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 4.032073378562927*${_u_distance} variable lattice_constant_converted equal 4.032073378562927*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 61.546928965765595*${_u_distance} variable xmax_converted equal 61.546928965765595*1 variable ymin_converted equal -61.550961039144156*${_u_distance} variable ymin_converted equal -61.550961039144156*1 variable ymax_converted equal 61.550961039144156*${_u_distance} variable ymax_converted equal 61.550961039144156*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032073378562927*${_u_distance} variable zmax_converted equal 4.032073378562927*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03207337856293 Lattice spacing in x,y,z = 4.03207 4.03207 4.03207 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 61.5469289657656 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.5469289657656 -61.5509610391442 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.5469289657656 -61.5509610391442 61.5509610391442 ${zmin_converted} ${zmax_converted} units box region whole block 0 61.5469289657656 -61.5509610391442 61.5509610391442 0 ${zmax_converted} units box region whole block 0 61.5469289657656 -61.5509610391442 61.5509610391442 0 4.03207337856293 units box create_box 2 whole Created orthogonal box = (0 -61.551 0) to (61.5469 61.551 4.03207) 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 61.5509610391442 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -8 0 orient y 8 13 0 orient z 0 0 1 lattice fcc 4.03207337856293 orient x 13 -8 0 orient y 8 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.54715 5.54715 4.03207 create_atoms 1 region upper Created 933 atoms create_atoms CPU = 0.000483036 secs group upper type 1 933 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.868951885113186 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.5509610391442 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 8 0 orient y -8 13 0 orient z 0 0 1 lattice fcc 4.03207337856293 orient x 13 8 0 orient y -8 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.54715 5.54715 4.03207 create_atoms 2 region lower Created 933 atoms create_atoms CPU = 0.000336885 secs group lower type 2 933 atoms in group lower displace_atoms lower move -6.868951885113186 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_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*4.03207337856293 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01603668928146 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, 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 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1840 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 17 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.578 | 5.578 | 5.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6137.9074 0 -6137.9074 1026.4121 337 0 -6164.3154 0 -6164.3154 -5101.7312 Loop time of 3.13231 on 1 procs for 337 steps with 1840 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 = -6137.90742664 -6164.31543507 -6164.31543507 Force two-norm initial, final = 30.1416 2.72193e-05 Force max component initial, final = 6.63553 8.53683e-06 Final line search alpha, max atom move = 1 8.53683e-06 Iterations, force evaluations = 337 662 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0519 | 3.0519 | 3.0519 | 0.0 | 97.43 Neigh | 0.016336 | 0.016336 | 0.016336 | 0.0 | 0.52 Comm | 0.038551 | 0.038551 | 0.038551 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02551 | | | 0.81 Nlocal: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10096 ave 10096 max 10096 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: 241028 ave 241028 max 241028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241028 Ave neighs/atom = 130.993 Neighbor list builds = 3 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) = 5.578 | 5.578 | 5.578 Mbytes Step Temp E_pair E_mol TotEng Press Volume 337 0 -6164.3154 0 -6164.3154 -5101.7312 30549.186 1337 0 -6164.5583 0 -6164.5583 -1127.0178 30394.258 Loop time of 9.28071 on 1 procs for 1000 steps with 1840 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 = -6164.31543507 -6164.55831708 -6164.5583171 Force two-norm initial, final = 125.543 0.0137005 Force max component initial, final = 103.082 0.00876135 Final line search alpha, max atom move = 0.147408 0.00129149 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.8075 | 8.8075 | 8.8075 | 0.0 | 94.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10251 | 0.10251 | 0.10251 | 0.0 | 1.10 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3706 | | | 3.99 Nlocal: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10179 ave 10179 max 10179 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: 241032 ave 241032 max 241032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241032 Ave neighs/atom = 130.996 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 16 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 5.709 | 5.709 | 5.709 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6164.5583 0 -6164.5583 -1127.0178 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1840 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: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10219 ave 10219 max 10219 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: 241238 ave 241238 max 241238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241238 Ave neighs/atom = 131.108 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) = 5.709 | 5.709 | 5.709 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 -6164.5583 -6164.5583 61.313042 123.10192 4.0269279 -1127.0178 -1127.0178 0.46008301 -3381.0734 -0.44008257 2.5717352 1046.6676 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1840 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: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10219 ave 10219 max 10219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120619 ave 120619 max 120619 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 241238 ave 241238 max 241238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241238 Ave neighs/atom = 131.108 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_063.2150/numatoms.out 1840 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6164.55831709757-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6164.55831709757-1840*${isolated_atom_energy} variable adjusted_pe_metal equal -6164.55831709757-1840*0 print "${adjusted_pe_metal} eV" file output/dump_063.2150/energy.out -6164.55831709757 eV print "${mindist_metal} Angstroms" file output/dump_063.2150/mindistance.out 2.57173519973527 Angstroms write_dump all cfg output/dump_063.2150/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_063.2150/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12