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 4.049763545393944*${_u_distance} variable lattice_constant_converted equal 4.049763545393944*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 60.2040632762107*${_u_distance} variable xmax_converted equal 60.2040632762107*1 variable ymin_converted equal -60.20811303975609*${_u_distance} variable ymin_converted equal -60.20811303975609*1 variable ymax_converted equal 60.20811303975609*${_u_distance} variable ymax_converted equal 60.20811303975609*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049763545393944*${_u_distance} variable zmax_converted equal 4.049763545393944*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04976354539394 Lattice spacing in x,y,z = 4.04976 4.04976 4.04976 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 60.2040632762107 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2040632762107 -60.2081130397561 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2040632762107 -60.2081130397561 60.2081130397561 ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2040632762107 -60.2081130397561 60.2081130397561 0 ${zmax_converted} units box region whole block 0 60.2040632762107 -60.2081130397561 60.2081130397561 0 4.04976354539394 units box create_box 2 whole Created orthogonal box = (0 -60.2081 0) to (60.2041 60.2081 4.04976) 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 60.2081130397561 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -5 0 orient y 5 14 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 14 -5 0 orient y 5 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.17591 5.17591 4.04976 create_atoms 1 region upper Created 886 atoms create_atoms CPU = 0.000247002 secs group upper type 1 886 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.689730936293327 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -60.2081130397561 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 5 0 orient y -5 14 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 14 5 0 orient y -5 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.17591 5.17591 4.04976 create_atoms 2 region lower Created 886 atoms create_atoms CPU = 0.000140905 secs group lower type 2 886 atoms in group lower displace_atoms lower move -6.689730936293327 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_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*4.04976354539394 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02488177269697 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 14 28 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 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1748 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 14 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.965 | 5.965 | 5.965 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5765.3787 0 -5765.3787 1438.1072 153 0 -5785.2026 0 -5785.2026 -4410.2671 Loop time of 2.19357 on 1 procs for 153 steps with 1748 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5765.37871091 -5785.20260603 -5785.20260603 Force two-norm initial, final = 24.3416 0.0197983 Force max component initial, final = 4.97318 0.00413456 Final line search alpha, max atom move = 3.05176e-05 1.26177e-07 Iterations, force evaluations = 153 316 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1476 | 2.1476 | 2.1476 | 0.0 | 97.90 Neigh | 0.015197 | 0.015197 | 0.015197 | 0.0 | 0.69 Comm | 0.019623 | 0.019623 | 0.019623 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0112 | | | 0.51 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11112 ave 11112 max 11112 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: 300944 ave 300944 max 300944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300944 Ave neighs/atom = 172.165 Neighbor list builds = 3 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) = 5.965 | 5.965 | 5.965 Mbytes Step Temp E_pair E_mol TotEng Press Volume 153 0 -5785.2026 0 -5785.2026 -4410.2671 29358.947 178 0 -5785.4117 0 -5785.4117 -463.81724 29204.373 Loop time of 0.607025 on 1 procs for 25 steps with 1748 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5785.20260603 -5785.41168644 -5785.41168644 Force two-norm initial, final = 110.346 0.0780823 Force max component initial, final = 81.5927 0.0401499 Final line search alpha, max atom move = 1.6103e-06 6.46533e-08 Iterations, force evaluations = 25 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58546 | 0.58546 | 0.58546 | 0.0 | 96.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0048409 | 0.0048409 | 0.0048409 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01672 | | | 2.75 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11107 ave 11107 max 11107 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: 301788 ave 301788 max 301788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301788 Ave neighs/atom = 172.648 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 14 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 6.103 | 6.103 | 6.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5785.4117 0 -5785.4117 -463.81724 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1748 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: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11107 ave 11107 max 11107 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: 302384 ave 302384 max 302384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302384 Ave neighs/atom = 172.989 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) = 6.103 | 6.103 | 6.103 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 -5785.4117 -5785.4117 60.021909 120.41623 4.040667 -463.81724 -463.81724 -0.15730852 -1393.4921 2.1977119 2.5889043 1027.3213 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1748 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 | | 1.192e-06 | | |100.00 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11107 ave 11107 max 11107 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 151192 ave 151192 max 151192 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 302384 ave 302384 max 302384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302384 Ave neighs/atom = 172.989 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.3076/numatoms.out 1748 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5785.41168643629-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5785.41168643629-1748*${isolated_atom_energy} variable adjusted_pe_metal equal -5785.41168643629-1748*0 print "${adjusted_pe_metal} eV" file output/dump_039.3076/energy.out -5785.41168643629 eV print "${mindist_metal} Angstroms" file output/dump_039.3076/mindistance.out 2.58890431079677 Angstroms write_dump all cfg output/dump_039.3076/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_039.3076/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02