ug bell

docs/assets/data/breadcrumbs.json

@@ -165,59 +165,104 @@
     "Gautschi User Guide",
     "Frequently Asked Questions"
   ],
+  "/userguides/bell/": [
+    "Home",
+    "Bell User Guide"
+  ],
+  "/userguides/bell/overview/": [
+    "Home",
+    "Bell User Guide",
+    "Overview of Bell"
+  ],
+  "/userguides/bell/biography/": [
+    "Home",
+    "Bell User Guide",
+    "Biography of Bell"
+  ],
+  "/userguides/bell/accounts/": [
+    "Home",
+    "Bell User Guide",
+    "Accounts"
+  ],
+  "/userguides/bell/software/": [
+    "Home",
+    "Bell User Guide",
+    "Software"
+  ],
+  "/userguides/bell/run/": [
+    "Home",
+    "Bell User Guide",
+    "Running Jobs"
+  ],
+  "/userguides/bell/storage/": [
+    "Home",
+    "Bell User Guide",
+    "File Storage and Transfer"
+  ],
+  "/userguides/bell/gateway/": [
+    "Home",
+    "Bell User Guide",
+    "Gateway (Open OnDemand)"
+  ],
+  "/userguides/bell/compile/": [
+    "Home",
+    "Bell User Guide",
+    "Compiling Source Code"
+  ],
+  "/userguides/bell/faqs/": [
+    "Home",
+    "Bell User Guide",
+    "Frequently Asked Questions"
+  ],
   "/userguides/gilbreth/": [
     "Home",
-    "Gilbreth"
+    "Gilbreth User Guide"
   ],
   "/userguides/gilbreth/overview/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "Gilbreth Overview"
   ],
   "/userguides/gilbreth/biography/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "Biography of Gilbreth"
   ],
   "/userguides/gilbreth/accounts/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "Accounts"
   ],
   "/userguides/gilbreth/software/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "Software"
   ],
   "/userguides/gilbreth/run_jobs/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "Running Jobs"
   ],
   "/userguides/gilbreth/storage/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "File Storage and Transfer"
   ],
   "/userguides/gilbreth/gateway/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "Gateway (Open OnDemand)"
   ],
   "/userguides/gilbreth/compile/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "Compiling Source Code"
   ],
   "/userguides/gilbreth/faqs/": [
     "Home",
-    "Gilbreth",
+    "Gilbreth User Guide",
     "Frequently Asked Questions"
   ],
-  "/https://www.rcac.purdue.edu/knowledge/bell": [
-    "Home",
-    "Bell"
-  ],
   "/https://www.rcac.purdue.edu/knowledge/negishi": [
     "Home",
     "Negishi"

docs/index.md

@@ -115,7 +115,7 @@ Follow these steps to get up and running on RCAC clusters.
 
     **128 cores/node | 256 GB RAM | 100 Gbps HDR Infiniband**
 
-    [:octicons-arrow-right-24: Bell User Guide](https://www.rcac.purdue.edu/knowledge/bell)
+    [:octicons-arrow-right-24: Bell User Guide](userguides/bell/index.md)
 
