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 4.210718545317654*${_u_distance} variable lattice_constant_converted equal 4.210718545317654*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 25.61280099309005*${_u_distance} variable xmax_converted equal 25.61280099309005*1 variable ymin_converted equal -51.22981270472542*${_u_distance} variable ymin_converted equal -51.22981270472542*1 variable ymax_converted equal 51.22981270472542*${_u_distance} variable ymax_converted equal 51.22981270472542*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.210718545317654*${_u_distance} variable zmax_converted equal 4.210718545317654*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.21071854531765 Lattice spacing in x,y,z = 4.21072 4.21072 4.21072 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 25.6128009930901 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.6128009930901 -51.2298127047254 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.6128009930901 -51.2298127047254 51.2298127047254 ${zmin_converted} ${zmax_converted} units box region whole block 0 25.6128009930901 -51.2298127047254 51.2298127047254 0 ${zmax_converted} units box region whole block 0 25.6128009930901 -51.2298127047254 51.2298127047254 0 4.21071854531765 units box create_box 2 whole Created orthogonal box = (0 -51.2298 0) to (25.6128 51.2298 4.21072) 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 51.2298127047254 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 -1 0 orient y 1 6 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 6 -1 0 orient y 1 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.84567 4.84567 4.21072 create_atoms 1 region upper Created 298 atoms create_atoms CPU = 0.000211 secs group upper type 1 298 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.7372431386341987 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -51.2298127047254 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 1 0 orient y -1 6 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 6 1 0 orient y -1 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.84567 4.84567 4.21072 create_atoms 2 region lower Created 298 atoms create_atoms CPU = 8.29697e-05 secs group lower type 2 298 atoms in group lower displace_atoms lower move -2.7372431386341987 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_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*4.21071854531765 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.10535927265882 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 23 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 586 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.914 | 4.914 | 4.914 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2174.1811 0 -2174.1811 2219.695 302 0 -2181.2122 0 -2181.2122 -908.63048 Loop time of 1.2626 on 1 procs for 302 steps with 586 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2174.18110909 -2181.21220147 -2181.21220147 Force two-norm initial, final = 16.839 9.43802e-06 Force max component initial, final = 6.36188 2.13002e-06 Final line search alpha, max atom move = 1 2.13002e-06 Iterations, force evaluations = 302 598 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.238 | 1.238 | 1.238 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01627 | 0.01627 | 0.01627 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008382 | | | 0.66 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5244 ave 5244 max 5244 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: 101576 ave 101576 max 101576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101576 Ave neighs/atom = 173.338 Neighbor list builds = 0 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) = 4.918 | 4.918 | 4.918 Mbytes Step Temp E_pair E_mol TotEng Press Volume 302 0 -2181.2122 0 -2181.2122 -908.63048 11050.096 1302 0 -2181.22 0 -2181.22 -14.848351 11024.607 Loop time of 4.84508 on 1 procs for 1000 steps with 586 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2181.21220147 -2181.22001807 -2181.22001808 Force two-norm initial, final = 9.58196 0.00334891 Force max component initial, final = 6.82861 0.0026143 Final line search alpha, max atom move = 0.748254 0.00195616 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5942 | 4.5942 | 4.5942 | 0.0 | 94.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.06071 | 0.06071 | 0.06071 | 0.0 | 1.25 Output | 4.1008e-05 | 4.1008e-05 | 4.1008e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1901 | | | 3.92 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5807 ave 5807 max 5807 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: 100976 ave 100976 max 100976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100976 Ave neighs/atom = 172.314 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 -0.09604918 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2181.22 0 -2181.22 -14.848351 Loop time of 9.53674e-07 on 1 procs for 0 steps with 586 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: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5812 ave 5812 max 5812 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: 101032 ave 101032 max 101032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101032 Ave neighs/atom = 172.41 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) = 5.056 | 5.056 | 5.056 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 -2181.22 -2181.22 25.58384 102.45963 4.2057613 -14.848351 -14.848351 0.37950023 -44.993321 0.068767753 2.7174482 524.4782 Loop time of 1.90735e-06 on 1 procs for 0 steps with 586 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 | | 1.907e-06 | | |100.00 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5812 ave 5812 max 5812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50516 ave 50516 max 50516 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101032 ave 101032 max 101032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101032 Ave neighs/atom = 172.41 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_018.9246/numatoms.out 586 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2181.22001807542-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2181.22001807542-586*${isolated_atom_energy} variable adjusted_pe_metal equal -2181.22001807542-586*-0.09604918 print "${adjusted_pe_metal} eV" file output/dump_018.9246/energy.out -2124.93519859542 eV print "${mindist_metal} Angstroms" file output/dump_018.9246/mindistance.out 2.71744822907999 Angstroms write_dump all cfg output/dump_018.9246/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_018.9246/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06