LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 16.628437587142773*${_u_distance} variable xmax_converted equal 16.628437587142773*1 variable ymin_converted equal -49.8893457499319*${_u_distance} variable ymin_converted equal -49.8893457499319*1 variable ymax_converted equal 49.8893457499319*${_u_distance} variable ymax_converted equal 49.8893457499319*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032988503575325*${_u_distance} variable zmax_converted equal 4.032988503575325*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03298850357533 Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 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 16.6284375871428 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6284375871428 -49.8893457499319 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6284375871428 -49.8893457499319 49.8893457499319 ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6284375871428 -49.8893457499319 49.8893457499319 0 ${zmax_converted} units box region whole block 0 16.6284375871428 -49.8893457499319 49.8893457499319 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -49.8893 0) to (16.6284 49.8893 4.03299) 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 49.8893457499319 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.89072 4.89072 4.03299 create_atoms 1 region upper Created 206 atoms create_atoms CPU = 0.000159979 secs group upper type 1 206 atoms in group upper mass 1 26.981538*${_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 -49.8893457499319 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.89072 4.89072 4.03299 create_atoms 2 region lower Created 206 atoms create_atoms CPU = 4.79221e-05 secs group lower type 2 206 atoms in group lower displace_atoms lower move -1.8553975315279474 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.03298850357533 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01649425178767 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 15 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 13.7567 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.373 | 5.373 | 5.373 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1157.9689 0 -1157.9689 3821.0008 201 0 -1172.4959 0 -1172.4959 -3579.83 Loop time of 2.20558 on 1 procs for 201 steps with 404 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1157.96888847 -1172.49592944 -1172.49592944 Force two-norm initial, final = 23.0815 2.10803e-06 Force max component initial, final = 7.1667 2.50927e-07 Final line search alpha, max atom move = 1 2.50927e-07 Iterations, force evaluations = 201 393 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1777 | 2.1777 | 2.1777 | 0.0 | 98.73 Neigh | 0.0041809 | 0.0041809 | 0.0041809 | 0.0 | 0.19 Comm | 0.019339 | 0.019339 | 0.019339 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004405 | | | 0.20 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10532 ave 10532 max 10532 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: 267908 ave 267908 max 267908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267908 Ave neighs/atom = 663.139 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) = 5.374 | 5.374 | 5.374 Mbytes Step Temp E_pair E_mol TotEng Press Volume 201 0 -1172.4959 0 -1172.4959 -3579.83 6691.3883 1201 0 -1172.5369 0 -1172.5369 -306.5451 6661.0802 Loop time of 11.9391 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 = -1172.49592944 -1172.53686293 -1172.536863 Force two-norm initial, final = 21.1719 0.00831188 Force max component initial, final = 17.3505 0.00817477 Final line search alpha, max atom move = 0.129988 0.00106262 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.606 | 11.606 | 11.606 | 0.0 | 97.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.095856 | 0.095856 | 0.095856 | 0.0 | 0.80 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2376 | | | 1.99 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10628 ave 10628 max 10628 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: 269448 ave 269448 max 269448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269448 Ave neighs/atom = 666.95 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.512 | 5.512 | 5.512 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1172.5369 0 -1172.5369 -306.5451 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: 10628 ave 10628 max 10628 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: 269592 ave 269592 max 269592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269592 Ave neighs/atom = 667.307 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:52) Per MPI rank memory allocation (min/avg/max) = 5.512 | 5.512 | 5.512 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 -1172.5369 -1172.5369 16.543966 99.778691 4.0352201 -306.5451 -306.5451 -0.2502729 -921.35238 1.9673489 2.5529492 251.22393 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: 10628 ave 10628 max 10628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134796 ave 134796 max 134796 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 269592 ave 269592 max 269592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269592 Ave neighs/atom = 667.307 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -1172.5368629957-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1172.5368629957-404*${isolated_atom_energy} variable adjusted_pe_metal equal -1172.5368629957-404*0 print "${adjusted_pe_metal} eV" file output/dump_028.0725/energy.out -1172.5368629957 eV print "${mindist_metal} Angstroms" file output/dump_028.0725/mindistance.out 2.55294924463149 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: 0:00:14