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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10395 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -83,6 +83,7 @@ shear: sideways shear applied to 2d solid, with and without a void
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srd: stochastic rotation dynamics (SRD) particles as solvent
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srd: stochastic rotation dynamics (SRD) particles as solvent
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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tri: triangular particles in rigid bodies
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tri: triangular particles in rigid bodies
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voronoi: test of Voronoi tesselation in compute voronoi/atom
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Here is how you might run and visualize one of the sample problems:
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Here is how you might run and visualize one of the sample problems:
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@ -0,0 +1,155 @@
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# Test of Kawasaki Dynamics on LJ test system
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units metal
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#newton off
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boundary p p p
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lattice fcc 1 origin 0.25 0.25 0.25
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atom_style atomic
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atom_modify sort 0 0.0
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region box block 0 10 0 10 0 10
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create_box 2 box
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create_atoms 1 box basis 1 2
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mass 1 50
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mass 2 50
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pair_style lj/cut 2.0
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pair_coeff 1 1 0.0 1.0
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pair_coeff 1 2 0.0 1.0
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pair_coeff 2 2 0.0 1.0
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neighbor 0.3 bin
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neigh_modify delay 10
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# set the cut-off to 2.5x the cutoff from the potential
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communicate single cutoff 5.0
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# atom radii per type
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variable r atom (type==1)*0.1+(type==2)*0.3
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# groups
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group type1 type 1
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group type2 type 2
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thermo 1
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# reduce computes
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#compute r1 type1 reduce sum c_v1[1]
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#compute r2 type2 reduce sum c_v1[1]
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#compute v1 all voronoi/atom radius v_r
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#
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# TEST 1: Sum of all voronoi cells is the simulation cell volume
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#
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compute v1 all voronoi/atom
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dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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compute r0 all reduce sum c_v1[1]
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thermo_style custom c_r0
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variable t1 equal c_r0
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run 0
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print "TEST_1 $(round(abs(v_t1-1000)/10))% Error. Sum of all voronoi cells is the simulation cell volume"
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uncompute v1
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uncompute r0
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undump d1
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#
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# TEST 2: Sum of all only_group voronoi cells is the simulation cell volume
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#
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compute v1 type2 voronoi/atom only_group
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dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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compute r0 type2 reduce sum c_v1[1]
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compute r1 type1 reduce sum c_v1[1]
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thermo_style custom c_r0 c_r1
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variable t2a equal c_r0
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variable t2b equal c_r1
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run 0
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print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error. Sum of all only_group voronoi cells is the simulation cell volume"
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print "TEST_2b $(round(v_t2b/10))% Error. Sum of all only_group not included voronoi cells is zero"
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uncompute v1
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uncompute r0
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uncompute r1
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undump d1
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#
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# TEST 3: Sum of all radius voronoi cells is the simulation cell volume
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#
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compute v1 all voronoi/atom radius v_r
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dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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compute r0 all reduce sum c_v1[1]
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thermo_style custom c_r0
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variable t3 equal c_r0
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run 0
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print "TEST_3 $(round(abs(v_t3-1000)/10))% Error. Sum of all radius voronoi cells is the simulation cell volume"
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uncompute v1
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uncompute r0
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undump d1
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#
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# TEST 4: Edge histogram tests
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#
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compute v1 type2 voronoi/atom edge_histo 6
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thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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run 1
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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
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print "TEST_4a $(round(v_t4a))% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)"
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uncompute v1
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compute v1 all voronoi/atom edge_histo 8
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thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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run 1
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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
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print "TEST_4b $(round(v_t4b))% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)"
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uncompute v1
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# perturbed fcc lattice
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displace_atoms all random 0.01 0.01 0.01 31423
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compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1
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thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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run 1
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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
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print "TEST_4c $(round(v_t4c))% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold"
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uncompute v1
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# bcc lattice
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delete_atoms group all
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lattice bcc 1 origin 0.25 0.25 0.25
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create_atoms 1 box
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compute v1 all voronoi/atom edge_histo 8
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thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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run 1
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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
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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)"
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uncompute v1
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# restore fcc lattice
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delete_atoms group all
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lattice fcc 1 origin 0.25 0.25 0.25
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create_atoms 1 box basis 1 2
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#
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# TEST 5: Sum of all voronoi cells is the triclinic simulation cell volume
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#
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# switch to triclinic box
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change_box all triclinic
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change_box all xy final 5.0 remap units box
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compute v1 all voronoi/atom
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dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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compute r0 all reduce sum c_v1[1]
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thermo_style custom c_r0
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variable t5 equal c_r0
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run 0
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print "TEST_5 $(round((v_t5-1000)/10))% Error. Sum of all voronoi cells is the triclinic simulation cell volume"
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uncompute v1
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uncompute r0
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undump d1
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# All tests done
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print TEST_DONE
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