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 4.039798453450203*${_u_distance} variable lattice_constant_converted equal 4.039798453450203*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 16.656515729782058*${_u_distance} variable xmax_converted equal 16.656515729782058*1 variable ymin_converted equal -49.97358698779962*${_u_distance} variable ymin_converted equal -49.97358698779962*1 variable ymax_converted equal 49.97358698779962*${_u_distance} variable ymax_converted equal 49.97358698779962*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.039798453450203*${_u_distance} variable zmax_converted equal 4.039798453450203*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0397984534502 Lattice spacing in x,y,z = 4.0398 4.0398 4.0398 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 16.6565157297821 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6565157297821 -49.9735869877996 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6565157297821 -49.9735869877996 49.9735869877996 ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6565157297821 -49.9735869877996 49.9735869877996 0 ${zmax_converted} units box region whole block 0 16.6565157297821 -49.9735869877996 49.9735869877996 0 4.0397984534502 units box create_box 2 whole Created orthogonal box = (0 -49.9736 0) to (16.6565 49.9736 4.0398) 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 49.9735869877996 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.89898 4.89898 4.0398 create_atoms 1 region upper Created 206 atoms create_atoms CPU = 0.000156879 secs group upper type 1 206 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.8553975315279474 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -49.9735869877996 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.89898 4.89898 4.0398 create_atoms 2 region lower Created 206 atoms create_atoms CPU = 5.10216e-05 secs group lower type 2 206 atoms in group lower displace_atoms lower move -1.8553975315279474 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Al__MO_279544746097_002 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.0397984534502 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0198992267251 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 17 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.939 | 4.939 | 4.939 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1144.0149 0 -1144.0149 3761.3335 220 0 -1158.3916 0 -1158.3916 -3552.788 Loop time of 1.70858 on 1 procs for 220 steps with 404 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1144.01492401 -1158.39158102 -1158.39158102 Force two-norm initial, final = 22.8687 6.48333e-07 Force max component initial, final = 7.10688 6.70966e-08 Final line search alpha, max atom move = 1 6.70966e-08 Iterations, force evaluations = 220 431 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6784 | 1.6784 | 1.6784 | 0.0 | 98.24 Neigh | 0.0044541 | 0.0044541 | 0.0044541 | 0.0 | 0.26 Comm | 0.019298 | 0.019298 | 0.019298 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006403 | | | 0.37 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8031 ave 8031 max 8031 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: 162508 ave 162508 max 162508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162508 Ave neighs/atom = 402.248 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) = 4.939 | 4.939 | 4.939 Mbytes Step Temp E_pair E_mol TotEng Press Volume 220 0 -1158.3916 0 -1158.3916 -3552.788 6725.342 1220 0 -1158.4287 0 -1158.4287 -368.00565 6696.518 Loop time of 8.11707 on 1 procs for 1000 steps with 404 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 = -1158.39158102 -1158.42872728 -1158.42872728 Force two-norm initial, final = 20.8891 0.00198557 Force max component initial, final = 17.0515 0.00186326 Final line search alpha, max atom move = 1 0.00186326 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7962 | 7.7962 | 7.7962 | 0.0 | 96.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.08322 | 0.08322 | 0.08322 | 0.0 | 1.03 Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2377 | | | 2.93 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8052 ave 8052 max 8052 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: 157768 ave 157768 max 157768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157768 Ave neighs/atom = 390.515 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1158.4287 0 -1158.4287 -368.00565 Loop time of 9.53674e-07 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8136 ave 8136 max 8136 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: 163064 ave 163064 max 163064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163064 Ave neighs/atom = 403.624 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) = 5.078 | 5.078 | 5.078 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 -1158.4287 -1158.4287 16.580835 99.947174 4.0408444 -368.00565 -368.00565 -0.44376875 -1103.5699 -0.0032997472 2.5577934 251.85991 Loop time of 2.14577e-06 on 1 procs for 0 steps with 404 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 | | 2.146e-06 | | |100.00 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8136 ave 8136 max 8136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81532 ave 81532 max 81532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163064 ave 163064 max 163064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163064 Ave neighs/atom = 403.624 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_028.0725/numatoms.out 404 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1158.42872728015-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1158.42872728015-404*${isolated_atom_energy} variable adjusted_pe_metal equal -1158.42872728015-404*0 print "${adjusted_pe_metal} eV" file output/dump_028.0725/energy.out -1158.42872728015 eV print "${mindist_metal} Angstroms" file output/dump_028.0725/mindistance.out 2.55779339666194 Angstroms write_dump all cfg output/dump_028.0725/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_028.0725/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09