Closed jpfairbanks closed 1 year ago
jpfairbanks
commented
1 year ago The judgements are where you declare variables, then the equations are where you declare equations in those variables. The judgements tell you the types of each variable including the dimension and space over which it is defined.
jpfairbanks
commented
1 year ago Just realized I named the model diffusion, but it is harmonic oscillator
jpfairbanks
commented
1 year ago Updated some field names
{
"header": {
"name": "harmonic_oscillator",
"schema": "modelreps.io/DecaExpr",
"description": "A Simple Harmonic Oscillator as a Diagrammatic Equation",
"schema_name": "DecaExpr",
"model_version": "v1.0"
},
"model": {
"context": [
{
"var": {
"name": "X"
},
"dim": "Form0",
"space": "Point"
},
{
"var": {
"name": "V"
},
"dim": "Form0",
"space": "Point"
},
{
"var": {
"name": "k"
},
"dim": "Constant",
"space": "Point"
}
],
"equations": [
{
"lhs": {
"var": {
"name": "X"
}
},
"rhs": {
"name": "V"
}
},
{
"lhs": {
"var": {
"name": "V"
}
},
"rhs": {
"args": [
{
"name": "-1"
},
{
"name": "k"
},
{
"name": "X"
}
]
}
}
]
}
}Combinatorial Representation of the model is
{
"Var": [
{
"_id": 1,
"type": "Form0",
"name": "X"
},
{
"_id": 2,
"type": "Form0",
"name": "Ẋ"
},
{
"_id": 3,
"type": "Constant",
"name": "k"
},
{
"_id": 4,
"type": "infer",
"name": "mult_1"
},
{
"_id": 5,
"type": "infer",
"name": "Ẋ̇"
},
{
"_id": 6,
"type": "Literal",
"name": "-1"
}
],
"TVar": [
{
"_id": 1,
"incl": 2
},
{
"_id": 2,
"incl": 5
}
],
"Op1": [
{
"_id": 1,
"src": 1,
"tgt": 2,
"op1": "∂ₜ"
},
{
"_id": 2,
"src": 2,
"tgt": 5,
"op1": "∂ₜ"
}
],
"Op2": [
{
"_id": 1,
"proj1": 6,
"proj2": 3,
"res": 4,
"op2": "*"
},
{
"_id": 2,
"proj1": 4,
"proj2": 1,
"res": 5,
"op2": "*"
}
],
"Σ": [],
"Summand": [],
"Type": [],
"Operator": [],
"Name": []
}I think we should probably support both the Syntactic and Combinatorial forms. Because some parts of the software will be easier to write with each representation.
jpfairbanks
commented
1 year ago The relevant parts of the Decapodes Source Code are:
DecaExpr definitions: https://github.com/AlgebraicJulia/Decapodes.jl/blob/a19e268808a657360b8e6b502cbad866d5c5222f/src/language.jl#L6
Schemas for the combinatorial representaions: https://github.com/AlgebraicJulia/Decapodes.jl/blob/a19e268808a657360b8e6b502cbad866d5c5222f/src/decapodeacset.jl#L6 and https://github.com/AlgebraicJulia/Decapodes.jl/blob/a19e268808a657360b8e6b502cbad866d5c5222f/src/decapodeacset.jl#L113
YohannParis
commented
1 year ago Could we not use short forms of names? for example:
var instead of variabledim instead of dimensionsCan we remove the header property and just put its content at the root level like other AMR?
Also this schema is missing id for each of the context.var
jpfairbanks
commented
1 year ago I have added a UWD example.
