From fb4510d25e5e4ff0a63e15085b15b1ae2b5e4b1e Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Wed, 23 Mar 2022 22:41:46 +0000
Subject: [PATCH 01/13] added nuclear data download

---
 .github/workflows/ci_with_install.yml | 48 +++++++++++++++++++++++++++
 .gitignore                            |  8 +++++
 2_run_openmc_dagmc_simulation.py      | 21 ++++++++----
 README.md                             | 12 +++----
 environment_cad.yml                   | 13 ++++++++
 environment_neutronics.yml            | 11 ++++++
 6 files changed, 98 insertions(+), 15 deletions(-)
 create mode 100644 .github/workflows/ci_with_install.yml
 create mode 100644 environment_cad.yml
 create mode 100644 environment_neutronics.yml

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
new file mode 100644
index 0000000..5b2b2a7
--- /dev/null
+++ b/.github/workflows/ci_with_install.yml
@@ -0,0 +1,48 @@
+
+# This CI will launch a Docker image that contains all the dependencies required
+# within that image the pytest test suite is run 
+
+
+name: CI with install
+
+on:
+  pull_request:    
+    branches:
+    - develop
+    - main
+ 
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    container:
+      image: continuumio/miniconda3
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      
+      - name: install dependencies package
+        run: |
+          apt update -y
+          apt-get install ffmpeg libsm6 libxext6  -y
+
+      - name: create environment 1
+        run: |
+          conda env create -f environment_cad.yml
+          conda activate env_cad
+
+      - name: run script 1 of 3
+        run: |
+          python 1_creation_of_dagmc_geometry.py
+
+      - name: create environment 1
+        run: |
+          conda env create -f environment_neutronics.yml
+          conda activate env_neutronics
+
+      - name: run script 2 of 3
+        run: |
+          2_run_openmc_dagmc_simulation.py
+
+      - name: run script 3 of 3
+        run: |
+          3_extract_results.py
diff --git a/.gitignore b/.gitignore
index b6e4761..e354119 100644
--- a/.gitignore
+++ b/.gitignore
@@ -127,3 +127,11 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# output files
+*.h5m
+*.html
+*.xml
+*.h5
+*.out
+*.xml
diff --git a/2_run_openmc_dagmc_simulation.py b/2_run_openmc_dagmc_simulation.py
index 580ce4d..ae22154 100644
--- a/2_run_openmc_dagmc_simulation.py
+++ b/2_run_openmc_dagmc_simulation.py
@@ -1,30 +1,31 @@
 import openmc
+import openmc_data_downloader as odd
+
 
 # Names of material tags can be found with the command line tool
 # mbsize -ll dagmc.h5m | grep 'NAME = mat:'
 
-
-mat_vacuum_vessel = openmc.Material(name="mat_vacuum_vessel")
+mat_vacuum_vessel = openmc.Material(name="vacuum_vessel")
 mat_vacuum_vessel.add_element("Fe", 1, "ao")
 mat_vacuum_vessel.set_density("g/cm3", 7.7)
 
-mat_upper_blanket = openmc.Material(name="mat_upper_blanket")
+mat_upper_blanket = openmc.Material(name="upper_blanket")
 mat_upper_blanket.add_element("Li", 1, "ao")
 mat_upper_blanket.set_density("g/cm3", 0.5)
 
-mat_lower_blanket = openmc.Material(name="mat_lower_blanket")
+mat_lower_blanket = openmc.Material(name="lower_blanket")
 mat_lower_blanket.add_element("Li", 1, "ao")
 mat_lower_blanket.set_density("g/cm3", 0.5)
 
-mat_lower_vacuum_vessel = openmc.Material(name="mat_lower_vacuum_vessel")
+mat_lower_vacuum_vessel = openmc.Material(name="lower_vacuum_vessel")
 mat_lower_vacuum_vessel.add_element("Fe", 1, "ao")
 mat_lower_vacuum_vessel.set_density("g/cm3", 7.7)
 
-mat_upper_vacuum_vessel = openmc.Material(name="mat_upper_vacuum_vessel")
+mat_upper_vacuum_vessel = openmc.Material(name="upper_vacuum_vessel")
 mat_upper_vacuum_vessel.add_element("Fe", 1, "ao")
 mat_upper_vacuum_vessel.set_density("g/cm3", 7.7)
 
