Merge pull request #222 from PhasicFlow/main

from main

.github/scripts/sync-wiki.py

@@ -0,0 +1,153 @@
+#!/usr/bin/env python3
+
+import os
+import re
+import yaml
+import sys
+
+# Constants
+REPO_URL = "https://github.com/PhasicFlow/phasicFlow"
+REPO_PATH = os.path.join(os.environ.get("GITHUB_WORKSPACE", ""), "repo")
+WIKI_PATH = os.path.join(os.environ.get("GITHUB_WORKSPACE", ""), "wiki")
+MAPPING_FILE = os.path.join(REPO_PATH, ".github/workflows/markdownList.yml")
+
+def load_mapping():
+    """Load the markdown to wiki page mapping file."""
+    try:
+        with open(MAPPING_FILE, 'r') as f:
+            data = yaml.safe_load(f)
+            return data.get('mappings', [])
+    except Exception as e:
+        print(f"Error loading mapping file: {e}")
+        return []
+
+def convert_relative_links(content, source_path):
+    """Convert relative links in markdown content to absolute URLs."""
+    # Find markdown links with regex pattern [text](url)
+    md_pattern = r'\[([^\]]+)\]\(([^)]+)\)'
+    
+    # Find HTML img tags
+    img_pattern = r'<img\s+src=[\'"]([^\'"]+)[\'"]'
+    
+    def replace_link(match):
+        link_text = match.group(1)
+        link_url = match.group(2)
+        
+        # Skip if already absolute URL or anchor
+        if link_url.startswith(('http://', 'https://', '#', 'mailto:')):
+            return match.group(0)
+        
+        # Get the directory of the source file
+        source_dir = os.path.dirname(source_path)
+        
+        # Create absolute path from repository root
+        if link_url.startswith('/'):
+            # If link starts with /, it's already relative to repo root
+            abs_path = link_url
+        else:
+            # Otherwise, it's relative to the file location
+            abs_path = os.path.normpath(os.path.join(source_dir, link_url))
+            if not abs_path.startswith('/'):
+                abs_path = '/' + abs_path
+        
+        # Convert to GitHub URL
+        github_url = f"{REPO_URL}/blob/main{abs_path}"
+        return f"[{link_text}]({github_url})"
+    
+    def replace_img_src(match):
+        img_src = match.group(1)
+        
+        # Skip if already absolute URL
+        if img_src.startswith(('http://', 'https://')):
+            return match.group(0)
+        
+        # Get the directory of the source file
+        source_dir = os.path.dirname(source_path)
+        
+        # Create absolute path from repository root
+        if img_src.startswith('/'):
+            # If link starts with /, it's already relative to repo root
+            abs_path = img_src
+        else:
+            # Otherwise, it's relative to the file location
+            abs_path = os.path.normpath(os.path.join(source_dir, img_src))
+            if not abs_path.startswith('/'):
+                abs_path = '/' + abs_path
+        
+        # Convert to GitHub URL (use raw URL for images)
+        github_url = f"{REPO_URL}/raw/main{abs_path}"
+        return f'<img src="{github_url}"'
+    
+    # Replace all markdown links
+    content = re.sub(md_pattern, replace_link, content)
+    
+    # Replace all img src tags
+    content = re.sub(img_pattern, replace_img_src, content)
+    
+    return content
+
+def process_file(source_file, target_wiki_page):
+    """Process a markdown file and copy its contents to a wiki page."""
+    source_path = os.path.join(REPO_PATH, source_file)
+    target_path = os.path.join(WIKI_PATH, f"{target_wiki_page}.md")
+    
+    print(f"Processing {source_path} -> {target_path}")
+    
+    try:
+        # Check if source exists
+        if not os.path.exists(source_path):
+            print(f"Source file not found: {source_path}")
+            return False
+        
+        # Read source content
+        with open(source_path, 'r') as f:
+            content = f.read()
+        
+        # Convert relative links
+        content = convert_relative_links(content, source_file)
+        
+        # Write to wiki page
+        with open(target_path, 'w') as f:
+            f.write(content)
+        
+        return True
+    
+    except Exception as e:
+        print(f"Error processing {source_file}: {e}")
+        return False
+
+def main():
+    # Check if wiki directory exists
+    if not os.path.exists(WIKI_PATH):
+        print(f"Wiki path not found: {WIKI_PATH}")
+        sys.exit(1)
+    
+    # Load mapping
+    mappings = load_mapping()
+    if not mappings:
+        print("No mappings found in the mapping file")
+        sys.exit(1)
+    
+    print(f"Found {len(mappings)} mappings to process")
+    
+    # Process each mapping
+    success_count = 0
+    for mapping in mappings:
+        source = mapping.get('source')
+        target = mapping.get('target')
+        
+        if not source or not target:
+            print(f"Invalid mapping: {mapping}")
+            continue
+        
+        if process_file(source, target):
+            success_count += 1
+    
+    print(f"Successfully processed {success_count} of {len(mappings)} files")
+    
+    # Exit with error if any file failed
+    if success_count < len(mappings):
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()