Given a relation macro
@relation (x:X, z:Z) where y:Y begin
R(x,y)
S(y,z)
T(z,y,u)
endThe UWD is given by the following database:
Catlab.Programs.RelationalPrograms.TypedUnnamedRelationDiagram{Symbol, Symbol, Symbol} with elements Box = 1:3, Port = 1:7, OuterPort = 1:2, Junction = 1:4, Type = 1:0, Name = 1:0, VarName = 1:0
┌─────┬──────┐
│ Box │ name │
├─────┼──────┤
│ 1 │ R │
│ 2 │ S │
│ 3 │ T │
└─────┴──────┘
┌──────┬─────┬──────────┬───────────┐
│ Port │ box │ junction │ port_type │
├──────┼─────┼──────────┼───────────┤
│ 1 │ 1 │ 1 │ X │
│ 2 │ 1 │ 3 │ Y │
│ 3 │ 2 │ 3 │ Y │
│ 4 │ 2 │ 2 │ Z │
│ 5 │ 3 │ 2 │ Z │
│ 6 │ 3 │ 3 │ Y │
│ 7 │ 3 │ 4 │ untyped │
└──────┴─────┴──────────┴───────────┘
┌───────────┬────────────────┬─────────────────┐
│ OuterPort │ outer_junction │ outer_port_type │
├───────────┼────────────────┼─────────────────┤
│ 1 │ 1 │ x │
│ 2 │ 2 │ z │
└───────────┴────────────────┴─────────────────┘
┌──────────┬───────────────┬──────────┐
│ Junction │ junction_type │ variable │
├──────────┼───────────────┼──────────┤
│ 1 │ X │ x │
│ 2 │ Z │ z │
│ 3 │ Y │ y │
│ 4 │ untyped │ u │
└──────────┴───────────────┴──────────┘The expression that creates it is serialized as:
{
"context": [
{
"var": "x",
"type": "X"
},
{
"var": "z",
"type": "Z"
}
],
"statements": [
{
"relation": "R",
"args": [
{
"var": "x",
"type": "X"
},
{
"var": "y",
"type": "Y"
}
]
},
{
"relation": "S",
"args": [
{
"var": "y",
"type": "Y"
},
{
"var": "z",
"type": "Z"
}
]
},
{
"relation": "T",
"args": [
{
"var": "z",
"type": "Z"
},
{
"var": "y",
"type": "Y"
},
{
"var": "u"
}
]
}
]
}Take a look at src/julia/composite_models_examples.jl for an example of building a composite model in AMR.
jpfairbanks
commented
1 year ago If this were a real julia package, some of the horrific namespacing would go away.
jpfairbanks
commented
1 year ago The composite model is:
Decapodes.SummationDecapode{Any, Any, Symbol} with elements Var = 1:14, TVar = 1:3, Op1 = 1:4, Op2 = 1:4, Σ = 1:1, Summand = 1:2, Type = 1:0, Operator = 1:0, Name = 1:0
┌─────┬───────────┬───────────────────┐
│ Var │ type │ name │
├─────┼───────────┼───────────────────┤
│ 1 │ Form0 │ X │
│ 2 │ Form0 │ V │
│ 3 │ Constant │ oscillator_k │
│ 4 │ infer │ oscillator_mult_1 │
│ 5 │ infer │ oscillator_Ẋ̇ │
│ 6 │ Literal │ -1 │
│ 7 │ Form0 │ Q │
│ 8 │ Constant │ heating_κ │
│ 9 │ Constant │ heating_λ │
│ 10 │ Parameter │ heating_Q₀ │
│ 11 │ infer │ heating_Q̇ │
│ 12 │ infer │ heating_•2 │
│ 13 │ infer │ heating_•3 │
│ 14 │ infer │ heating_•4 │
└─────┴───────────┴───────────────────┘
┌──────┬──────┐
│ TVar │ incl │
├──────┼──────┤
│ 1 │ 2 │
│ 2 │ 5 │
│ 3 │ 11 │
└──────┴──────┘
┌─────┬─────┬─────┬─────┐
│ Op1 │ src │ tgt │ op1 │
├─────┼─────┼─────┼─────┤
│ 1 │ 1 │ 2 │ ∂ₜ │
│ 2 │ 2 │ 5 │ ∂ₜ │
│ 3 │ 7 │ 11 │ ∂ₜ │
│ 4 │ 14 │ 13 │ λ │
└─────┴─────┴─────┴─────┘
┌─────┬───────┬───────┬─────┬─────┐
│ Op2 │ proj1 │ proj2 │ res │ op2 │
├─────┼───────┼───────┼─────┼─────┤
│ 1 │ 6 │ 3 │ 4 │ * │
│ 2 │ 4 │ 1 │ 5 │ * │
│ 3 │ 8 │ 2 │ 12 │ * │
│ 4 │ 7 │ 10 │ 14 │ - │
└─────┴───────┴───────┴─────┴─────┘
┌───┬─────┐
│ Σ │ sum │
├───┼─────┤
│ 1 │ 11 │
└───┴─────┘
┌─────────┬─────────┬───────────┐
│ Summand │ summand │ summation │
├─────────┼─────────┼───────────┤
│ 1 │ 12 │ 1 │
│ 2 │ 13 │ 1 │
└─────────┴─────────┴───────────┘
Made some progress today:
{
"header": {
"description": "A Simple Harmonic Oscillator as a Diagrammatic Equation",
"name": "harmonic_oscillator",
"_type": "Header",
"model_version": "v1.0",
"schema": "modelreps.io/DecaExpr",
"schema_name": "DecaExpr"
},
"_type": "ASKEMDecaExpr",
"model": {
"context": [
{
"dim": "Form0",
"var": {
"name": "X",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Form0",
"var": {
"name": "V",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Constant",
"var": {
"name": "k",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
}
],
"_type": "Decapodes.DecaExpr",
"equations": [
{
"rhs": {
"name": "V",
"_type": "Var"
},
"lhs": {
"var": {
"name": "X",
"_type": "Var"
},
"_type": "Tan"
},
"_type": "Eq"
},
{
"rhs": {
"args": [
{
"name": "-1",
"_type": "Decapodes.Lit"
},
{
"name": "k",
"_type": "Var"
},
{
"name": "X",
"_type": "Var"
}
],
"_type": "Decapodes.Mult"
},
"lhs": {
"var": {
"name": "V",
"_type": "Var"
},
"_type": "Tan"
},
"_type": "Eq"
}
]
}
}Current status is that the UWDs, Decapodes, and Composite models are all serializable and deserializable. The current definition of correctness for serialization is that write, read, write == write.
