Add examples

Author: reb-ddm

examples/boolean_predicates/example_agents.ka

@@ -0,0 +1,9 @@
+%agent: A(x{u p})
+// global boolean parameter
+// P
+%guard_param: P [false]
+
+#[P] . -> A(x{u}) @ 1
+A(x{u}) -> A(x{p}) @ 1
+
+%obs: 'Ap' |A(x{p})|

examples/boolean_predicates/example_agents_params.ka

@@ -0,0 +1,9 @@
+%agent: A(x{u p})
+%agent: B()
+// global boolean parameter
+// P1, P2
+
+#[P1 && P2] . -> A(x{u}) @ 1
+#[P1 || P2] . -> B(x{u}) @ 1
+
+%obs: 'Ap' |A(x{p})|

examples/boolean_predicates/example_automatic_conflicts.ka

@@ -0,0 +1,13 @@
+
+
+%agent: A(x,y,z)
+%agent: E(t)
+
+%conflict: A x y
+
+%init: 100 A(),E()
+
+A(x[.]), E(t[.]) -> A(x[1]), E(t[1]) @ 1
+A(y[.]), E(t[.]) -> A(y[1]), E(t[1]) @ 1
+
+A(x[_], y[_], z[.]), E(t[.]) -> A(x[_], y[_], z[1]), E(t[1]) @ 1

examples/boolean_predicates/example_conflict_macro.ka

@@ -0,0 +1,18 @@
+%agent: A(x{u p} y)
+%conflict: A x y
+// global boolean parameter
+// P
+%guard_param: B [false]
+%guard_param: P [true]
+%guard_param: C [false]
+%guard_param: x [true]
+%guard_param: y [true]
+
+
+#[P] . -> A(x{u}) @ 1
+'~namef' A(x{u}) -> A(x{p}) @ 1
+#[x && y] A(x[.]), A(x[.]) -> A(x[1]), A(x[1]) @ 1
+#[B || C] A(y[.]), A(y[.]) -> A(y[1]), A(y[1]) @ 1
+
+
+%obs: 'Ap' |A(x{p})|

examples/boolean_predicates/example_covering_classes.ka

@@ -0,0 +1,4 @@
+%init: 50 A(x{u},y{u},z{u})
+
+#[a] A(x{u}, y{u}) -> A(x{u},y{p}) @ 1
+#[a || b] A(y{u}, z{u}) -> A(y{u},z{p}) @ 1

examples/boolean_predicates/example_double_bonds.ka

@@ -0,0 +1,26 @@
+
+
+// Define agents
+%agent: A(x,y,z)
+// global boolean parameter
+%guard_param: P [true]
+// P = x and y are in conflict
+
+// Initial conditions
+%init: 100 A()
+
+A(x[.],y[.]), A(x[.],y[.]) -> A(x[.],y[1]), A(x[.],y[1]) @ 1
+A(x[.],y[.]), A(x[.],y[.]) -> A(x[1],y[.]), A(x[1],y[.]) @ 1
+
+// if there is no conflict
+#[[not] P] A(x[.]), A(x[.]) -> A(x[1]), A(x[1]) @ 1
+#[[not] P] A(y[.]), A(y[.]) -> A(y[1]), A(y[1]) @ 1
+
+// else
+#[P] A(x[1],y[.]), A(x[1],y[.]) -> A(x[2],y[1]), A(x[2],y[1]) @ 1
+#[P] A(x[.],y[1]), A(x[.],y[1]) -> A(x[1],y[2]), A(x[1],y[2]) @ 1
+
+// Measure amount of A double bonds
+%obs: 'Trimer' |A(x[1],y[2]),A(x[1],y[2])|
+
+// Static analysis must show that P => no double bonds

examples/boolean_predicates/example_sequential_bond_macro.ka

@@ -0,0 +1,15 @@
+%agent: A(x{u p} y)
+%sequential_bond: A x y
+// global boolean parameter
+// P
+
+
+. -> A(x{u}) @ 1
+A(x{u}) -> A(x{p}) @ 1
+A(x[.]), A(x[.]) -> A(x[1]), A(x[1]) @ 1
+A(y[.]), A(y[.]) -> A(y[1]), A(y[1]) @ 1
+A(x[.],y[.]), A(x[.],y[.]) -> A(x[.],y[1]), A(x[.],y[1]) @ 1
+
+
+
+%obs: 'Ap' |A(x{p})|

examples/boolean_predicates/example_site_across_bounds.ka

@@ -0,0 +1,27 @@
+
+
+// Define agents
+%agent: A(a,b{u p})
+%agent: B(x,y{u p})
+%agent: C(z,k{u p})
+// global boolean parameter
+//%guard_param: P [true]
+
+// Initial conditions
+%init: 100 A(),B(),C()
+
+A(a[.]),B(x[.]) -> A(a[1]),B(x[1]) @ 1
+A(a[1],b{u}),B(x[1],y{u}) <-> A(a[1],b{p}),B(x[1],y{p}) @ 1
+#[P]
+A(a[.]),C(z[.],k{u}) -> A(a[1]),C(z[1],k{u}) @ 1
+#[Q || [not] J]
+A(a[1]),C(z[1],k{u}) -> A(a[.]),C(z[.],k{p}) @ 1
+#[J && Q]
+A(a[.]),C(z[.],k{p}) -> A(a[1]),C(z[1],k{p}) @ 1
+#[P || J || [not] Q]
+A(a[1],b{u}),C(z[1],k{p}) -> A(a[1],b{p}),C(z[1],k{p}) @ 1
+#[Q]
+A(a[1]),C(z[1]),B(x[.]) -> A(a[1]),C(z[.]),B(x[1]) @ 1
+
+'not_sym1' A(a[1],b{p}),B(x[1],y{u}) -> .,. @ 1
+'not_sym2' A(a[1],b{u}),B(x[1],y{p}) -> .,. @ 1

examples/boolean_predicates/example_working_set_macro.ka

@@ -0,0 +1,16 @@
+%agent: A(x{u p} y)
+//%conflict: A x y
+%guard_param: A [true]
+%guard_param: B [true]
+%guard_param: B [true]
+
+
+%working_set: [
+'create A' #[A && B] . -> A(x{u}) @ 1
+'phosphorization' A(x{u}) -> A(x{p}) @ 1
+'binding x' A(x[.]), A(x[.]) -> A(x[1]), A(x[1]) @ 1
+]
+'binding y' A(y[.]), A(y[.]) -> A(y[1]), A(y[1]) @ 1
+
+
+%obs: 'Ap' |A(x{p})|