.github/workflows/markdownList.yml

@@ -0,0 +1,18 @@
+# This file maps source markdown files to their target wiki pages
+# format:
+# - source: path/to/markdown/file.md
+#   target: Wiki-Page-Name
+mappings:
+  - source: benchmarks/readme.md
+    target: Performance-of-phasicFlow
+  - source: benchmarks/helicalMixer/readme.md
+    target: Helical-Mixer-Benchmark
+  - source: benchmarks/rotatingDrum/readme.md
+    target: Rotating-Drum-Benchmark
+  - source: doc/mdDocs/howToBuild-V1.0.md
+    target: How-to-build-PhasicFlow‐v‐1.0
+  - source: tutorials/README.md
+    target: Tutorials
+  - source: doc/mdDocs/phasicFlowFeatures.md
+    target: Features-of-PhasicFlow
+  # Add more mappings as needed

.github/workflows/sync-wiki.yml

@@ -0,0 +1,60 @@
+name: Sync-Wiki
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "**/*.md"
+      - ".github/workflows/sync-wiki.yml"
+      - ".github/workflows/markdownList.yml"
+      - ".github/scripts/sync-wiki.py"
+  workflow_dispatch:
+
+jobs:
+  sync-wiki:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          path: repo
+      - name: Checkout Wiki
+        uses: actions/checkout@v3
+        with:
+          repository: ${{ github.repository }}.wiki
+          path: wiki
+        continue-on-error: true
+      - name: Create Wiki Directory if Not Exists
+        run: |
+          if [ ! -d "wiki" ]; then
+            mkdir -p wiki
+            cd wiki
+            git init
+            git config user.name "${{ github.actor }}"
+            git config user.email "${{ github.actor }}@users.noreply.github.com"
+            git remote add origin "https://github.com/${{ github.repository }}.wiki.git"
+          fi
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Install dependencies
+        run: pip install pyyaml
+      - name: Sync markdown files to Wiki
+        run: |
+          python $GITHUB_WORKSPACE/repo/.github/scripts/sync-wiki.py
+        env:
+          GITHUB_REPOSITORY: ${{ github.repository }}
+      - name: Push changes to wiki
+        run: |
+          cd wiki
+          git config user.name "${{ github.actor }}"
+          git config user.email "${{ github.actor }}@users.noreply.github.com"
+          git add .
+          if git status --porcelain | grep .; then
+            git commit -m "Auto sync wiki from main repository"
+            git push --set-upstream https://${{ github.actor }}:${{ github.token }}@github.com/${{ github.repository }}.wiki.git master -f
+          else
+            echo "No changes to commit"
+          fi

benchmarks/helicalMixer/readme.md

@@ -0,0 +1 @@
+# Helical Mixer Benchmark (phasicFlow v-1.0)

benchmarks/readme.md

@@ -0,0 +1,7 @@
+
+# Benchmarks
+
+Benchmakrs has been done on two different simulations: a simulation with simple geometry (rotating drum) and a simulation with complex geometry (helical mixer).
+
+- [rotating drum](./rotatingDrum/readme.md)
+- [helical mixer](./helicalMixer/readme.md)

