From b85090f04837d26f7de8f4cdbb3ef52159c1bf5a Mon Sep 17 00:00:00 2001
From: Tianbai Xiao <tianbaixiao@gmail.com>
Date: Thu, 4 Feb 2021 09:58:43 +0100
Subject: [PATCH] Update docs

---
 docs/make.jl                     |   9 ++++-
 docs/src/assets/icnn.png         | Bin 0 -> 16009 bytes
 docs/src/fortran1.md             |   2 +-
 docs/src/kitml1.md               |  63 +++++++++++++++++++++++++++++++
 docs/src/{kitml.md => kitml2.md} |  18 +--------
 docs/src/reference.md            |   3 +-
 6 files changed, 74 insertions(+), 21 deletions(-)
 create mode 100644 docs/src/assets/icnn.png
 create mode 100644 docs/src/kitml1.md
 rename docs/src/{kitml.md => kitml2.md} (92%)

diff --git a/docs/make.jl b/docs/make.jl
index 846c02e1..81adb977 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -50,8 +50,13 @@ parallel_page = [
     "CUDA" => "para_cuda.md",
 ]
 
+ml_page = [
+    "KitML" => "kitml1.md",
+    "UBE" => "kitml2.md",
+]
+
 fortran_page = [
-    "KitFort.jl" => "fortran1.md",
+    "KitFort" => "fortran1.md",
     "Benchmark" => "fortran2.md",
 ]
 
@@ -71,7 +76,7 @@ makedocs(
         "Tutorial" => tutorial_page,
         "Parallelization" => parallel_page,
         "Utility" => utility_page,
-        "SciML" => "kitml.md",
+        "SciML" => ml_page,
         "Fortran" => fortran_page,
         "Index" => "function_index.md",
         "Python" => "python.md",
diff --git a/docs/src/assets/icnn.png b/docs/src/assets/icnn.png
new file mode 100644
index 0000000000000000000000000000000000000000..03d2566ad95aec0e4e8af0ff4693166fbc420e2e
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HcmV?d00001

diff --git a/docs/src/fortran1.md b/docs/src/fortran1.md
index 3646356c..98b0d9ce 100644
--- a/docs/src/fortran1.md
+++ b/docs/src/fortran1.md
@@ -1,4 +1,4 @@
-# KitFort.jl
+# KitFort and high performance computing
 
 Numerical simulations of nonlinear models and differential equations are essentially connected with supercomputers and high-performance computing (HPC).
 The performance of a supercomputer or a software program is commonly measured in floating-point operations per second (FLOPS).
diff --git a/docs/src/kitml1.md b/docs/src/kitml1.md
new file mode 100644
index 00000000..49174d53
--- /dev/null
+++ b/docs/src/kitml1.md
@@ -0,0 +1,63 @@
+# KitML and scientific machine learning
+
+Machine learning is building its momentum in scientific computing.
+Given the nonlinear structure of differential and integral equations, it is promising to incorporate the universal function approximator from machine learning models into the governing equations and achieve the balance between efficiency and accuracy.
+KitML is designed as a scientific machine learning toolbox, which devotes to fusing mechanical and neural models.
+For example, the Boltzmann collision operator can be divided into a combination of relaxation model and neural network, i.e. the so-called universal Boltzmann equation.
+```math
+\frac{df}{dt} = \int_{\mathcal{R}^{3}} \int_{\mathcal{S}^{2}} \mathcal{B}(\cos \beta, g)\left[f\left(\mathbf{u}^{\prime}\right) f\left(\mathbf{u}_{*}^{\prime}\right)-f(\mathbf{u}) f\left(\mathbf{u}_{*}\right)\right] d \mathbf{\Omega} d \mathbf{u}_{*} \simeq \nu(\mathcal{M}-f)+\mathrm{NN}_{\theta}(\mathcal{M}-f)
+```
+The UBE has the following benefits. 
+First, it automatically ensures the asymptotic limits. 
+Let's consider the Chapman-Enskog method for solving Boltzmann equation, where the distribution function is approximated with expansion series.
+```math
+f \simeq f^{(0)}+f^{(1)}+f^{(2)}+\cdots, \quad f^{(0)}=\mathcal{M}
+```
+Take the zeroth order truncation, and consider an illustrative multi-layer perceptron.
+```math
+\mathrm{NN}_{\theta}(x)=\operatorname{layer}_{n}\left(\ldots \text { layer }_{2}\left({\sigma}\left(\text { layer }_{1}(x)\right)\right)\right), \quad \operatorname{layer}(x)=w x
+```
+Given the zero input from ``M − f``, the contribution from collision term is absent, and the moment equation naturally leads to the Euler equations.
+```math
+\frac{\partial}{\partial t}\left(\begin{array}{c}
+\rho \\
+\rho \mathbf{U} \\
+\rho E
+\end{array}\right)+\nabla_{\mathbf{x}} \cdot\left(\begin{array}{c}
+\rho \mathbf{U} \\
+\rho \mathbf{U} \otimes \mathbf{U} \\
+\mathbf{U}(\rho E+p)
+\end{array}\right)=\int\left(\begin{array}{c}
+1 \\
+\mathbf{u} \\
+\frac{1}{2} \mathbf{u}^{2}
+\end{array}\right)\left(\mathcal{M}_{t}+\mathbf{u} \cdot \nabla_{\mathbf{x}} \mathcal{M}\right) d \mathbf{u}=0
+```
+
+KitML provides two functions to construct universal Boltzmann equation, and it works seamlessly with any modern ODE solver in [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl).
+```@docs
+ube_dfdt
+ube_dfdt!
+```
+
+Besides, we provide an input convex neural network (ICNN) developed by Amos et al.
+
+The neural network parameters are constrained such that the output of the network is a convex function of the inputs. 
+The structure of the ICNN is shown as follows, and it allows for efficient inference via optimization over some inputs to the network given others, and can be applied to settings including structured prediction, data imputation, reinforcement learning, and others. 
+It is important for entropy-based modelling, since the minimization principle works exclusively with convex function.
+
+![](./assets/icnn.png)
+
+```@docs
+ICNNLayer
+ICNNChain
+```
+Besides, we also provide scientific machine learning training interfaces and I/O methods.
+They are consistent with both [Flux.jl](https://github.com/FluxML/Flux.jl) and [DiffEqFlux.jl](https://github.com/SciML/DiffEqFlux.jl) ecosystem.
+
+```@docs
+sci_train
+sci_train!
+load_data
+save_model
+```
\ No newline at end of file
diff --git a/docs/src/kitml.md b/docs/src/kitml2.md
similarity index 92%
rename from docs/src/kitml.md
rename to docs/src/kitml2.md
index cd75d43c..41067bb5 100644
--- a/docs/src/kitml.md
+++ b/docs/src/kitml2.md
@@ -1,24 +1,16 @@
-# Scientific Machine Learning and KitML
+# Universal Boltzmann equation
 