-mat_blanket = openmc.Material(name="mat_blanket")
+mat_blanket = openmc.Material(name="blanket")
 mat_blanket.add_element("Li", 1, "ao")
 mat_blanket.set_density("g/cm3", 0.5)
 
@@ -39,6 +40,12 @@
     ]
 )
 
+#downloads the nuclear data and sets the openmc_cross_sections environmental variable
+odd.just_in_time_library_generator(
+    libraries='ENDFB-7.1-NNDC',
+    materials=materials
+)
+
 # makes use of the dagmc geometry
 dag_univ = openmc.DAGMCUniverse("dagmc.h5m")
 
diff --git a/README.md b/README.md
index ba7852c..75f3342 100644
--- a/README.md
+++ b/README.md
@@ -14,10 +14,8 @@ cd cad-to-dagmc-to-openmc-example
 
 Make an environment for the model preparation
 ```
-conda create --name paramak_env python=3.9
-conda activate paramak_env
-conda install -c fusion-energy -c cadquery -c conda-forge paramak
-pip install jupyter_cadquery
+conda env create -f environment_cad.yml
+conda activate env_cad
 ```
 
 Then run the script for making the DAGMC model.
@@ -44,10 +42,8 @@ paraview dagmc.vtk
 First make an environment for simulation.
 
 ```
-conda create --name openmc_dagmc_env python=3.9
-conda activate openmc_dagmc_env
-conda install -c conda-forge openmc
-pip install openmc_mesh_tally_to_vtk
+conda env create -f environment_neutronics.yml
+conda activate env_neutronics
 ```
 
 Then run the simulation which will produce a statepoint.10.h5 file that contains the simulation outputs
diff --git a/environment_cad.yml b/environment_cad.yml
new file mode 100644
index 0000000..25f1216
--- /dev/null
+++ b/environment_cad.yml
@@ -0,0 +1,13 @@
+
+
+name: env_cad
+channels:
+  - fusion-energy
+  - cadquery
+  - conda-forge
+dependencies:
+  - python=3.9
+  - paramak=0.7.2
+  - pip
+  - pip:
+    - jupyter-cadquery
diff --git a/environment_neutronics.yml b/environment_neutronics.yml
new file mode 100644
index 0000000..4c1cbd6
--- /dev/null
+++ b/environment_neutronics.yml
@@ -0,0 +1,11 @@
+
+
+name: env_neutronics
+channels:
+  - conda-forge
+dependencies:
+  - python=3.9
+  - openmc=0.13.0
+  - pip
+  - pip:
+    - openmc_data_downloader

From fc487c55f6c4a37545d8202a97756834914708b3 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Wed, 23 Mar 2022 22:44:58 +0000
Subject: [PATCH 02/13] fixed typos

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 75f3342..d0f4660 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,6 @@
-This example simulates a simplfied model of an inertial confinement fusion reactor.
+[![CI with install](https://github.com/shimwell/cad-to-dagmc-to-openmc-example/actions/workflows/ci_with_install.yml/badge.svg)](https://github.com/shimwell/cad-to-dagmc-to-openmc-example/actions/workflows/ci_with_install.yml)
+
+This example simulates a simplified model of an inertial confinement fusion reactor.
 
 - A CAD model is made and automatically converted to a DAGMC geometry that is then used in OpenMC for a neutronics simulation.
 - The neutronics simulation obtains the tritium breeding ratio and a 3D map of tritium production.

From d46a0e20c7248dc7166346b4d88af82a2ad2e877 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Wed, 23 Mar 2022 22:45:12 +0000
Subject: [PATCH 03/13] added missing package

---
 environment_neutronics.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment_neutronics.yml b/environment_neutronics.yml
index 4c1cbd6..c3562ca 100644
--- a/environment_neutronics.yml
+++ b/environment_neutronics.yml
@@ -9,3 +9,4 @@ dependencies:
   - pip
   - pip:
     - openmc_data_downloader
+    - openmc_mesh_tally_to_vtk

From 80a80c509f9275e812c39097e4f69752639f49c6 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Wed, 23 Mar 2022 22:47:00 +0000
Subject: [PATCH 04/13] reduced number of particles