benchmarks/rotatingDrum/readme.md

@@ -0,0 +1,96 @@
+# Rotating Drum Benchmark (phasicFlow v-1.0)
+
+## Overview
+
+This benchmark compares the performance of phasicFlow with a well-stablished commercial DEM software for simulating a rotating drum with varying particle counts (250k to 8M particles). The benchmark measures both computational efficiency and memory usage across different hardware configurations.
+
+## Simulation Setup
+
+<div align="center">
+    <img src="./images/commericalDEMsnapshot.png"/>
+    <div align="center">  
+        <p>Figure 1. Commercial DEM simulation snapshot</p>
+    </div>
+</div>
+
+<div align="center">
+    <img src="./images/phasicFlow_snapshot.png"/>
+    <div align="center">  
+        <p>Figure 2. phasicFlow simulation snapshot and visualized using Paraview</p>
+    </div>
+</div>
+
+### Hardware Specifications
+
+<div align="center">
+    Table 1. Hardware specifications used for benchmarking.
+</div>
+
+|  System     |           CPU            |             GPU              | Operating System |
+| :---------: | :----------------------: | :--------------------------: | :--------------: |
+|   Laptop    | Intel i9-13900HX 2.2 GHz | NVIDIA GeForce RTX 4050Ti 6G | Windows 11 24H2  |
+| Workstation | Intel Xeon 4210 2.2 GHz  |     NVIDIA RTX A4000 16G     |   Ubuntu 22.04   |
+
+### Simulation Parameters
+
+<div align="center">
+    Table 2. Parameters for rotating drum simulations.
+</div>
+
+| Case     | Particle Diameter | Particle Count | Drum Length | Drum Radius |
+| :-------: | :---------------: | :--------------: | :------------------: | :------------------: |
+| 250k     | 6 mm              | 250,000        | 0.8 m       | 0.2 m       |
+| 500k     | 5 mm              | 500,000        | 0.8 m       | 0.2 m       |
+| 1M       | 4 mm              | 1,000,000      | 0.8 m       | 0.2 m       |
+| 2M       | 3 mm              | 2,000,000      | 1.2 m       | 0.2 m       |
+| 4M       | 3 mm              | 4,000,000      | 1.6 m       | 0.2 m       |
+| 8M       | 2 mm              | 8,000,000      | 1.6 m       | 0.2 m       |
+
+The time step for all simulations was set to 1.0e-5 seconds and the simulation ran for 4 seconds.
+
+## Performance Comparison
+
+### Execution Time
+
+<div align="center">
+    Table 3. Total calculation time (minutes) for different configurations.
+</div>
+
+|     Software      | 250k   | 500k   | 1M     | 2M     | 4M     | 8M      |
+| :---------------: | :----: | :-----: | :-----: | :-----: | :-----: | :------: |
+| phasicFlow-4050Ti | 54 min | 111 min | 216 min | 432 min | -       | -        |
+| Commercial DEM-4050Ti | 68 min | 136 min | 275 min | 570 min | -       | -        |
+| phasicFlow-A4000  | 38 min | 73 min  | 146 min | 293 min | 589 min | 1188 min |
+
+The execution time scales linearly with particle count. phasicFlow demonstrates approximately:
+
+- 20% faster calculation than the well-established commercial DEM software on the same hardware
+- 30% performance improvement when using the NVIDIA RTX A4000 compared to the RTX 4050Ti
+
+<div align="center">
+    <img src="./images/performance1.png"/>
+    <p>Figure 3. Calculation time comparison between phasicFlow and the well-established commercial DEM software.</p>
+</div>
+
+### Memory Usage
+
+<div align="center">
+    Table 4. Memory consumption for different configurations.
+</div>
+
+|     Software      | 250k   | 500k   | 1M      | 2M      | 4M      | 8M      |
+| :---------------: | :-----: | :-----: | :-----: | :-----: | :-----: | :-----: |
+| phasicFlow-4050Ti | 252 MB  | 412 MB  | 710 MB  | 1292 MB | -       | -       |
+| Commercial DEM-4050Ti | 485 MB | 897 MB | 1525 MB | 2724 MB | -       | -       |
+| phasicFlow-A4000  | 344 MB  | 480 MB  | 802 MB  | 1386 MB | 2590 MB | 4966 MB |
+
+Memory efficiency comparison:
+
+- phasicFlow uses approximately 0.7 GB of memory per million particles
+- Commercial DEM software uses approximately 1.2 GB of memory per million particles
+- phasicFlow shows ~42% lower memory consumption compared to the commercial alternative
+- The memory usage scales linearly with particle count in both software packages. But due to memory limitations on GPUs, it is possible to run larger simulation on GPUs with phasicFlow.
+
+## Run Your Own Benchmarks
+
+The simulation case setup files are available in this folder for users interested in performing similar benchmarks on their own hardware. These files can be used to reproduce the tests and compare performance across different systems.

