.245291509425472 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -76.419286710155 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 5 0 orient y -5 8 0 orient z 0 0 1 lattice fcc 4.0499994456768 orient x 8 5 0 orient y -5 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.58089 5.58089 4.05 create_atoms 2 region lower Created 714 atoms create_atoms CPU = 0.000136137 secs group lower type 2 714 atoms in group lower displace_atoms lower move -4.245291509425472 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005 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*4.0499994456768 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0249997228384 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 9 36 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 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1412 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4723.288 0 -4723.288 -1082.3734 276 0 -4732.7436 0 -4732.7436 -2133.1332 Loop time of 2.93902 on 1 procs for 276 steps with 1412 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 = -4723.28795379 -4732.74360854 -4732.74360854 Force two-norm initial, final = 9.91827 7.21989e-06 Force max component initial, final = 2.1362 5.15602e-07 Final line search alpha, max atom move = 1 5.15602e-07 Iterations, force evaluations = 276 541 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8805 | 2.8805 | 2.8805 | 0.0 | 98.01 Neigh | 0.008507 | 0.008507 | 0.008507 | 0.0 | 0.29 Comm | 0.033053 | 0.033053 | 0.033053 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01701 | | | 0.58 Nlocal: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10571 ave 10571 max 10571 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: 245424 ave 245424 max 245424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245424 Ave neighs/atom = 173.813 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) = 5.54 | 5.54 | 5.54 Mbytes Step Temp E_pair E_mol TotEng Press Volume 276 0 -4732.7436 0 -4732.7436 -2133.1332 23650.368 1276 0 -4732.7794 0 -4732.7794 -318.45087 23595.468 Loop time of 12.1164 on 1 procs for 1000 steps with 1412 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 = -4732.74360854 -4732.7794033 -4732.7794033 Force two-norm initial, final = 42.8972 0.00219666 Force max component initial, final = 32.6236 0.0010308 Final line search alpha, max atom move = 0.452637 0.000466577 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.603 | 11.603 | 11.603 | 0.0 | 95.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11915 | 0.11915 | 0.11915 | 0.0 | 0.98 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3939 | | | 3.25 Nlocal: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11079 ave 11079 max 11079 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: 245440 ave 245440 max 245440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245440 Ave neighs/atom = 173.824 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 -0.061233718112 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 5.678 | 5.678 | 5.678 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4732.7794 0 -4732.7794 -318.45087 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1412 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: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11085 ave 11085 max 11085 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: 245552 ave 245552 max 245552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245552 Ave neighs/atom = 173.904 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) = 5.678 | 5.678 | 5.678 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 -4732.7794 -4732.7794 38.15333 152.83857 4.0463473 -318.45087 -318.45087 0.069893643 -955.48116 0.058662699 2.6121489 628.60858 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1412 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: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11085 ave 11085 max 11085 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122776 ave 122776 max 122776 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 245552 ave 245552 max 245552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245552 Ave neighs/atom = 173.904 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_064.0108/numatoms.out 1412 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4732.77940330137-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4732.77940330137-1412*${isolated_atom_energy} variable adjusted_pe_metal equal -4732.77940330137-1412*-0.061233718112 print "${adjusted_pe_metal} eV" file output/dump_064.0108/energy.out -4646.31739332723 eV print "${mindist_metal} Angstroms" file output/dump_064.0108/mindistance.out 2.61214890012218 Angstroms write_dump all cfg output/dump_064.0108/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_064.0108/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15