 -   :material-server:{ .lg .middle } __Negishi__
 

docs/snippets/examples/apps/ansysfluent.md

@@ -0,0 +1,43 @@
+# Ansys Fluent
+
+[Ansys](https://www.ansys.com) is a CAE/multiphysics engineering simulation software that utilizes finite element analysis for numerically solving a wide variety of mechanical problems. The software contains a list of packages and can simulate many structural properties such as strength, toughness, elasticity, thermal expansion, fluid dynamics as well as acoustic and electromagnetic attributes.
+
+## Ansys Licensing
+
+The Ansys licensing on our community clusters is maintained by Purdue ECN group. There are two types of licenses: teaching and research. For more information, please refer to [ECN Ansys licensing page](https://engineering.purdue.edu/ECN/Support/KB/Docs/ANSYSFLUENTLicensing). If you are interested in purchasing your own research license, please send email to **software@ecn.purdue.edu**.
+
+## Ansys Workflow
+
+Ansys software consists of several sub-packages such as Workbench and Fluent. Most simulations are performed using the Ansys Workbench console, a GUI interface to manage and edit the simulation workflow. It requires X11 forwarding for remote display so a SSH client software with X11 support or a remote desktop portal is required. Please see [Logging In](../../../accounts.md#logging-in-to-bell) section for more details. To ensure preferred performance, [ThinLinc](../../../accounts.md#thinlinc) remote desktop connection is highly recommended.
+
+Typically users break down larger structures into small components in geometry with each of them modeled and tested individually. A user may start by defining the dimensions of an object, adding weight, pressure, temperature, and other physical properties.
+
+Ansys Fluent is a computational fluid dynamics (CFD) simulation software known for its advanced physics modeling capabilities and accuracy. Fluent offers unparalleled analysis capabilities and provides all the tools needed to design and optimize new equipment and to troubleshoot existing installations.
+
+In the following sections, we provide step-by-step instructions to lead you through the process of using Fluent. We will create a classical elbow pipe model and simulate the fluid dynamics when water flows through the pipe. The project files have been generated and can be downloaded via [fluent\_tutorial.zip](https://www.rcac.purdue.edu/knowledge/run/examples/apps/ansys/fluent_tutorial.zip).
+
+## Loading Ansys Module
+
+Different versions of Ansys are installed on the clusters and can be listed with `module spider` or `module avail` command in the terminal.
+
+```
+$ module avail ansys/
+---------------------- Core Applications -----------------------------
+   ansys/2019R3    ansys/2020R1    ansys/2021R2    ansys/2022R1 (D)
+```
+
+Before launching Ansys Workbench, a specific version of Ansys module needs to be loaded. For example, you can `module load ansys/2021R2` to use the latest Ansys 2021R2. If no version is specified, the default module -> (D) (`ansys/2022R1` in this case) will be loaded. You can also check the loaded modules with `module list` command.
+
+## Launching Ansys Workbench
+
+Open a terminal on Bell, enter `rcac-runwb2` to launch Ansys Workbench.
+
+!!! Note
+      You can also use `runwb2` to launch Ansys Workbench. The main difference between `runwb2`and `rcac-runwb2` is that the latter sets the project folder to be in your scratch space. Ansys has an known bug that it might crash when the project folder is set to `$HOME` on our systems.
+
+## In This Section
+
+- [Case Calculating with Fluent](ansysfluent/case_calculating_with_fluent.md)
+- [Fluent Text User Interface and Journal File](ansysfluent/fluent_text_user_interface_and_journal_file.md)
+- [Preparing Case Files for Fluent](ansysfluent/preparing_case_files_for_fluent.md)
+- [Submitting Fluent jobs to SLURM](ansysfluent/submit_fluent_jobs_to_slurm.md)