benchmarks/rotatingDrum/rotatingDrum_1mParticles/settings/geometryDict

@@ -35,7 +35,7 @@ surfaces
         
         radius2     0.2;                   // radius at p2
         
-        resolution  24;                    // number of divisions
+        resolution  60;                    // number of divisions
         
         material    wallMat;               // material name of this wall
         

benchmarks/rotatingDrum/rotatingDrum_1mParticles/settings/particlesDict

@@ -27,7 +27,7 @@ positionParticles
 
     orderedInfo
     {
-        diameter   0.004;           // minimum space between centers of particles
+        distance   0.004;           // minimum space between centers of particles
         
         numPoints  1000000;          // number of particles in the simulation 
         

benchmarks/rotatingDrum/rotatingDrum_250kParticles/settings/geometryDict

@@ -35,7 +35,7 @@ surfaces
         
         radius2     0.2;                   // radius at p2
         
-        resolution  24;                    // number of divisions
+        resolution  60;                    // number of divisions
         
         material    wallMat;               // material name of this wall
         

benchmarks/rotatingDrum/rotatingDrum_250kParticles/settings/particlesDict

@@ -27,7 +27,7 @@ positionParticles
 
     orderedInfo
     {
-        diameter   0.006;           // minimum space between centers of particles
+        distance   0.006;           // minimum space between centers of particles
         
         numPoints  250000;          // number of particles in the simulation 
         

benchmarks/rotatingDrum/rotatingDrum_2mParticles/settings/geometryDict

@@ -35,7 +35,7 @@ surfaces
         
         radius2     0.2;                   // radius at p2
         
-        resolution  24;                    // number of divisions
+        resolution  60;                    // number of divisions
         
         material    wallMat;               // material name of this wall
         

benchmarks/rotatingDrum/rotatingDrum_2mParticles/settings/particlesDict

@@ -27,7 +27,7 @@ positionParticles
 
     orderedInfo
     {
-        diameter   0.003;           // minimum space between centers of particles
+        distance   0.003;           // minimum space between centers of particles
         
         numPoints  2000000;          // number of particles in the simulation 
         

benchmarks/rotatingDrum/rotatingDrum_4mParticles/settings/geometryDict

@@ -35,7 +35,7 @@ surfaces
         
         radius2     0.2;                   // radius at p2
         
-        resolution  24;                    // number of divisions
+        resolution  60;                    // number of divisions
         
         material    wallMat;               // material name of this wall
         

benchmarks/rotatingDrum/rotatingDrum_4mParticles/settings/particlesDict

@@ -27,7 +27,7 @@ positionParticles
 
     orderedInfo
     {
-        diameter   0.003;           // minimum space between centers of particles
+        distance   0.003;           // minimum space between centers of particles
         
         numPoints  4000000;          // number of particles in the simulation 
         

benchmarks/rotatingDrum/rotatingDrum_500kParticles/settings/geometryDict

@@ -35,7 +35,7 @@ surfaces
         
         radius2     0.2;                   // radius at p2
         
-        resolution  24;                    // number of divisions
+        resolution  60;                    // number of divisions
         
         material    wallMat;               // material name of this wall
         

benchmarks/rotatingDrum/rotatingDrum_500kParticles/settings/particlesDict

@@ -27,7 +27,7 @@ positionParticles
 
     orderedInfo
     {
-        diameter   0.005;           // minimum space between centers of particles
+        distance   0.005;           // minimum space between centers of particles
         
