LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# Test of Kawasaki Dynamics on LJ test system

units		metal
#newton off
boundary	p p p

lattice         fcc 1 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 1 1 1
atom_style	atomic

# indexed atom variables in test 5 need a map

atom_modify     sort 0 0.0 map hash

region          box block 0 10  0 10 0 10
create_box      2 box
Created orthogonal box = (0 0 0) to (10 10 10)
  1 by 2 by 2 MPI processor grid
create_atoms    1 box basis 1 2
Created 4000 atoms
  Time spent = 0.000644922 secs

mass 1 50
mass 2 50

pair_style      lj/cut 2.0
pair_coeff      1 1 0.0 1.0
pair_coeff      1 2 0.0 1.0
pair_coeff      2 2 0.0 1.0

neighbor	0.3 bin
neigh_modify	delay 10

# set the cut-off to 2.5x the cutoff from the potential
comm_modify     cutoff 5.0

# atom radii per type
variable r atom (type==1)*0.1+(type==2)*0.3

# groups
group type1 type 1
3000 atoms in group type1
group type2 type 2
1000 atoms in group type2

thermo 1
# reduce computes
#compute r1 type1 reduce sum c_v1[1]
#compute r2 type2 reduce sum c_v1[1]

#compute v1 all voronoi/atom radius v_r

#
# TEST 1: Sum of all voronoi cells is the simulation cell volume
#

compute v1 all voronoi/atom
dump    d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
compute r0 all   reduce sum c_v1[1]
thermo_style custom c_r0
variable t1 equal c_r0
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 = 2.3
  ghost atom cutoff = 5
  binsize = 1.15, bins = 9 9 9
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      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) = 9.228 | 9.228 | 9.228 Mbytes
c_r0 
        1000 
Loop time of 2.08616e-06 on 4 procs for 0 steps with 4000 atoms

167.8% CPU use with 4 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   |            | 2.086e-06  |            |       |100.00

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    100000 ave 100000 max 100000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 400000
Ave neighs/atom = 100
Neighbor list builds = 0
Dangerous builds = 0
print "TEST_1  $(round(abs(v_t1-1000)/10))% Error.  Sum of all voronoi cells is the simulation cell volume"
TEST_1  0% Error.  Sum of all voronoi cells is the simulation cell volume
uncompute v1
uncompute r0
undump    d1

#
# TEST 2: Sum of all only_group voronoi cells is the simulation cell volume
#

compute v1 type2 voronoi/atom only_group
dump    d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
compute r0 type2   reduce sum c_v1[1]
compute r1 type1   reduce sum c_v1[1]
thermo_style custom c_r0 c_r1
variable t2a equal c_r0
variable t2b equal c_r1
run  0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 9.228 | 9.228 | 9.228 Mbytes
c_r0 c_r1 
        1000            0 
Loop time of 4.52995e-06 on 4 procs for 0 steps with 4000 atoms

132.5% CPU use with 4 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   |            | 4.53e-06   |            |       |100.00

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    100000 ave 100000 max 100000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 400000
Ave neighs/atom = 100
Neighbor list builds = 0
Dangerous builds = 0
print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error.  Sum of all only_group voronoi cells is the simulation cell volume"
TEST_2a 0% Error.  Sum of all only_group voronoi cells is the simulation cell volume
print "TEST_2b $(round(v_t2b/10))% Error.  Sum of all only_group not included voronoi cells is zero"
TEST_2b 0% Error.  Sum of all only_group not included voronoi cells is zero
uncompute v1
uncompute r0
uncompute r1
undump    d1

#
# TEST 3: Sum of all radius voronoi cells is the simulation cell volume
#

compute v1 all voronoi/atom radius v_r
dump    d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
compute r0 all   reduce sum c_v1[1]
thermo_style custom c_r0
variable t3 equal c_r0
run  0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 9.228 | 9.228 | 9.228 Mbytes
c_r0 
        1000 
Loop time of 1.84774e-06 on 4 procs for 0 steps with 4000 atoms

