git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10395 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/README

@@ -83,6 +83,7 @@ shear:    sideways shear applied to 2d solid, with and without a void
 srd:      stochastic rotation dynamics (SRD) particles as solvent
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
 tri:      triangular particles in rigid bodies
+voronoi:  test of Voronoi tesselation in compute voronoi/atom
 
 Here is how you might run and visualize one of the sample problems:
 

examples/voronoi/in.voronoi

@@ -0,0 +1,155 @@
+# 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
+
+atom_modify     sort 0 0.0
+
+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
+communicate     single 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 6
+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: 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 t5 equal c_r0
+run  0
+print "TEST_5  $(round((v_t5-1000)/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