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 4.073718130588532*${_u_distance}
variable lattice_constant_converted equal 4.073718130588532*1
variable xmin_converted equal 0.0*${_u_distance}
variable xmin_converted equal 0.0*1
variable xmax_converted equal 47.681648239396516*${_u_distance}
variable xmax_converted equal 47.681648239396516*1
variable ymin_converted equal -47.68572195752711*${_u_distance}
variable ymin_converted equal -47.68572195752711*1
variable ymax_converted equal 47.68572195752711*${_u_distance}
variable ymax_converted equal 47.68572195752711*1
variable zmin_converted equal 0.0*${_u_distance}
variable zmin_converted equal 0.0*1
variable zmax_converted equal 4.073718130588532*${_u_distance}
variable zmax_converted equal 4.073718130588532*1
lattice            fcc ${lattice_constant_converted}
lattice            fcc 4.07371813058853
Lattice spacing in x,y,z = 4.07372 4.07372 4.07372
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 47.6816482393965 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 47.6816482393965 -47.6857219575271 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 47.6816482393965 -47.6857219575271 47.6857219575271 ${zmin_converted} ${zmax_converted} units box
region             whole block 0 47.6816482393965 -47.6857219575271 47.6857219575271 0 ${zmax_converted} units box
region             whole block 0 47.6816482393965 -47.6857219575271 47.6857219575271 0 4.07371813058853 units box
create_box         2 whole
Created orthogonal box = (0 -47.6857 0) to (47.6816 47.6857 4.07372)
  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 47.6857219575271 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1
lattice            fcc 4.07371813058853 orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.22062 5.22062 4.07372
create_atoms       1 region upper
Created 550 atoms
  create_atoms CPU = 0.00029707 secs
group              upper type 1
550 atoms in group upper
mass               1 26.981538*${_u_mass}
mass               1 26.981538*1
displace_atoms     upper move 5.267114959823831 0 0.3333333333333333 units lattice
region             lower block INF INF ${ymin_converted}  0.0 INF INF units box
region             lower block INF INF -47.6857219575271  0.0 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 11 4 0 orient y -4 11 0 orient z 0 0 1
lattice            fcc 4.07371813058853 orient x 11 4 0 orient y -4 11 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.22062 5.22062 4.07372
create_atoms       2 region lower
Created 550 atoms
  create_atoms CPU = 0.000150919 secs
group              lower type 2
550 atoms in group lower
displace_atoms     lower move -5.267114959823831 0 -0.3333333333333333 units lattice
mass               2 26.981538*${_u_mass}
mass               2 26.981538*1
pair_style         kim EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089)
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*4.07371813058853
delete_atoms       overlap ${delete_distance} all all
delete_atoms       overlap 2.03685906529426 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 = 9.2864
  ghost atom cutoff = 9.2864
  binsize = 4.6432, bins = 11 21 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 9.2864
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Deleted 26 atoms, new total = 1074
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 = 9.2864
  ghost atom cutoff = 9.2864
  binsize = 4.6432, bins = 11 21 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 9.2864
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.428 | 5.428 | 5.428 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -3269.8063            0   -3269.8063   -1446.6985 
     347            0   -3282.3485            0   -3282.3485   -5447.3707 
Loop time of 4.43722 on 1 procs for 347 steps with 1074 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 = 
        -3269.80633569     -3282.34845981     -3282.34845981
  Force two-norm initial, final = 11.7495 9.09493e-06
  Force max component initial, final = 3.58464 1.01332e-06
  Final line search alpha, max atom move = 1 1.01332e-06
  Iterations, force evaluations = 347 681

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.3807     | 4.3807     | 4.3807     |   0.0 | 98.73
Neigh   | 0.003979   | 0.003979   | 0.003979   |   0.0 |  0.09
Comm    | 0.034956   | 0.034956   | 0.034956   |   0.0 |  0.79
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.01759    |            |       |  0.40

Nlocal:    1074 ave 1074 max 1074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8734 ave 8734 max 8734 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:  211572 ave 211572 max 211572 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 211572
Ave neighs/atom = 196.994
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) = 5.429 | 5.429 | 5.429 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
     347            0   -3282.3485            0   -3282.3485   -5447.3707    18525.101 
    1347            0   -3282.5517            0   -3282.5517   -1608.8772    18378.189 
Loop time of 13.6663 on 1 procs for 1000 steps with 1074 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 = 
        -3282.34845981     -3282.55169498     -3282.55169498
  Force two-norm initial, final = 71.33 0.000772832
  Force max component initial, final = 53.5108 0.000608891
  Final line search alpha, max atom move = 1 0.000608891
  Iterations, force evaluations = 1000 1996

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 13.27      | 13.27      | 13.27      |   0.0 | 97.10
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.09287    | 0.09287    | 0.09287    |   0.0 |  0.68
Output  | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.303      |            |       |  2.22

Nlocal:    1074 ave 1074 max 1074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8756 ave 8756 max 8756 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:  211980 ave 211980 max 211980 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 211980
Ave neighs/atom = 197.374
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 0.143095413925774
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 = 9.2864
  ghost atom cutoff = 9.2864
  binsize = 4.6432, bins = 11 21 1
  3 neighbor lists, perpetual/occasional/extra = 1 2 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 9.2864
      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) = 5.567 | 5.567 | 5.567 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -3282.5517            0   -3282.5517   -1608.8772 
Loop time of 1.19209e-06 on 1 procs for 0 steps with 1074 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:    1074 ave 1074 max 1074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8783 ave 8783 max 8783 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:  212128 ave 212128 max 212128 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 212128
Ave neighs/atom = 197.512
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) = 5.567 | 5.567 | 5.567 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   -3282.5517   -3282.5517    47.464685    95.371444    4.0598851   -1608.8772   -1608.8772  -0.05284044   -4826.5812 0.0024786969    2.5702689     838.0909 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 1074 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:    1074 ave 1074 max 1074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8783 ave 8783 max 8783 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    106064 ave 106064 max 106064 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  212128 ave 212128 max 212128 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 212128
Ave neighs/atom = 197.512
Neighbor list builds = 0
Dangerous builds = 0
variable           num_atoms equal "count(all)"
print              "${num_atoms}" file output/dump_039.9662/numatoms.out
1074
variable  adjusted_pe_metal  equal ${pe_metal}-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3282.55169497945-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3282.55169497945-1074*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3282.55169497945-1074*0.143095413925774
print              "${adjusted_pe_metal} eV" file output/dump_039.9662/energy.out
-3436.23616953573 eV
print              "${mindist_metal} Angstroms" file output/dump_039.9662/mindistance.out
2.57026886330015 Angstroms
write_dump         all cfg output/dump_039.9662/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_039.9662/success.out
This indicates that LAMMPS ran successfully
Total wall time: 0:00:18