docs/snippets/examples/apps/ansysfluent/case_calculating_with_fluent.md

@@ -0,0 +1,57 @@
+# Case Calculating with Fluent
+
+## Calculation with Fluent
+
+Now all the files are ready for the Fluent calculations. Both “Geometry” and “Mesh” cells should have green checks. We can set up the CFD simulation parameters in the Ansys Fluent by double-clicking the “Setup” cell.
+
+Ansys Fluent Launcher can be started by selecting “editing” on the “Setup” cell with many startup options (e.g. Precision, Parallel, Display). Note that “Dimension” is fixed to “3D” because we are using a 3D model in this project.
+
+<p style="text-align: center;">
+  <img src="/assets/images/userguides/bell/run-examples-apps-ansys-4-Ansys-Fluent-Launcher-options.png" alt="Ansys Fluent Launcher options" width="60%">
+</p>
+
+<p style="text-align: center;">Ansys Fluent Launcher options.</p>
+
+After the Fluent is opened, an Ansys Fluent settings file `FFF.set` is written under the folder `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/FFF/Fluent/`.
+
+Then we are going to set up all the necessary parameters for Fluent computation. Here are the key steps for the setup:
+
+1. Setting up the domain:
+      * Change the units for length to be consistent with the Mesh;
+      * Check the mesh statistics and quality;
+2. Setting up physics:
+      * Solver: “Energy”, “Viscous Model”, “Near-Wall Treatment”;
+      * Materials;
+      * Zones;
+      * Boundaries: Inlet, Outlet, Internal, Symmetry, Wall;
+3. Solving:
+      * Solution Methods;
+      * Reports;
+      * Initialization;
+      * Iterations and output frequency.
+
+Then the calculation will be carried out and the results will be written out into `FFF-1.cas.gz` under folder `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/FFF/Fluent/`.
+
+This file contains all the settings and simulation results which can be loaded for post analysis and re-computation (more details will be introduced in the following sections). If only configurations and settings within the Fluent are needed, we can open independent Fluent or submit Fluent jobs with bash commands by loading the existing case in order to facilitate the computation process.
+
+Parameters used in demo case (use default if not assigned):
+
+1. Domain Setup: Length Units=”mm”;
+2. Solver: Energy=”on”; Viscous Model=”k-epsilon”; Near-Wall Treatment=”Enhanced Wall Treatment”;
+3. Materials: water (Density=1000[kg/m^3]; Specific Heat=4216[J/kg-k]; Thermal Conductivity=0.677[w/m-k]; Viscosity=8e-4[kg/m-s]);
+4. Zones=”fluid (water)”;
+5. Inlet=”velocity-inlet-large” (Velocity Magnitude=0.4m/s, Specification Method=”Intensity and Hydraulic Diameter”, Turbulent Intensity=5%; Hydraulic Diameter=100mm; Thermal Temperature=293.15k) &”velocity-inlet-small” (Velocity Magnitude=1.2m/s, Specification Method=”Intensity and Hydraulic Diameter”, Turbulent Intensity=5%; Hydraulic Diameter=25mm; Thermal Temperature=313.15k); Internal=”interior-fluid”; Symmetry=”symmetry”; Wall=”wall-fluid”;
+6. Solution Methods: Gradient=”Green-Gauss Node Based”;
+7. Report: plot residual and “Facet Maximum” for “pressure-outlet”
+8. Hybrid Initialization;
+9. 300 iterations.
+
+## Results analysis
+
+The best methods to view and analyze the simulation should be the Ansys Fluent (directly after computation) or the Ansys CFD-Post (entering “Results” in Ansys Workbench). Both methods are straightforward so we will not cover this part in this tutorial. Here is a final simulation result showing the temperature of the symmetry after 300 iterations for reference:
+
+<p style="text-align: center;">
+  <img src="/assets/images/userguides/bell/run-examples-apps-ansys-5-Simulated-temperature-profile-of-the-symmetry.png" alt="Simulated temperature" width="80%">
+</p>
+
+<p style="text-align: center;">Simulated temperature profile of the symmetry.</p>

docs/snippets/examples/apps/ansysfluent/fluent_text_user_interface_and_journal_file.md

