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lammps/examples/voronoi/in.voronoi
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# 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
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
create_atoms 1 box basis 1 2
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
group type2 type 2
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
print "TEST_1 $(round(abs(v_t1-1000)/10))% 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
print "TEST_2a $(round(abs(v_t2a-1000)/10))% 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"
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
print "TEST_3 $(round(abs(v_t3-1000)/10))% 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
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)"
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
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)"
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
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"
uncompute v1
# bcc lattice
delete_atoms group all
lattice bcc 1 origin 0.25 0.25 0.25
create_atoms 1 box
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
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 $(round(v_t4d))% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)"
uncompute v1
# restore fcc lattice
delete_atoms group all
lattice fcc 1 origin 0.25 0.25 0.25
create_atoms 1 box basis 1 2
#
# TEST 5: Occupation analysis
#
print "START5"
# start with pristine lattice
variable i1 equal 13
variable i2 equal 257
compute v1 all voronoi/atom occupation
compute r0 all reduce sum c_v1[1]
compute r1 all reduce sum c_v1[2]
variable d5a equal c_v1[${i1}][1]
variable d5b equal c_v1[${i2}][1]
variable d5c equal c_v1[${i1}][2]
variable d5d equal c_v1[${i2}][2]
thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
run 0
# expect 1 1 1 1 (one atom per cell each)
variable t5a equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
# move atom i1 next to atom i2
variable oxd equal x[${i1}]
variable oyd equal y[${i1}]
variable ozd equal z[${i1}]
# we need to freeze this value
variable ox equal ${oxd}
variable oy equal ${oyd}
variable oz equal ${ozd}
# these coords dont change so dynamic evaluation is ok
variable nx equal x[${i2}]
variable ny equal y[${i2}]
variable nz equal z[${i2}]
set atom ${i1} x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
run 0
# expect 0 2 2 2 (vacancy at the original i1 site, interstitial at i2 and both atoms are now sharing a site)
variable t5b equal abs(${d5a}-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
# move atom back
set atom ${i1} x ${ox} y ${oy} z ${oz}
run 0
# expect 1 1 1 1 (restored to the initial state)
variable t5c equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
print "TEST_5 $((v_t5a+v_t5b+v_t5c)*100)% 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
change_box all xy final 5.0 remap units box
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
print "TEST_6 $(round((v_t6-1000)/10))% Error. Sum of all voronoi cells is the triclinic simulation cell volume"
uncompute v1
uncompute r0
undump d1
# All tests done
print TEST_DONE
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