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 4.045259781181812*${_u_distance} variable lattice_constant_converted equal 4.045259781181812*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 39.841188356184496*${_u_distance} variable xmax_converted equal 39.841188356184496*1 variable ymin_converted equal -79.68642197215017*${_u_distance} variable ymin_converted equal -79.68642197215017*1 variable ymax_converted equal 79.68642197215017*${_u_distance} variable ymax_converted equal 79.68642197215017*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045259781181812*${_u_distance} variable zmax_converted equal 4.045259781181812*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04525978118181 Lattice spacing in x,y,z = 4.04526 4.04526 4.04526 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 39.8411883561845 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.8411883561845 -79.6864219721502 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.8411883561845 -79.6864219721502 79.6864219721502 ${zmin_converted} ${zmax_converted} units box region whole block 0 39.8411883561845 -79.6864219721502 79.6864219721502 0 ${zmax_converted} units box region whole block 0 39.8411883561845 -79.6864219721502 79.6864219721502 0 4.04525978118181 units box create_box 2 whole Created orthogonal box = (0 -79.6864 0) to (39.8412 79.6864 4.04526) 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 79.6864219721502 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -4 0 orient y 4 9 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 9 -4 0 orient y 4 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.33954 5.33954 4.04526 create_atoms 1 region upper Created 778 atoms create_atoms CPU = 0.000363111 secs group upper type 1 778 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.431986010808247 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -79.6864219721502 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 4 0 orient y -4 9 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 9 4 0 orient y -4 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.33954 5.33954 4.04526 create_atoms 2 region lower Created 778 atoms create_atoms CPU = 0.000231981 secs group lower type 2 778 atoms in group lower displace_atoms lower move -4.431986010808247 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_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*4.04525978118181 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0226298905909 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 38 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1542 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 38 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.558 | 5.558 | 5.558 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5230.771 0 -5230.771 1741.9788 479 0 -5247.1121 0 -5247.1121 -1069.2432 Loop time of 5.30705 on 1 procs for 479 steps with 1542 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5230.77099367 -5247.1120538 -5247.1120538 Force two-norm initial, final = 25.2251 1.22258e-05 Force max component initial, final = 6.5554 2.1091e-06 Final line search alpha, max atom move = 1 2.1091e-06 Iterations, force evaluations = 479 952 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.216 | 5.216 | 5.216 | 0.0 | 98.28 Neigh | 0.0041981 | 0.0041981 | 0.0041981 | 0.0 | 0.08 Comm | 0.05491 | 0.05491 | 0.05491 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03192 | | | 0.60 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10593 ave 10593 max 10593 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: 216804 ave 216804 max 216804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216804 Ave neighs/atom = 140.599 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) = 5.558 | 5.558 | 5.558 Mbytes Step Temp E_pair E_mol TotEng Press Volume 479 0 -5247.1121 0 -5247.1121 -1069.2432 25685.796 1479 0 -5247.1345 0 -5247.1345 253.31982 25642.301 Loop time of 11.6324 on 1 procs for 1000 steps with 1542 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5247.1120538 -5247.1344809 -5247.1344809 Force two-norm initial, final = 33.8722 0.00569598 Force max component initial, final = 27.8683 0.00565991 Final line search alpha, max atom move = 0.855619 0.00484273 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.151 | 11.151 | 11.151 | 0.0 | 95.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10783 | 0.10783 | 0.10783 | 0.0 | 0.93 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3732 | | | 3.21 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10578 ave 10578 max 10578 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: 216268 ave 216268 max 216268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216268 Ave neighs/atom = 140.252 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 38 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.696 | 5.696 | 5.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5247.1345 0 -5247.1345 253.31982 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1542 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: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10583 ave 10583 max 10583 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: 216316 ave 216316 max 216316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216316 Ave neighs/atom = 140.283 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) = 5.696 | 5.696 | 5.696 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 -5247.1345 -5247.1345 39.829315 159.37284 4.0396137 253.31982 253.31982 0.35353577 759.60748 -0.0015502876 2.4983385 713.02713 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1542 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: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10583 ave 10583 max 10583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108158 ave 108158 max 108158 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 216316 ave 216316 max 216316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216316 Ave neighs/atom = 140.283 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_047.9250/numatoms.out 1542 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5247.13448090234-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5247.13448090234-1542*${isolated_atom_energy} variable adjusted_pe_metal equal -5247.13448090234-1542*0 print "${adjusted_pe_metal} eV" file output/dump_047.9250/energy.out -5247.13448090234 eV print "${mindist_metal} Angstroms" file output/dump_047.9250/mindistance.out 2.49833847883242 Angstroms write_dump all cfg output/dump_047.9250/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_047.9250/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:17