update/de-cruft notes directory

13 files changed, 142 insertions, 41 deletions

diff --git a/notes/background.txt b/notes/background.txt
index 700926d..72991e3 100644
--- a/notes/background.txt
+++ b/notes/background.txt
@@ -4,6 +4,12 @@
 "CellML Model Repository"
 http://models.cellml.org/cellml
 
+OpenCell tool for CellML
+https://www.cellml.org/tools/opencell
+
+NeuroML
+https://en.wikipedia.org/wiki/NeuroML
+
 "BioModels Database"
 http://www.ebi.ac.uk/biomodels-main/
 
@@ -82,3 +88,10 @@ Luna Lang
     so far, vaporware
     http://www.luna-lang.org/
 
+### Other
+
+"HOW TO SIMULATE THE UNIVERSE IN 134 EASY STEPS"
+Nicky Case, 2016
+http://ncase.me/OVC2016/
+
+also: http://blog.ncase.me/evolution-not-revolution/
diff --git a/notes/dae_libs.txt b/notes/dae_libs.txt
new file mode 100644
index 0000000..762d21b
--- /dev/null
+++ b/notes/dae_libs.txt
@@ -0,0 +1,9 @@
+
+##### Solvers/"Codes"
+
+SUNDIALS
+    http://computation.llnl.gov/projects/sundials
+
+DAEPACK
+    http://yoric.mit.edu/DAEPACK
+
diff --git a/notes/goals.txt b/notes/goals.txt
deleted file mode 100644
index d3e4bc4..0000000
--- a/notes/goals.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-- simple wiki/database tool with web front end
-- some support or UI for compound models
-- code generation:
-    - julia
-    - javascript
-    - rust?
-    - C?
-    - modelica
-- Elm interactive front-end / debugger
diff --git a/notes/ideas.txt b/notes/ideas.txt
deleted file mode 100644
index 2f5d5ac..0000000
--- a/notes/ideas.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-- FRP-based integration of models (via signals)
-- Elm-based browser simulation environment
-- fast simulator/plotter in Rust
-- try to integrate or use "Luna" language
diff --git a/notes/implementation_libs.txt b/notes/julia_libs.txt
index 94a961f..3ab17c8 100644
--- a/notes/implementation_libs.txt
+++ b/notes/julia_libs.txt
@@ -32,13 +32,3 @@ PEGParser.jl
 
 ParserCombinator.jl
     More Haskell-like. Meh.
-
-##### GUI Demos
-
-numeric.js
-    Has an ODE solver. Use with Elm?
-
-Tangle.js
-    Brett's JS widget-y thing. Very simple.
-    How did he do plots/graphs for those demos?
-    http://worrydream.com/Tangle/guide.html
diff --git a/notes/examples.txt b/notes/list_of_examples.txt
index 5f5d4d3..b8b416f 100644
--- a/notes/examples.txt
+++ b/notes/list_of_examples.txt
@@ -1,16 +1,15 @@
 
 Newer list:
-https://en.wikipedia.org/wiki/Radioactive_decay#One-decay_process
-https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model
-logistic function
-Black–Scholes
-https://en.wikipedia.org/wiki/Sethi_model 
-von Bertalanffy growth equation
+- https://en.wikipedia.org/wiki/Radioactive_decay#One-decay_process
+- https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model
+- logistic function
+- Black–Scholes
+- https://en.wikipedia.org/wiki/Sethi_model 
+- von Bertalanffy growth equation
 
 ### Models
 
 Simple, equation based:
-- World3 (from limits to growth report)
 - classic predator-prey (Lotka–Volterra)
 - attractors
 - that vegan paper
@@ -57,3 +56,9 @@ https://www.wikidata.org/wiki/Q173227 (physical constant)
 ### Units
 