         numPoints  500000;          // number of particles in the simulation 
         

benchmarks/rotatingDrum/rotatingDrum_8mParticles/settings/geometryDict

@@ -35,7 +35,7 @@ surfaces
         
         radius2     0.2;                   // radius at p2
         
-        resolution  24;                    // number of divisions
+        resolution  60;                    // number of divisions
         
         material    wallMat;               // material name of this wall
         

benchmarks/rotatingDrum/rotatingDrum_8mParticles/settings/particlesDict

@@ -27,7 +27,7 @@ positionParticles
 
     orderedInfo
     {
-        diameter   0.003;           // minimum space between centers of particles
+        distance   0.003;           // minimum space between centers of particles
         
         numPoints  6000000;          // number of particles in the simulation 
         

doc/mdDocs/howToBuild-V1.0.md

@@ -0,0 +1,136 @@
+# How to build PhasicFlow-v-1.0
+
+You can build PhasicFlow for CPU or GPU. You can have a single build or oven multiple builds on a machine. Here you learn how to have a single build of PhasicFlow, in various modes of execution. You can install PhasicFlow-v-1.0 on **Ubuntu-22.04 LTS** and **Ubuntu-24.04 LTS**. Installing it on older versions of Ubuntu needs some additional steps to meet the requirements which are not covered here. 
+
+If you want to install PhasicFlow on **Windows OS**, just see [this page](https://www.cemf.ir/installing-phasicflow-v-1-0-on-ubuntu/) for more information. 
+
+# Required packages
+
+You need a list of packages installed on your computer before building PhasicFlow:
+
+* git, for cloning the code and package management
+* g++, for compiling the code
+* cmake, for generating build system
+* Cuda-12.x or above (if GPU is targeted), for compiling the code for CUDA execution.
+ 
+### Installing packages 
+
+Execute the following commands to install the required packages (Except Cuda). tbb is installed automatically.
+
+```bash
+sudo apt update
+sudo apt install -y git g++ cmake cmake-qt-gui
+```
+
+### Installing Cuda for GPU execution 
+
+If you want to build PhasicFlow to be executed on an nvidia-GPU, you need to install the latest version of Cuda compiler (Version 12.x or above), which is compatible with your hardware and OS, on your computer.
+
+# How to build? 
+
+Here you will learn how to build PhasicFlow for single execution mode. Follow the steps below to install it on your computer. 
+Tested operating systems are:
+* Ubuntu-22.04 LTS
+* Ubuntu-24.04 LTS
+
+### Step 1: Package check
+Make sure that you have installed all the required packages on your computer. See above for more information.
+
+
+### Step 2: Cloning PhasicFlow
+Create the PhasicFlow folder in your home folder and then clone the source code into that folder:
+```bash
+cd ~
+mkdir PhasicFlow
+cd PhasicFlow
+git clone https://github.com/PhasicFlow/phasicFlow.git
+mv phasicFlow phasicFlow-v-1.0
+```
+### Step 3: Environmental variables
+Opne the bashrc file using the following command:
+
+```bash
+$ gedit ~/.bashrc
+```
+
+and add the following line to the end of the file, **save** and **close** it.
+
+```bash
+source $HOME/PhasicFlow/phasicFlow-v-1.0/cmake/bashrc
+```
+
+this will introduce a new source file for setting the environmental variables of PhasicFlow. If you want to load these variables in the current open terminal, you need to source it. Or, simply **close the terminal** and **open a new terminal**.
+
+### Step 4: Building PhasicFlow
+Follow one of the followings to build PhasicFlow for one mode of execution.
+
+#### Serial build for CPU
+In a **new terminal** enter the following commands:
+```bash
+cd ~/PhasicFlow/phasicFlow-v-1.0
+mkdir build
+cd build
+cmake ../ -DpFlow_Build_Serial=On -DCMAKE_BUILD_TYPE=Release
+make install -j4
+```
+For faster builds, use `make install -j`. This will use all the CPU cores on your computer for building. 
+
+#### OpenMP build for CPU
+
+```bash
+cd ~/PhasicFlow/phasicFlow-v-1.0
+mkdir build
+cd build
+cmake ../ -DpFlow_Build_OpenMP=On -DCMAKE_BUILD_TYPE=Release
+make install -j4
+```
+
+#### GPU build for parallel execution on CUDA-enabled GPUs
+
+```bash
+cd ~/PhasicFlow/phasicFlow-v-1.0
+mkdir build
+cd build
+cmake ../ -DpFlow_Build_Cuda=On -DCMAKE_BUILD_TYPE=Release
+cmake ../ -DpFlow_Build_Cuda=On -DCMAKE_BUILD_TYPE=Release
+make install -j4
+```
+
+After building, `bin`, `include`, and `lib` folders will be created in `~/PhasicFlow/phasicFlow-v-1.0/` folder. Now you are ready to use PhasicFlow.
+
+**note 1**: When compiling the code in parallel, you need to have enough RAM on your computer. As a rule, you need 1 GB free RAM per each processor on your computer for compiling in parallel.
+You may want to use fewer number of cores on your computer by using the following command:
+
+```bash
+make install -j3
+```
+
+the above command only uses 3 cores for compiling. 
+
+**note 2**: By default PhasicFlow is compiled with **double** as floating point variable. You can compile it with **float**. Just in the command line of camke added `-DpFlow_Build_Double=Off` flag to compile it with float. For example if you are building for cuda, you can enter the following command:
+
+```bash
+cmake ../ -DpFlow_Build_Cuda=On -DpFlow_Build_Double=Off
+```
+
+### Step 5: Testing
+
+In the current terminal or a new terminal enter the following command:
+
+```bash
+checkPhasicFlow
+```
+
+This command shows the host and device environments and software version. If PhasicFlow was build correctly, you would get the following output:
+
+```
+Initializing host/device execution spaces . . . 
+  Host execution space is Serial
+  Device execution space is Serial
+
+  You are using phasicFlow v-1.0 (copyright(C): www.cemf.ir)
+  In this build, double is used for floating point operations and uint32for indexing.
+  This is not a build for MPI execution
+
+Finalizing host/device execution space ....
+```