-Machine learning is building its momentum in scientific computing.
-Given the nonlinear structure of differential and integral equations, it is promising to incorporate the universal function approximator from machine learning models into the governing equations and achieve the balance between efficiency and accuracy.
 In the following, we present a universal differential equation strategy to construct the neural network enhanced Boltzmann equation.
 The complicated fivefold integral operator is replaced by a combination of relaxation and neural models.
 It promises a completely differential structure and thus the neural ODE type training and computing becomes possible.
 The approach reduces the computational cost up to three orders of magnitude and preserves the perfect accuracy.
 The detailed theory and implementation can be found in [Tianbai Xiao and Martin Frank, Using neural networks to accelerate the solution of the Boltzmann equation](https://arxiv.org/pdf/2010.13649.pdf).
 
-```@docs
-ube_dfdt
-ube_dfdt!
-```
-
 First we load all the packages needed and set up the configurations.
 ```julia
 using OrdinaryDiffEq, Flux, DiffEqFlux, Plots
 using KitBase, KitML
 
-# config
 begin
     case = "homogeneous"
     maxTime = 3
@@ -47,7 +39,6 @@ end
 
 The dataset is produced by the fast spectral method, which solves the nonlinear Boltzmann integral with fast Fourier transformation.
 ```julia
-# dataset
 begin
     tspan = (0.0, maxTime)
     tran = linspace(tspan[1], tspan[2], tlen)
@@ -124,7 +115,6 @@ end
 Then we define the neural network and construct the unified model with mechanical and neural parts.
 The training is conducted by DiffEqFlux.jl with ADAM optimizer.
 ```julia
-# neural model
 begin
     model_univ = DiffEqFlux.FastChain(
         DiffEqFlux.FastDense(nu, nu * nh, tanh),
@@ -152,18 +142,13 @@ begin
     end
 end
 
-# train
 res = DiffEqFlux.sciml_train(loss, p_model, ADAM(), cb = cb, maxiters = 200)
 res = DiffEqFlux.sciml_train(loss, res.minimizer, ADAM(), cb = cb, maxiters = 200)
-
-# residual history
-plot(log.(his))
 ```
 
 Once we have trained a hybrid Boltzmann collision term, we could solve it as a normal differential equation with any desirable solvers.
 Consider the Midpoint rule as an example, the solution algorithm and visualization can be organized.
 ```julia
-# solution
 ube = ODEProblem(KitML.ube_dfdt, f0_1D, tspan, [M0_1D, τ0, (model_univ, res.minimizer)]);
 sol = solve(
     ube,
@@ -173,7 +158,6 @@ sol = solve(
     saveat = tran,
 );
 
-# result
 plot(
     vSpace.u[:, vSpace.nv÷2, vSpace.nw÷2],
     data_boltz_1D[:, 1],
diff --git a/docs/src/reference.md b/docs/src/reference.md
index 2385a85b..ae348efc 100644
--- a/docs/src/reference.md
+++ b/docs/src/reference.md
@@ -9,4 +9,5 @@
 - Xiao, T., Cai, Q., & Xu, K. (2017). A well-balanced unified gas-kinetic scheme for multiscale flow transport under gravitational field. Journal of Computational Physics, 332, 475-491.
 - Xiao, T., Xu, K., & Cai, Q. (2019). A unified gas-kinetic scheme for multiscale and multicomponent flow transport. Applied Mathematics and Mechanics, 40(3), 355-372.
 - Xiao, T., Liu, C., Xu, K., & Cai, Q. (2020). A velocity-space adaptive unified gas kinetic scheme for continuum and rarefied flows. Journal of Computational Physics, 415, 109535.
-- Xiao, T., & Frank, M. (2020). Using neural networks to accelerate the solution of the Boltzmann equation. arXiv:2010.13649.
\ No newline at end of file
+- Xiao, T., & Frank, M. (2020). Using neural networks to accelerate the solution of the Boltzmann equation. arXiv:2010.13649.
+- Amos, B., Xu, L., & Kolter, J. Z. (2017, July). Input convex neural networks. In International Conference on Machine Learning (pp. 146-155). PMLR.
\ No newline at end of file