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 77.05013717404609*${_u_distance}
variable xmax_converted equal 77.05013717404609*1
variable ymin_converted equal -77.05417016254967*${_u_distance}
variable ymin_converted equal -77.05417016254967*1
variable ymax_converted equal 77.05417016254967*${_u_distance}
variable ymax_converted equal 77.05417016254967*1
variable zmin_converted equal 0.0*${_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 77.0501371740461 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 77.0501371740461 -77.0541701625497 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 77.0501371740461 -77.0541701625497 77.0541701625497 ${zmin_converted} ${zmax_converted} units box
region             whole block 0 77.0501371740461 -77.0541701625497 77.0541701625497 0 ${zmax_converted} units box
region             whole block 0 77.0501371740461 -77.0541701625497 77.0541701625497 0 4.03298850357533 units box
create_box         2 whole
Created orthogonal box = (0 -77.0542 0) to (77.0501 77.0542 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 77.0541701625497 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1
lattice            fcc 4.03298850357533 orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.6996 5.6996 4.03299
create_atoms       1 region upper
Created 1461 atoms
  create_atoms CPU = 0.000379086 secs
group              upper type 1
1461 atoms in group upper
mass               1 26.981538*${_u_mass}
mass               1 26.981538*1
displace_atoms     upper move 8.59723792854426 0 0.3333333333333333 units lattice
region             lower block INF INF ${ymin_converted}  0.0 INF INF units box
region             lower block INF INF -77.0541701625497  0.0 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 14 13 0 orient y -13 14 0 orient z 0 0 1
lattice            fcc 4.03298850357533 orient x 14 13 0 orient y -13 14 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.6996 5.6996 4.03299
create_atoms       2 region lower
Created 1461 atoms
  create_atoms CPU = 0.000261068 secs
group              lower type 2
1461 atoms in group lower
displace_atoms     lower move -8.59723792854426 0 -0.3333333333333333 units lattice
mass               2 26.981538*${_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 = 12 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 13.7567
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Deleted 30 atoms, new total = 2892
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 = 12 23 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) = 20.37 | 20.37 | 20.37 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -8356.6035            0   -8356.6035    764.59333 
     415            0   -8442.2052            0   -8442.2052   -6644.3071 
Loop time of 29.8792 on 1 procs for 415 steps with 2892 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 = 
        -8356.60353865     -8442.20523774     -8442.20523774
  Force two-norm initial, final = 35.3187 2.81282e-05
  Force max component initial, final = 5.87209 4.99457e-06
  Final line search alpha, max atom move = 1 4.99457e-06
  Iterations, force evaluations = 415 797

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 29.6       | 29.6       | 29.6       |   0.0 | 99.07
Neigh   | 0.10976    | 0.10976    | 0.10976    |   0.0 |  0.37
Comm    | 0.12624    | 0.12624    | 0.12624    |   0.0 |  0.42
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.04293    |            |       |  0.14

Nlocal:    2892 ave 2892 max 2892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    34036 ave 34036 max 34036 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:  1.90696e+06 ave 1.90696e+06 max 1.90696e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1906958
Ave neighs/atom = 659.391
Neighbor list builds = 4
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) = 20.37 | 20.37 | 20.37 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
     415            0   -8442.2052            0   -8442.2052   -6644.3071    47887.983 
    1415            0   -8442.7223            0   -8442.7223   -2720.0102    47632.557 
Loop time of 76.8964 on 1 procs for 1000 steps with 2892 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 = 
        -8442.20523774     -8442.72228476     -8442.72228489
  Force two-norm initial, final = 165.832 0.0892763
  Force max component initial, final = 155.704 0.0538277
  Final line search alpha, max atom move = 0.0416114 0.00223985
  Iterations, force evaluations = 1000 1993

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 75.793     | 75.793     | 75.793     |   0.0 | 98.56
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.30472    | 0.30472    | 0.30472    |   0.0 |  0.40
Output  | 1.812e-05  | 1.812e-05  | 1.812e-05  |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.799      |            |       |  1.04

Nlocal:    2892 ave 2892 max 2892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    34004 ave 34004 max 34004 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:  1.91094e+06 ave 1.91094e+06 max 1.91094e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1910944
Ave neighs/atom = 660.769
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 = 12 23 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) = 19.26 | 19.26 | 19.26 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -8442.7223            0   -8442.7223   -2720.0102 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 2892 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:    2892 ave 2892 max 2892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    33956 ave 33956 max 33956 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:  1.91203e+06 ave 1.91203e+06 max 1.91203e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1912032
Ave neighs/atom = 661.145
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) = 19.26 | 19.26 | 19.26 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   -8442.7223   -8442.7223    77.209975    154.10834    4.0031728   -2720.0102   -2720.0102    1.7251722   -8163.5531    1.7971734    2.5607726    181.47783 
Loop time of 1.19209e-06 on 1 procs for 0 steps with 2892 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:    2892 ave 2892 max 2892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    33956 ave 33956 max 33956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    956016 ave 956016 max 956016 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  1.91203e+06 ave 1.91203e+06 max 1.91203e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1912032
Ave neighs/atom = 661.145
Neighbor list builds = 0
Dangerous builds = 0
variable           num_atoms equal "count(all)"
print              "${num_atoms}" file output/dump_085.7578/numatoms.out
2892
variable  adjusted_pe_metal  equal ${pe_metal}-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -8442.72228489069-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -8442.72228489069-2892*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -8442.72228489069-2892*0
print              "${adjusted_pe_metal} eV" file output/dump_085.7578/energy.out
-8442.72228489069 eV
print              "${mindist_metal} Angstroms" file output/dump_085.7578/mindistance.out
2.56077260185921 Angstroms
write_dump         all cfg output/dump_085.7578/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_085.7578/success.out
This indicates that LAMMPS ran successfully
Total wall time: 0:01:47