doc/mdDocs/howToBuild.md

@@ -1,151 +0,0 @@
-# How to build PhasicFlow {#howToBuildPhasicFlow}
-
-You can build PhasicFlow for CPU or GPU. You can have a single build or oven multiple builds on a machine. Here you learn how to have a single build of PhasicFlow, in various modes of execution. 
-
-# Required packages
-You need a list of packaged installed on your computer before building PhasicFlow:
-* git, for cloning the code and package management
-* g++, for compiling the code
-* cmake, for generating build system
-* tbb, a parallel library for STL algorithms
-* Cuda (if GPU is targeted), for compiling the code for CUDA execution.
-* Kokkos, the parallelization backend of PhasicFlow 
-
-### git 
-if git is not installed on your computer, enter the following commands 
-```
-$ sudo apt update
-$ sudo apt install git
-```
- 
-
-### g++ (C++ compiler)
-The code is tested with g++ (gnu C++ compiler). The default version of g++ on Ubuntu 18.04 LTS or upper is sufficient for compiling. If it is not installed on your operating system, enter the following command:
-
-``` 
-$ sudo apt update
-$ sudo apt install g++
-```
-
-
-### CMake
-You also need to have CMake-3.22 or higher installed on your computer.
-``` 
-$ sudo apt update
-$ sudo apt install cmake
-```
-
-### tbb (2020.1-2 or higher)
-For **Ubuntu 20.04 LTS or higher versions**, you can install tbb using apt. For now, some parallel algorithms on host side rely on tbb parallel library (C++ parallel backend). Use e following commands to install it:
-```
-$ sudo apt update
-$ sudo apt install libtbb-dev
-```
-If you are compiling on **Ubuntu-18.04 LTS**, you need to enter the following commands to get the right version (2020.1-2 or higher) of tbb:
-```
-$ wget "http://archive.ubuntu.com/ubuntu/pool/universe/t/tbb/libtbb2_2020.1-2_amd64.deb"
-$ sudo dpkg --install libtbb2_2020.1-2_amd64.deb
-$ wget "http://archive.ubuntu.com/ubuntu/pool/universe/t/tbb/libtbb-dev_2020.1-2_amd64.deb"
-$ sudo dpkg --install libtbb-dev_2020.1-2_amd64.deb
-```
-### Cuda
-If you want to build PhasicFlow to be executed on an nvidia-GPU, you need to install the latest version of Cuda compiler, which is compatible with your hardware and OS, on your computer. 
-
-# How to build? 
-Here you will learn how to build PhasicFlow for single execution mode. Follow the steps below to install it on your computer. 
-Tested operating systems are:
-* Ubuntu 18.04 LTS
-* Ubuntu 20.04 LTS
-* Ubuntu 22.04 LTS
-
-### Step 1: Package check
-Make sure that you have installed all the required packages on your computer. See above for more information.
-
-### Step 2: Cloning Kokkos
-It is assumed that Kokkos source is located in the home folder of your computer. Clone the latest version of Kokkos into your home folder:
-```
-$ cd ~
-$ mkdir Kokkos
-$ cd Kokkos
-$ git clone https://github.com/kokkos/kokkos.git
-```