@@ -0,0 +1,100 @@
+# Fluent Text User Interface and Journal File
+
+## Fluent Text User Interface (TUI)
+
+If you pay attention to the “Console” window in the Fluent window when setting up and carrying out the calculation, corresponding commands can be found and executed one after another. Almost all the setting processes can be accomplished by the command lines, which is called Fluent Text User Interface (TUI). Here are the main commands in Fluent TUI:
+
+```
+
+
+  adjoint/                parallel/               solve/
+  define/                 plot/                   surface/
+  display/                preferences/            turbo-workflow/
+  exit                    print-license-usage     views/
+  file/                   report/
+  mesh/                   server/
+
+```
+
+For example, instead of opening a case by clicking buttons in Ansys Fluent, we can type `/file read-case case_file_name.cas.gz` to open the saved case.
+
+## Fluent Journal Files
+
+A Fluent journal file is a series of TUI commands stored in a text file. The file can be written in a text editor or generated by Fluent as a transcript of the commands given to Fluent during your session.
+
+A journal file generated by Fluent will include any GUI operations (in a TUI form, though). This is quite useful if you have a series of tasks that you need to execute, as it provides a shortcut. To record a journal file, start recording with File -> Write -> Start Journal..., perform whatever tasks you need, and then stop recording with File -> Write -> Stop Journal...
+
+You can also write your own journal file into a text file. The basic rule for a Fluent journal file is to reproduce the TUI commands that controlled the configuration and calculation of Fluent in their order. You can add a comment in a line starting with a `;` (semicolon).
+
+Here are some reasons why you should use a Fluent journal file:
+
+1. Using journal files with bash scripting can allow you to automate your jobs.
+2. Using journal files can allow you to parameterize your models easily and automatically.
+3. Using a journal file can set parameters you do not have in your case file e.g. autosaving.
+4. Using a journal file can allow you to safely save, stop and restart your jobs easily.
+
+!!! Note
+    The order of your journal file commands is **highly important**. The correct sequences must be followed and some stages have multiple options e.g. different initialization methods.
+
+Here is a sample Fluent journal file for the demo case:
+
+```
+
+
+  ;testJournal.jou
+  ;Set the TUI version for Fluent
+  /file/set-tui-version "22.1"
+  ;Read the case. The default folder
+  /file read-case /home/jin456/Fluent_files/tutorial_case1/elbow_files/dp0/FFF/Fluent/FFF-1.cas.gz
+  ;Initialize the case with Hybrid Initialization
+  /solve/initialize/hyb-initialization
+  ;Set Number of Iterations to 1000, Reporting Interval to 10 iterations and Profile Update Interval to 1 iteration
+  /solve/iterate 1000 10 1
+  ;Outputting solver performance data upon completion of the simulation
+  /parallel timer usage
+  ;Write out the simulation results.
+  /file write-case-data /home/jin456/Fluent_files/tutorial_case1/elbow_files/dp0/FFF/Fluent/result.cas.h5
+  ;After computation, exit Flent
+  /exit
+
+```
+
+Before running this Fluent journal file, you need to make sure: 1) the ansys module has been loaded (it’s highly recommended to load the same version of Ansys when you built the case project); 2) the project case file (`***.cas.gz`) has been created.
+
+Then we can use Fluent to run this journal file by simply using:`fluent 3ddp -t$NTASKS -g -i testJournal.jou` in the terminal. Here, `3d` indicates this is a 3d model, `dp` indicates double precision, `-t$NTASKS` tells Fluent how many Solver Processes it will take (e.g. `-t4`), `-g` means to run without the GUI or graphics, `-i` testJournal.jou tells Fluent to read the specific journal file.
+
+Here is a table for the available command line Options for Linux/UNIX and Windows Platforms in Ansys Fluent.
+
+Options for Fluent TUI
+
+| Option | Platform | Description |
+| --- | --- | --- |
+| `-cc` | all | Use the classic color scheme |
+| `-ccp x` | Windows only | Use the Microsoft Job Scheduler where x is the head node name. |
+| `-cnf=x` | all | Specify the hosts or machine list file |
+| `-driver` | all | Sets the graphics driver (available drivers vary by platform - opengl or x11 or null(Linux/UNIX) - opengl or msw or null (Windows)) |
+| `-env` | all | Show environment variables |
+| `-fgw` | all | Disables the embedded graphics |
+| `-g` | all | Run without the GUI or graphics (Linux/UNIX); Run with the GUI minimized (Windows) |
+| `-gr` | all | Run without graphics |
+| `-gu` | all | Run without the GUI but with graphics (Linux/UNIX); Run with the GUI minimized but with graphics (Windows) |
+| `-help` | all | Display command line options |
+| `-hidden` | Windows only | Run in batch mode |
+| `-host_ip=host:ip` | all | Specify the IP interface to be used by the host process |
+| `-i journal` | all | Reads the specified journal file |
+| `-lsf` | Linux/UNIX only | Run FLUENT using LSF |
+| `-mpi=` | all | Specify MPI implementation |
+| `-mpitest` | all | Will launch an MPI program to collect network performance data |
+| `-nm` | all | Do not display mesh after reading |
+| `-pcheck` | Linux/UNIX only | Checks all nodes |
+| `-post` | all | Run the FLUENT post-processing-only executable |
+| `-p` | all | Choose the interconnect  = default or myr or inf |
+| `-r` | all | List all releases installed |
+| `-rx` | all | Specify release number |
+| `-sge` | Linux/UNIX only | Run FLUENT under Sun Grid Engine |
+| `-sge queue` | Linux/UNIX only | Name of the queue for a given computing grid |
+| `-sgeckpt ckpt_obj` | Linux/UNIX only | Set checkpointing object to ckpt\_objfor SGE |
+| `-sgepe fluent_pe min_n-max_n` | Linux/UNIX only | Set the parallel environment for SGE to fluent\_pe, min\_nand max\_n are number of min and max nodes requested |
+| `-tx` | all | Specify the number of processors x |
+
+For more information for Fluent text user interface and journal files, please refer to [Fluent FAQ]( https://www.cfd-online.com/Wiki/Fluent_FAQ).