162.4% CPU use with 4 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   |            | 1.848e-06  |            |       |100.00

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    100000 ave 100000 max 100000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 400000
Ave neighs/atom = 100
Neighbor list builds = 0
Dangerous builds = 0
print "TEST_3  $(round(abs(v_t3-1000)/10))% Error.  Sum of all radius voronoi cells is the simulation cell volume"
TEST_3  0% Error.  Sum of all radius voronoi cells is the simulation cell volume
uncompute v1
uncompute r0
undump    d1

#
# TEST 4: Edge histogram tests
#

compute v1 type2 voronoi/atom edge_histo 8
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
run  1
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 
           0            0            0        12000            0            0            0 
           0            0            0        12000            0            0            0 
Loop time of 0.181586 on 4 procs for 1 steps with 4000 atoms

Performance: 0.476 ns/day, 50.441 hours/ns, 5.507 timesteps/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0015094  | 0.0015393  | 0.0016015  |   0.1 |  0.85
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00039601 | 0.00046033 | 0.00049233 |   0.0 |  0.25
Output  | 0.17947    | 0.1795     | 0.17956    |   0.0 | 98.85
Modify  | 4.7684e-07 | 7.1526e-07 | 9.5367e-07 |   0.0 |  0.00
Other   |            | 9e-05      |            |       |  0.05

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    100000 ave 100000 max 100000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 400000
Ave neighs/atom = 100
Neighbor list builds = 0
Dangerous builds = 0
variable t4a equal (abs(c_v1[4]-12000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/120
print "TEST_4a $(round(v_t4a))% Error.  Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)"
TEST_4a 0% Error.  Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)
uncompute v1
compute v1 all voronoi/atom edge_histo 8
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
run  1
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 
           0            0            0        48000            0            0            0 
           0            0            0        48000            0            0            0 
Loop time of 0.184754 on 4 procs for 1 steps with 4000 atoms

Performance: 0.468 ns/day, 51.321 hours/ns, 5.413 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0015123  | 0.0015253  | 0.0015385  |   0.0 |  0.83
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00038028 | 0.00039649 | 0.00040984 |   0.0 |  0.21
Output  | 0.18271    | 0.18273    | 0.1828     |   0.0 | 98.91
Modify  | 7.1526e-07 | 8.9407e-07 | 9.5367e-07 |   0.0 |  0.00
Other   |            | 0.0001001  |            |       |  0.05

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    100000 ave 100000 max 100000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 400000
Ave neighs/atom = 100
Neighbor list builds = 0
Dangerous builds = 0
variable t4b equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
print "TEST_4b $(round(v_t4b))% Error.  Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)"
TEST_4b 0% Error.  Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)
uncompute v1

# perturbed fcc lattice
displace_atoms all random 0.01 0.01 0.01 31423
compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
run  1
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 
           0            0            0        48000            0            0            0 
           0            0            0        48000            0            0            0 
Loop time of 0.191424 on 4 procs for 1 steps with 4000 atoms

Performance: 0.451 ns/day, 53.173 hours/ns, 5.224 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0016205  | 0.0016853  | 0.0018284  |   0.2 |  0.88
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00041676 | 0.00055587 | 0.00062323 |   0.0 |  0.29
Output  | 0.18905    | 0.18907    | 0.18915    |   0.0 | 98.77
Modify  | 1.1921e-06 | 1.2517e-06 | 1.4305e-06 |   0.0 |  0.00
Other   |            | 0.0001094  |            |       |  0.06

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    100000 ave 100016 max 99984 min
Histogram: 1 0 0 1 0 0 1 0 0 1