---
 2_run_openmc_dagmc_simulation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/2_run_openmc_dagmc_simulation.py b/2_run_openmc_dagmc_simulation.py
index ae22154..6d2d6bf 100644
--- a/2_run_openmc_dagmc_simulation.py
+++ b/2_run_openmc_dagmc_simulation.py
@@ -69,7 +69,7 @@
 # specifies the simulation computational intensity
 settings = openmc.Settings()
 settings.batches = 10
-settings.particles = 100000
+settings.particles = 10000
 settings.inactive = 0
 settings.run_mode = "fixed source"
 settings.source = my_source

From e79c6a8acc4390f5ea6f875b886f70bbf495959e Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Wed, 23 Mar 2022 22:52:34 +0000
Subject: [PATCH 05/13] added conda init

---
 .github/workflows/ci_with_install.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 5b2b2a7..3b2cfb2 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -20,6 +20,10 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
       
+      - name: conda init
+        run: |
+          conda init bash
+
       - name: install dependencies package
         run: |
           apt update -y

From 57b3772fd169772e28895a41d306e132a81f8cf3 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 24 Mar 2022 09:38:04 +0000
Subject: [PATCH 06/13] init code with .sh script

---
 .github/workflows/ci_with_install.yml | 2 +-
 conda_init_for_ci.sh                  | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)
 create mode 100644 conda_init_for_ci.sh

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 3b2cfb2..01f79e1 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -22,7 +22,7 @@ jobs:
       
       - name: conda init
         run: |
-          conda init bash
+          bash -i conda_init_for_ci.sh
 
       - name: install dependencies package
         run: |
diff --git a/conda_init_for_ci.sh b/conda_init_for_ci.sh
new file mode 100644
index 0000000..0704985
--- /dev/null
+++ b/conda_init_for_ci.sh
@@ -0,0 +1 @@
+conda init
\ No newline at end of file

From 04291be0f68cb0b0121d8f1694c89da04a7fbb91 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 24 Mar 2022 10:09:13 +0000
Subject: [PATCH 07/13] added vtk

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index e354119..485366d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -135,3 +135,4 @@ dmypy.json
 *.h5
 *.out
 *.xml
+*.vtk

From f14a3a3dccd7618a32eabe3a66738eae8a61bb43 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 24 Mar 2022 10:09:26 +0000
Subject: [PATCH 08/13] added conda requirement

---
 README.md | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index d0f4660..e0ba418 100644
--- a/README.md
+++ b/README.md
@@ -6,13 +6,27 @@ This example simulates a simplified model of an inertial confinement fusion reac
 - The neutronics simulation obtains the tritium breeding ratio and a 3D map of tritium production.
 - The simulation outputs are post processed to display the results and produce a VTK file for visualization.
 
+# Prerequisites
+
+This minimal example makes use of Conda to manage and install the packages.
+
+You will need one of these conda distributions to be installed or work within a [Docker image](https://hub.docker.com/r/continuumio/miniconda3)
+
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+
+- [Anaconda](https://www.anaconda.com/)
+
+- [Miniforge](https://github.com/conda-forge/miniforge)
+
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+
 # First clone the repository
 ```bash
 git clone https://github.com/shimwell/cad-to-dagmc-to-openmc-example.git
 cd cad-to-dagmc-to-openmc-example
 ```
 
-# Making the DAGMC model.
+# Making the DAGMC model
 
 Make an environment for the model preparation
 ```
@@ -29,7 +43,6 @@ Then open the ```dagmc.html``` file in an internet browser to view the CAD creat
 
 ![CAD geometry image](https://user-images.githubusercontent.com/8583900/159698975-d82544c7-635b-4117-b4bc-4d61a8cf9ecc.png)
 
-
 Optionally you can inspect the DAGMC file at this stage by converting the h5m file to a vtk file and opening this with [Paraview](https://www.paraview.org/)
 ```
 mbconvert dagmc.h5m dagmc.vtk
@@ -37,9 +50,7 @@ paraview dagmc.vtk
 ```
 ![DAGMC model image](https://user-images.githubusercontent.com/8583900/159698979-3665e14b-ca42-4df2-8a1e-deee6597efc0.png)
 
-
-
-# Simulating the model in OpenMC.
+# Simulating the model in OpenMC
 
 First make an environment for simulation.
 
@@ -58,7 +69,7 @@ Then run the post processing script that should output the Tritium Breeding Rati
 python 3_extract_results.py
 ```
 