 https://www.wikidata.org/wiki/Q15088658 (measured value)
+
+### Existing / Import
+- World3 (from limits to growth report)
+- Tennessee Eastman Process Control Challenge Problem
+    http://yoric.mit.edu/DAEPACK/Examples/Eastman
+- OpenWorm (in NeuroML)
diff --git a/notes/modelica33r1_spec.txt b/notes/modelica33r1_grammar.txt
index 2df42dd..2df42dd 100644
--- a/notes/modelica33r1_spec.txt
+++ b/notes/modelica33r1_grammar.txt
diff --git a/notes/modelica.txt b/notes/modelica_limitations.txt
index 69457c1..5c4294d 100644
--- a/notes/modelica.txt
+++ b/notes/modelica_limitations.txt
@@ -1,2 +1,2 @@
-
 Double derivative (eg, "der(der(x)) = a") is not allowed.
+Partial derivatives are not allowed.
diff --git a/notes/parsing.txt b/notes/parsing.txt
index 6a13b76..a3c29ef 100644
--- a/notes/parsing.txt
+++ b/notes/parsing.txt
@@ -3,3 +3,6 @@ Parser Refs:
 http://notes.willcrichton.net/parsing-strategies-in-rust/
 http://smallcultfollowing.com/babysteps/blog/2015/09/14/lalrpop/
 https://github.com/nikomatsakis/lalrpop/
+
+
+libsyntax: rust lib for parsing rust itself
diff --git a/notes/solve_for.txt b/notes/solve_for.txt
new file mode 100644
index 0000000..b1cf81d
--- /dev/null
+++ b/notes/solve_for.txt
@@ -0,0 +1,58 @@
+
+    x = a*y + c
+    y = 4 * c
+
+    solve for [c] in terms of [a, x]
+        first solve for other unknowns: [y]
+
+    x = a*(4*c) + c
+
+    x = c * (1 + 4*a)
+    c = (1 + 4*a) / x
+
+N equations in M unknowns, P constants
+
+    0 = x + y
+    0 = y*2 + 1 - x
+
+-----------------------------------
+
+solve_for(self, P: Vec<String>, M: Vec<String>, Q: HashMap<String, Expr>)
+
+
+returns a ModelicaModel with fixed components; equations are LHS identifier, in
+    correct order, no extends, no connections, name suffixed " (rewritten)",
+    components as Parameter (w/ val), Input, or Output
+    
+
+V variables
+Q constants (become kwargs)
+P bound vars (independent, inputs/passed, become like constants)
+M unknowns (dependent, outputs)
+N' total equations
+N equations with unknowns
+
+  V = Q + P + M
+  check: each Q is Integer or Float     UnderSpecifiedConstant
+  filter N' to get N    OverConstrained if extra equations
+  check: N >= M         UnderConstrained
+
+while len(eqns) > 0:
+  1. find first eqn with single unknown, and pop it
+  2. rebalance to get unknown on LHS
+  3. remove unknown from unknown list
+
+return: sort equations to match order
+
+solve_for(var) impl for SimpleEquation => Result<SimpleEquation, String>
+    check: var only on one side     VariableNotFound or NaiveImplementation
+    put var on LHS
+    recursively apply rules to symmetrically unwrap LHS onto RHS
+    if try to unwrap Abs:           NaiveImplementation
+
+-----------------------------------
+systems of differential equations:
+  will be N equations of N variables, in terms of implied time
+
+should be no unknowns; odex thing is just varying initial equations
+have JS boxes to show ranges of initial conditions
diff --git a/notes/spec.txt b/notes/spec.txt
deleted file mode 100644
index 405629b..0000000
--- a/notes/spec.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-
-variable types:
-    state
-    parameter
-    constant
-    independent (?)
-    dependent (?)
-    time (special case?)
-
-"variables"? or "symbols"? or "quantities"?
diff --git a/notes/tangle_demo.txt b/notes/tangle_demo.txt
new file mode 100644
index 0000000..463abe1
--- /dev/null
+++ b/notes/tangle_demo.txt
@@ -0,0 +1,31 @@
+
+
+/experiments/%model/tangle.html
+/experiments/%model/tangle-model.js
+
+<script type="text/javascript" src="Tangle.js"></script>
+
+this part in body's onLoad; after live script has downloaded.
+var table = new Tangle (document.getElementById("MODELNAME"), {
+    initialize: function () {
+        this.CONSTANT = INIT;
+        this.IN_VAR = INIT;
+    },
+    update: function () {
+        var vals = model();
+        this.OUT_VAR = vals[0];
+        this.OUT_VAR = vals[1];
+        [...]
+    },
+});
+
+<p id="MODELNAME">
+<!-- TODO: some built-in js that checks if in/out vars are the same, and
+     alerts if not? -->
+<!-- EDIT ME: this part is template -->
+When the parameters are <span data-var="VARSLUG"> for VARSLUG</span>, [...],
+    and the variables are <span data-var="cookies" class="TKAdjustableNumber">
+    for VAR</span>, then you get <span data-var=OUTVAR> for OUTVAR</span>
+<!-- END EDIT ME -->
+
+
diff --git a/notes/webface.txt b/notes/webface.txt
index 2932f8e..78306bd 100644
--- a/notes/webface.txt
+++ b/notes/webface.txt
@@ -21,3 +21,18 @@ hyperphysics
 plotly.js: d3.js and stack.gl
     https://plot.ly/javascript/
     https://github.com/plotly/plotly.js
+
+
+##### GUI Demos
+
+numeric.js
+    Has an ODE solver. Use with Elm?
+
+Tangle.js
+    Brett's JS widget-y thing. Very simple.
+    How did he do plots/graphs for those demos?
+    http://worrydream.com/Tangle/guide.html
+
+KaTeX LaTeX rendering
+    Faster than mathjax?
+    https://github.com/Khan/KaTeX