Here is the example of a nested hierarchical model:
{
"components": [
{
"interface": [
"X",
"Ẋ"
],
"_type": "OpenModel",
"model": {
"header": {
"description": "A Simple Harmonic Oscillator as a Diagrammatic Equation",
"name": "harmonic_oscillator",
"_type": "Header",
"model_version": "v1.0",
"schema": "modelreps.io/DecaExpr",
"schema_name": "DecaExpr"
},
"_type": "ASKEMDecaExpr",
"model": {
"context": [
{
"dim": "Form0",
"var": {
"name": "X",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Form0",
"var": {
"name": "V",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Constant",
"var": {
"name": "k",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
}
],
"_type": "DecaExpr",
"equations": [
{
"rhs": {
"name": "V",
"_type": "Var"
},
"lhs": {
"var": {
"name": "X",
"_type": "Var"
},
"_type": "Tan"
},
"_type": "Eq"
},
{
"rhs": {
"args": [
{
"name": "-1",
"_type": "Lit"
},
{
"name": "k",
"_type": "Var"
},
{
"name": "X",
"_type": "Var"
}
],
"_type": "Mult"
},
"lhs": {
"var": {
"name": "V",
"_type": "Var"
},
"_type": "Tan"
},
"_type": "Eq"
}
]
}
}
},
{
"components": [
{
"interface": [
"V",
"Q₊"
],
"_type": "OpenModel",
"model": {
"header": {
"description": "velocity makes it get hot",
"name": "DragHeat",
"_type": "Header",
"model_version": "v1.0",
"schema": "modelreps.io/SummationDecapode",
"schema_name": "SummationDecapode"
},
"_type": "ASKEMDecaExpr",
"model": {
"context": [
{
"dim": "Form0",
"var": {
"name": "V",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Form0",
"var": {
"name": "Q₊",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Constant",
"var": {
"name": "κ",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
}
],
"_type": "DecaExpr",
"equations": [
{
"rhs": {
"f": "*",
"arg1": {
"name": "κ",
"_type": "Var"
},
"_type": "App2",
"arg2": {
"name": "V",
"_type": "Var"
}
},
"lhs": {
"name": "Q₊",
"_type": "Var"
},
"_type": "Eq"
}
]
}
}
},
{
"interface": [
"Q₋",
"Q"
],
"_type": "OpenModel",
"model": {
"header": {
"description": "heat dissipates to the enviornment",
"name": "NetwonCooling",
"_type": "Header",
"model_version": "v1.0",
"schema": "modelreps.io/SummationDecapode",
"schema_name": "SummationDecapode"
},
"_type": "ASKEMDecaExpr",
"model": {
"context": [
{
"dim": "Form0",
"var": {
"name": "Q₋",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Parameter",
"var": {
"name": "Q₀",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Form0",
"var": {
"name": "Q",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Constant",
"var": {
"name": "λ",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
}
],
"_type": "DecaExpr",
"equations": [
{
"rhs": {
"f": "λ",
"arg": {
"f": "-",
"arg1": {
"name": "Q",
"_type": "Var"
},
"_type": "App2",
"arg2": {
"name": "Q₀",
"_type": "Var"
}
},
"_type": "App1"
},
"lhs": {
"name": "Q₋",
"_type": "Var"
},
"_type": "Eq"
}
]
}
}
},
{
"interface": [
"X",
"Y",
"T"
],
"_type": "OpenModel",
"model": {
"header": {
"description": "variables be addin",
"name": "LinearSuperpositon",
"_type": "Header",
"model_version": "v1.0",
"schema": "modelreps.io/SummationDecapode",
"schema_name": "SummationDecapode"
},
"_type": "ASKEMDecaExpr",
"model": {
"context": [
{
"dim": "Form0",
"var": {
"name": "X",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Form0",
"var": {
"name": "Y",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
},
{
"dim": "Form0",
"var": {
"name": "T",
"_type": "Var"
},
"space": "Point",
"_type": "Judgement"
}
],
"_type": "DecaExpr",
"equations": [
{
"rhs": {
"args": [
{
"name": "X",
"_type": "Var"
},
{
"name": "Y",
"_type": "Var"
}
],
"_type": "Plus"
},
"lhs": {
"name": "T",
"_type": "Var"
},
"_type": "Eq"
}
]
}
}
}
],
"composition_pattern": {
"statements": [
{
"variables": [
{
"var": "V",
