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 38.820906825703744*${_u_distance} variable xmax_converted equal 38.820906825703744*1 variable ymin_converted equal -77.64602436995281*${_u_distance} variable ymin_converted equal -77.64602436995281*1 variable ymax_converted equal 77.64602436995281*${_u_distance} variable ymax_converted equal 77.64602436995281*1 variable zmin_converted equal 0.0*${_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 38.8209068257037 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 38.8209068257037 -77.6460243699528 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 38.8209068257037 -77.6460243699528 77.6460243699528 ${zmin_converted} ${zmax_converted} units box region whole block 0 38.8209068257037 -77.6460243699528 77.6460243699528 0 ${zmax_converted} units box region whole block 0 38.8209068257037 -77.6460243699528 77.6460243699528 0 4.21071854531765 units box create_box 2 whole Created orthogonal box = (0 -77.646 0) to (38.8209 77.646 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 77.6460243699528 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.02388 5.02388 4.21072 create_atoms 1 region upper Created 681 atoms create_atoms CPU = 0.000309944 secs group upper type 1 681 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.148795005781799 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -77.6460243699528 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.02388 5.02388 4.21072 create_atoms 2 region lower Created 681 atoms create_atoms CPU = 0.000159025 secs group lower type 2 681 atoms in group lower displace_atoms lower move -4.148795005781799 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 9 35 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 11 atoms, new total = 1351 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 = 9 35 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) = 5.498 | 5.498 | 5.498 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5016.4297 0 -5016.4297 2167.36 406 0 -5030.3849 0 -5030.3849 -461.08954 Loop time of 4.35951 on 1 procs for 406 steps with 1351 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5016.42966814 -5030.3848815 -5030.3848815 Force two-norm initial, final = 25.4522 5.66842e-07 Force max component initial, final = 6.47151 1.79253e-07 Final line search alpha, max atom move = 1 1.79253e-07 Iterations, force evaluations = 406 804 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2743 | 4.2743 | 4.2743 | 0.0 | 98.05 Neigh | 0.011614 | 0.011614 | 0.011614 | 0.0 | 0.27 Comm | 0.048517 | 0.048517 | 0.048517 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02509 | | | 0.58 Nlocal: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10160 ave 10160 max 10160 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: 234604 ave 234604 max 234604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234604 Ave neighs/atom = 173.652 Neighbor list builds = 2 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) = 5.506 | 5.506 | 5.506 Mbytes Step Temp E_pair E_mol TotEng Press Volume 406 0 -5030.3849 0 -5030.3849 -461.08954 25384.646 1406 0 -5030.3909 0 -5030.3909 55.915091 25350.691 Loop time of 10.9257 on 1 procs for 1000 steps with 1351 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 = -5030.3848815 -5030.39090113 -5030.39090114 Force two-norm initial, final = 12.6972 0.00201322 Force max component initial, final = 9.00505 0.00168102 Final line search alpha, max atom move = 1 0.00168102 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.443 | 10.443 | 10.443 | 0.0 | 95.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11344 | 0.11344 | 0.11344 | 0.0 | 1.04 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3696 | | | 3.38 Nlocal: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10725 ave 10725 max 10725 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: 234610 ave 234610 max 234610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234610 Ave neighs/atom = 173.657 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 = 9 35 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) = 5.644 | 5.644 | 5.644 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5030.3909 0 -5030.3909 55.915091 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1351 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: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10727 ave 10727 max 10727 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: 234660 ave 234660 max 234660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234660 Ave neighs/atom = 173.694 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) = 5.644 | 5.644 | 5.644 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 -5030.3909 -5030.3909 38.794155 155.29205 4.207986 55.915091 55.915091 -0.048597683 167.90004 -0.1061721 2.7253939 835.82608 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1351 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: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10727 ave 10727 max 10727 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117330 ave 117330 max 117330 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 234660 ave 234660 max 234660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234660 Ave neighs/atom = 173.694 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.0576/numatoms.out 1351 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5030.39090113531-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5030.39090113531-1351*${isolated_atom_energy} variable adjusted_pe_metal equal -5030.39090113531-1351*-0.09604918 print "${adjusted_pe_metal} eV" file output/dump_025.0576/energy.out -4900.62845895531 eV print "${mindist_metal} Angstroms" file output/dump_025.0576/mindistance.out 2.72539393882715 Angstroms write_dump all cfg output/dump_025.0576/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_025.0576/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15