-Open up the VTK file with paraview
+Open up the VTK file with Paraview and slice the data to see the high tritium breeding region
 ```bash
 paraview tritium_production_map.vtk
 ```

From 7db66f0478c6d34c82f8aadad98417f75faa1d56 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 24 Mar 2022 10:09:46 +0000
Subject: [PATCH 09/13] moved init after env creation

---
 .github/workflows/ci_with_install.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 01f79e1..a27f874 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -20,9 +20,6 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
       
-      - name: conda init
-        run: |
-          bash -i conda_init_for_ci.sh
 
       - name: install dependencies package
         run: |
@@ -34,6 +31,10 @@ jobs:
           conda env create -f environment_cad.yml
           conda activate env_cad
 
+      - name: conda init
+        run: |
+          bash -i conda_init_for_ci.sh
+
       - name: run script 1 of 3
         run: |
           python 1_creation_of_dagmc_geometry.py

From 1ab92005ffc2218bc59fe462aaa70f7a403a1aa7 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 24 Mar 2022 10:29:25 +0000
Subject: [PATCH 10/13] removed activate part

---
 .github/workflows/ci_with_install.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index a27f874..d339524 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -29,7 +29,6 @@ jobs:
       - name: create environment 1
         run: |
           conda env create -f environment_cad.yml
-          conda activate env_cad
 
       - name: conda init
         run: |
@@ -42,7 +41,6 @@ jobs:
       - name: create environment 1
         run: |
           conda env create -f environment_neutronics.yml
-          conda activate env_neutronics
 
       - name: run script 2 of 3
         run: |

From 032b1b509c2f0b32e2717789c6b7b4ba0e5b22a0 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 24 Mar 2022 10:30:15 +0000
Subject: [PATCH 11/13] added source bashrc

---
 .github/workflows/ci_with_install.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index d339524..bcfacb2 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -29,6 +29,9 @@ jobs:
       - name: create environment 1
         run: |
           conda env create -f environment_cad.yml
+          conda init bash
+          source ~/.bashrc    
+          conda activate env_cad
 
       - name: conda init
         run: |
@@ -41,6 +44,9 @@ jobs:
       - name: create environment 1
         run: |
           conda env create -f environment_neutronics.yml
+          conda init bash
+          source ~/.bashrc   
+          conda activate env_neutronics
 
       - name: run script 2 of 3
         run: |

From 5338c314662f0a3a446d1d277dfdddd39afb196e Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 24 Mar 2022 12:04:12 +0000
Subject: [PATCH 12/13] trying .source instead of source

---
 .github/workflows/ci_with_install.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index bcfacb2..baeacd6 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -19,7 +19,6 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
-      
 
       - name: install dependencies package
         run: |
@@ -30,7 +29,7 @@ jobs:
         run: |
           conda env create -f environment_cad.yml
           conda init bash
-          source ~/.bashrc    
+          .source ~/.bashrc    
           conda activate env_cad
 
       - name: conda init
@@ -45,7 +44,7 @@ jobs:
         run: |
           conda env create -f environment_neutronics.yml
           conda init bash
-          source ~/.bashrc   
+          .source ~/.bashrc   
           conda activate env_neutronics
 
       - name: run script 2 of 3

From facadd2a071fb08f81deb41f15cd284f5e851447 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 24 Mar 2022 12:28:38 +0000
Subject: [PATCH 13/13] [skip ci] removed ci badge while conda activate is
 fixed

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e0ba418..a7504be 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-[![CI with install](https://github.com/shimwell/cad-to-dagmc-to-openmc-example/actions/workflows/ci_with_install.yml/badge.svg)](https://github.com/shimwell/cad-to-dagmc-to-openmc-example/actions/workflows/ci_with_install.yml)
+<!-- [![CI with install](https://github.com/shimwell/cad-to-dagmc-to-openmc-example/actions/workflows/ci_with_install.yml/badge.svg)](https://github.com/shimwell/cad-to-dagmc-to-openmc-example/actions/workflows/ci_with_install.yml) -->
 
 This example simulates a simplified model of an inertial confinement fusion reactor.