"type": "Form0",
"_type": "Typed"
},
{
"var": "Q₊",
"_type": "Untyped"
}
],
"_type": "Statement",
"relation": "drag"
},
{
"variables": [
{
"var": "Q₋",
"_type": "Untyped"
},
{
"var": "Q",
"type": "Form0",
"_type": "Typed"
}
],
"_type": "Statement",
"relation": "cooling"
},
{
"variables": [
{
"var": "Q₊",
"_type": "Untyped"
},
{
"var": "Q₋",
"_type": "Untyped"
},
{
"var": "Q̇",
"_type": "Untyped"
}
],
"_type": "Statement",
"relation": "superposition"
}
],
"context": [
{
"var": "V",
"type": "Form0",
"_type": "Typed"
},
{
"var": "Q",
"type": "Form0",
"_type": "Typed"
}
],
"_type": "UWDExpr"
},
"header": {
"description": "A formula for heating - cooling",
"name": "heating_dynamics",
"_type": "Header",
"model_version": "v0.1",
"schema": "modelreps.io/Composite",
"schema_name": "CompositeModelExpr"
},
"_type": "CompositeModelExpr"
}
],
"composition_pattern": {
"statements": [
{
"variables": [
{
"var": "X",
"type": "Form0",
"_type": "Typed"
},
{
"var": "V",
"type": "Form0",
"_type": "Typed"
}
],
"_type": "Statement",
"relation": "oscillator"
},
{
"variables": [
{
"var": "V",
"type": "Form0",
"_type": "Typed"
},
{
"var": "Q",
"type": "Form0",
"_type": "Typed"
}
],
"_type": "Statement",
"relation": "heating"
}
],
"context": [
{
"var": "X",
"type": "Form0",
"_type": "Typed"
},
{
"var": "Q",
"type": "Form0",
"_type": "Typed"
}
],
"_type": "UWDExpr"
},
"header": {
"description": "A hierarchical composite model of frictional heating",
"name": "hierarchical_composite",
"_type": "Header",
"model_version": "v0.1",
"schema": "modelreps.io/Composite",
"schema_name": "CompositeModelExpr"
},
"_type": "CompositeModelExpr"
}I pulled out all the data definitions from all the files using awk
The types used in the Decapodes part are
@data CompositeModel <: AbstractTerm begin
OpenModel(model::ASKEMDecapodes.ASKEMDecaExpr, interface::Vector{Symbol})
OpenDecapode(model::ASKEMDecapodes.ASKEMDecapode, interface::Vector{Symbol})
CompositeModelExpr(header::Header, composition_pattern::UWDExpr, components::Vector{CompositeModel})
end
@data ASKEMDeca <: AbstractTerm begin
ASKEMDecaExpr(header::AMR.Header, model::Decapodes.DecaExpr)
ASKEMDecapode(header::AMR.Header, model::Decapodes.SummationDecapode)
end
@data Var <: AbstractTerm begin
Untyped(var::Symbol)
Typed(var::Symbol, type::Symbol)
end
@data UWDTerm <: AbstractTerm begin
Statement(relation::Symbol, variables::Vector{Var})
UWDExpr(context::Vector{Var}, statements::Vector{Statement})
UWDModel(header::AMR.Header, uwd::UWDExpr)
end
@as_record struct Header <: AbstractTerm
name::String
schema::String
description::String
schema_name::String
model_version::String
endAnd from Decapodes they are
@data Term begin
Var(name::Symbol)
Lit(name::Symbol)
Judgement(var::Var, dim::Symbol, space::Symbol)
AppCirc1(fs::Vector{Symbol}, arg::Term)
App1(f::Symbol, arg::Term)
App2(f::Symbol, arg1::Term, arg2::Term)
Plus(args::Vector{Term})
Mult(args::Vector{Term})
Tan(var::Term)
end
@data Equation begin
Eq(lhs::Term, rhs::Term)
end
@as_record struct DecaExpr
context::Vector{Judgement}
equations::Vector{Equation}
endSo these are all the types you would need to implement in order to properly process a model.
jpfairbanks
commented
1 year ago This PR has moved to its own package https://github.com/AlgebraicJulia/SyntacticModels.jl please provide feedback on issues on that repo.
bgyori
commented
1 year ago Should the JSON examples that were part of this original PR still be added under multiphysics/examples in a new PR? We could also work on creating (ideally generating automatically from the implementation) a JSON schema for validation purposes.
This uses PR #50 and requires a patch to decapodes https://github.com/AlgebraicJulia/Decapodes.jl/pull/132.