Update docs and README

README.md

@@ -68,24 +68,24 @@ cd deepflame-dev
 ### 4. Install dependencies and DeepFlame based on your need
 DeepFlame supports three compilation choices: no torch, LibTorch, and PyTorch. 
 >**Note**: You are encouaged to try all three options, but remember to install the next version in a new terminal to clean previous environment variables.
-#### 4.1 No Torch version 
-If your are using DeepFlame's cvODE solver without DNN model, just install [LibCantera](https://anaconda.org/conda-forge/libcantera-devel) via [conda](https://docs.conda.io/en/latest/miniconda.html#linux-installers).
+
+#### 4.1 PyTorch version (**RECOMMEND**)
+PyTorch version aims to support Python-based progamming for DeepFlame. First install [LibCantera](https://anaconda.org/conda-forge/libcantera-devel) via [conda](https://docs.conda.io/en/latest/miniconda.html#linux-installers). Run the following commands to install:
 ```
-conda create -n df-notorch
-conda activate df-notorch
+conda create -n df-pytorch python=3.8
+conda activate df-pytorch
 conda install -c cantera libcantera-devel
-```
->**Note**: Check your Miniconda3/envs/libcantera directory and make sure the install was successful (lib/ include/ etc. exist).
-
-If the conda env `df-notorch` is activated, install DeepFlame by running: 
+conda install pytorch torchvision torchaudio cudatoolkit=11.6 -c pytorch -c conda-forge 
+conda install pybind11
 
+. install.sh --use_pytorch
 ```
-. install.sh 
-```
-If `df-notorch` not activated (or you have a self-complied libcantera), specify the path to your libcantera:
+>**Note**: You may come accross an error regarding shared library *libmkl_rt.so.2* when libcantera is installed through cantera channel. If so, go to your conda environment and check the existance of *libmkl_rt.so.2* and *libmkl_rt.so.1*, and then link *libmkl_rt.so.2* to *libmkl_rt.so.1*.
 ```
-. install.sh --libcantera_dir /your/path/to/libcantera/
+cd ~/miniconda3/envs/df-pytorch/lib
+ln -s libmkl_rt.so.1 libmkl_rt.so.2
 ```
+>**Note**: Check your Miniconda3/envs/libcantera directory and make sure the install was successful (lib/ include/ etc. exist).
 
 #### 4.2 LibTorch version
 If you choose to use LibTorch (C++ API for Torch), first create the conda env and install [LibCantera](https://anaconda.org/conda-forge/libcantera-devel):
@@ -104,24 +104,30 @@ or you can pass your own libtorch path to DeepFlame.
 . install.sh --libtorch_dir /path/to/libtorch/
 ```
 
-#### 4.3 PyTorch version
-PyTorch version aims to support Python-based progamming for DeepFlame. Run the following commands to install:
+
+> **Note**: Some compiling issues may happen due to system compatability. Instead of using conda installed Cantera C++ lib and the downloaded Torch C++ lib, try to compile your own Cantera and Torch C++ libraries.
+
+
+
+#### 4.3 No Torch version 
+If your are using DeepFlame's cvODE solver without DNN model, just install [LibCantera](https://anaconda.org/conda-forge/libcantera-devel) via [conda](https://docs.conda.io/en/latest/miniconda.html#linux-installers).
 ```
-conda create -n df-pytorch python=3.8
-conda activate df-pytorch
+conda create -n df-notorch
+conda activate df-notorch
 conda install -c cantera libcantera-devel
-conda install pytorch torchvision torchaudio cudatoolkit=11.6 -c pytorch -c conda-forge 
-conda install pybind11
+```
+
+
+If the conda env `df-notorch` is activated, install DeepFlame by running: 
 
-. install.sh --use_pytorch
 ```
->**Note**: You may come accross an error regarding shared library *libmkl_rt.so.2* when libcantera is installed through cantera channel. If so, go to your conda environment and check the existance of *libmkl_rt.so.2* and *libmkl_rt.so.1*, and then link *libmkl_rt.so.2* to *libmkl_rt.so.1*.
+. install.sh 
 ```
-cd ~/miniconda3/envs/df-pytorch/lib
-ln -s libmkl_rt.so.1 libmkl_rt.so.2
+If `df-notorch` not activated (or you have a self-complied libcantera), specify the path to your libcantera:
+```
+. install.sh --libcantera_dir /your/path/to/libcantera/
 ```
 
-> **Note**: Some compiling issues may happen due to system compatability. Instead of using conda installed Cantera C++ lib and the downloaded Torch C++ lib, try to compile your own Cantera and Torch C++ libraries.
 
 ## Running DeepFlame examples
 1. Source your OpenFOAM, for example (depends on your OpenFOAM path):

docs/source/installation/index.rst

@@ -38,32 +38,6 @@ DeepFlame supports three compilation choices: no torch, LibTorch, and PyTorch.
     .. Note:: You are encouaged to try all three options, but remember to install the next version in a new terminal to clean previous environment variables.
 
 
-No Torch version
--------------------------
-
-If your are using DeepFlame's CVODE solver without DNN model, just install LibCantera via `conda <https://docs.conda.io/en/latest/miniconda.html#linux-installers>`_.
-
-.. code-block:: bash
-
-    conda create -n df-notorch
-    conda activate df-notorch
-    conda install -c cantera libcantera-devel
-
-.. Note:: Check your ``Miniconda3/envs/libcantera`` directory and make sure the install was successful (lib/ include/ etc. exist).
-
-
-If the conda env ``df-notorch`` is activated, install DeepFlame by running:
-
-.. code-block:: bash
-
-    . install.sh 
-
-If ``df-notorch`` not activated (or you have a self-complied libcantera), specify the path to your libcantera:
-
-.. code-block:: bash
-
-    . install.sh --libcantera_dir /your/path/to/libcantera/
-
 
 PyTorch version (**RECOMMEND**)
 -------------------------------
@@ -107,3 +81,28 @@ Then you can pass your own libtorch path to DeepFlame.
 
 .. Note::  Some compiling issues may happen due to system compatability. Instead of using conda installed Cantera C++ lib and the downloaded Torch C++ lib, try to compile your own Cantera and Torch C++ libraries.
 
+No Torch version
+-------------------------
+
+If your are using DeepFlame's CVODE solver without DNN model, just install LibCantera via `conda <https://docs.conda.io/en/latest/miniconda.html#linux-installers>`_.
+
+.. code-block:: bash
+
+    conda create -n df-notorch
+    conda activate df-notorch
+    conda install -c cantera libcantera-devel
+
+.. Note:: Check your ``Miniconda3/envs/libcantera`` directory and make sure the install was successful (lib/ include/ etc. exist).
+
+
+If the conda env ``df-notorch`` is activated, install DeepFlame by running:
+
+.. code-block:: bash
+
+    . install.sh 
+
+If ``df-notorch`` not activated (or you have a self-complied libcantera), specify the path to your libcantera:
+
+.. code-block:: bash
+
+    . install.sh --libcantera_dir /your/path/to/libcantera/