Total # of neighbors = 400000
Ave neighs/atom = 100
Neighbor list builds = 0
Dangerous builds = 0
variable t4c equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
print "TEST_4c $(round(v_t4c))% Error.  Edge histogram of a perturbed face centered cubic lattice with edge_threshold"
TEST_4c 0% Error.  Edge histogram of a perturbed face centered cubic lattice with edge_threshold
uncompute v1

# bcc lattice
delete_atoms group all
Deleted 4000 atoms, new total = 0
lattice         bcc 1 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 1 1 1
create_atoms    1 box
Created 2000 atoms
  Time spent = 0.000178576 secs
compute v1 all voronoi/atom edge_histo 8
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
run  1
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 
           0            0            0        12000            0        16000            0 
           0            0            0        12000            0        16000            0 
Loop time of 0.0871635 on 4 procs for 1 steps with 2000 atoms

Performance: 0.991 ns/day, 24.212 hours/ns, 11.473 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.00038028 | 0.00038761 | 0.00040364 |   0.0 |  0.44
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00020146 | 0.00021631 | 0.00022292 |   0.0 |  0.25
Output  | 0.086468   | 0.086487   | 0.086541   |   0.0 | 99.22
Modify  | 4.7684e-07 | 7.1526e-07 | 9.5367e-07 |   0.0 |  0.00
Other   |            | 7.224e-05  |            |       |  0.08

Nlocal:    500 ave 500 max 500 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    8500 ave 8500 max 8500 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    28000 ave 28000 max 28000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 112000
Ave neighs/atom = 56
Neighbor list builds = 0
Dangerous builds = 0
variable t4d equal (abs(c_v1[4]-12000)+abs(c_v1[6]-16000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[7])/280
print "TEST_4d $(round(v_t4d))% Error.  Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)"
TEST_4d 0% Error.  Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)
uncompute v1

# restore fcc lattice
delete_atoms group all
Deleted 2000 atoms, new total = 0
lattice         fcc 1 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 1 1 1
create_atoms    1 box basis 1 2
Created 4000 atoms
  Time spent = 0.000248909 secs

#
# TEST 5: Occupation analysis
#

print "START5"
START5

# start with pristine lattice
variable i1 equal 13
variable i2 equal 257
compute v1 all voronoi/atom occupation
compute r0 all   reduce sum c_v1[1]
compute r1 all   reduce sum c_v1[2]
variable d5a equal c_v1[${i1}][1]
variable d5a equal c_v1[13][1]
variable d5b equal c_v1[${i2}][1]
variable d5b equal c_v1[257][1]
variable d5c equal c_v1[${i1}][2]
variable d5c equal c_v1[13][2]
variable d5d equal c_v1[${i2}][2]
variable d5d equal c_v1[257][2]
thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d

run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 
        4000         4000            1            1            1            1 
Loop time of 1.84774e-06 on 4 procs for 0 steps with 4000 atoms

189.4% CPU use with 4 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   |            | 1.848e-06  |            |       |100.00

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    100000 ave 100000 max 100000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 400000
Ave neighs/atom = 100
Neighbor list builds = 0
Dangerous builds = 0
# expect 1 1 1 1 (one atom per cell each)
variable t5a equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
variable t5a equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
variable t5a equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)

# move atom i1 next to atom i2
variable oxd equal x[${i1}]
variable oxd equal x[13]
variable oyd equal y[${i1}]
variable oyd equal y[13]
variable ozd equal z[${i1}]
variable ozd equal z[13]
# we need to freeze this value
variable ox equal ${oxd}
variable ox equal 3.25
variable oy equal ${oyd}
variable oy equal 0.25
variable oz equal ${ozd}
variable oz equal 0.25
# these coords dont change so dynamic evaluation is ok
variable nx equal x[${i2}]
variable nx equal x[257]
variable ny equal y[${i2}]
variable ny equal y[257]
variable nz equal z[${i2}]
variable nz equal z[257]
set atom ${i1} x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
set atom 13 x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
set atom 13 x 4.4500000000000001776 y $(v_ny+0.2) z $(v_nz+0.2)
set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z $(v_nz+0.2)
set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z 1.4499999999999999556
  1 settings made for x
  1 settings made for y
  1 settings made for z

run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 7.675 | 7.675 | 7.675 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 
        4000         4002            0            2            2            2 
Loop time of 1.72853e-06 on 4 procs for 0 steps with 4000 atoms

188.0% CPU use with 4 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   |            | 1.729e-06  |            |       |100.00

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    99999.2 ave 100075 max 99967 min
Histogram: 2 1 0 0 0 0 0 0 0 1

Total # of neighbors = 399997
Ave neighs/atom = 99.9993
Neighbor list builds = 0
Dangerous builds = 0
# expect 0 2 2 2 (vacancy at the original i1 site, interstitial at i2 and both atoms are now sharing a site)
variable t5b equal abs(${d5a}-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
variable t5b equal abs(0-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
variable t5b equal abs(0-0)+abs(2-2)+abs(${d5c}-2)+abs(${d5d}-2)
variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(${d5d}-2)
variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(2-2)

# move atom back
set atom ${i1} x ${ox} y ${oy} z ${oz}
set atom 13 x ${ox} y ${oy} z ${oz}
set atom 13 x 3.25 y ${oy} z ${oz}
set atom 13 x 3.25 y 0.25 z ${oz}
set atom 13 x 3.25 y 0.25 z 0.25
  1 settings made for x
  1 settings made for y
  1 settings made for z

run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 7.675 | 7.675 | 7.675 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 
        4000         4000            1            1            1            1 
Loop time of 1.49012e-06 on 4 procs for 0 steps with 4000 atoms

218.1% CPU use with 4 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   |            | 1.49e-06   |            |       |100.00

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17000 ave 17000 max 17000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    100000 ave 100000 max 100000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 400000
Ave neighs/atom = 100
Neighbor list builds = 0
Dangerous builds = 0
# expect 1 1 1 1 (restored to the initial state)
variable t5c equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
variable t5c equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
variable t5c equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)

print "TEST_5  $((v_t5a+v_t5b+v_t5c)*100)% Error.  Detection of vacancies and interstitials using the {occupation} keyword."
TEST_5  0% Error.  Detection of vacancies and interstitials using the {occupation} keyword.

uncompute v1
uncompute r0
uncompute r1

#
# TEST 6: Sum of all voronoi cells is the triclinic simulation cell volume
#

# switch to triclinic box
change_box all triclinic
  triclinic box = (0 0 0) to (10 10 10) with tilt (0 0 0)
change_box all xy final 5.0 remap units box
  triclinic box = (0 0 0) to (10 10 10) with tilt (5 0 0)

compute v1 all voronoi/atom
dump    d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
compute r0 all   reduce sum c_v1[1]
thermo_style custom c_r0
variable t6 equal c_r0
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 = 2.3
  ghost atom cutoff = 5
  binsize = 1.15, bins = 14 9 9
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton/tri
      stencil: half/bin/3d/newton/tri
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.493 | 9.493 | 9.493 Mbytes
c_r0 
        1000 
Loop time of 1.96695e-06 on 4 procs for 0 steps with 4000 atoms

165.2% CPU use with 4 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   |            | 1.967e-06  |            |       |100.00

Nlocal:    1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    17900 ave 17900 max 17900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    108000 ave 108000 max 108000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 432000
Ave neighs/atom = 108
Neighbor list builds = 0
Dangerous builds = 0
print "TEST_6  $(round((v_t6-1000)/10))% Error.  Sum of all voronoi cells is the triclinic simulation cell volume"
TEST_6  0% Error.  Sum of all voronoi cells is the triclinic simulation cell volume
uncompute v1
uncompute r0
undump    d1

# All tests done

print TEST_DONE
TEST_DONE
Total wall time: 0:00:02