-or simply download and extract the source code of Kokkos in `~/Kokkos` folder. In the end, the top level CMakeLists.txt file should be located in `~/Kokkos/kokkos` folder. 
-
-### Step 3: Cloning PhasicFlow
-Create the PhasicFlow folder in your home folder and then clone the source code into that folder:
-```
-$ cd ~
-$ mkdir PhasicFlow
-$ cd PhasicFlow
-$ git clone https://github.com/PhasicFlow/phasicFlow.git
-```
-### Step 4: Environmental variables
-Opne the bashrc file using the following command:
-
-`$ gedit ~/.bashrc`
-
-and add the following line to the end of the file, **save** and **close** it.
-
-`source $HOME/PhasicFlow/phasicFlow/cmake/bashrc`
-
-this will introduce a new source file for setting the environmental variables of PhasicFlow. If you want to load these variables in the current open terminal, you need to source it. Or, simply **close the terminal** and **open a new terminal**.
-
-### Step 5: Building PhasicFlow
-Follow one of the followings to build PhasicFlow for one mode of execution.
-#### Serial build for CPU
-In a **new terminal** enter the following commands:
-```
-$ cd ~/PhasicFlow/phasicFlow
-$ mkdir build
-$ cd build
-$ cmake ../ -DpFlow_Build_Serial=On
-$ make install
-```
-For faster builds, use `make install -j`. This will use all the CPU cores on your computer for building. 
-#### OpenMP build for CPU
-```
-$ cd ~/PhasicFlow/phasicFlow
-$ mkdir build
-$ cd build
-$ cmake ../ -DpFlow_Build_OpenMP=On
-$ make install
-```
-#### GPU build for parallel execution on CUDA-enabled GPUs
-```
-$ cd ~/PhasicFlow/phasicFlow
-$ mkdir build
-$ cd build
-$ cmake ../ -DpFlow_Build_Cuda=On
-$ make install
-```
-
-After building, `bin`, `include`, and `lib` folders will be created in `~/PhasicFlow/phasicFlow/` folder. Now you are ready to use PhasicFlow.
-
-**note 1**: When compiling the code in parallel, you need to have enough RAM on your computer. As a rule, you need 1 GB free RAM per each processor in your computer for compiling in parallel.
-You may want to use fewer number of cores on your computer by using the following command:
-
-`$ make install -j 3`
-
-the above command only uses 3 cores for compiling. 
-
-**note 2**: By default PhasicFlow is compiled with **double** as floating point variable. You can compile it with **float**. Just in the command line of camke added `-DpFlow_Build_Double=Off` flag to compile it with float. For example if you are building for cuda, you can enter the following command:
-
-`$ cmake ../ -DpFlow_Build_Cuda=On -DpFlow_Build_Double=Off`
-
-### Step 6: Testing
-In the current terminal or a new terminal enter the following command:
-
-`$ checkPhasicFlow`
-
-This command shows the host and device environments and software version. If PhasicFlow was build correctly, you would get the following output:
-```
-Initializing host/device execution spaces . . . 
-  Host execution space is Serial
-  Device execution space is Cuda
-
-  ou are using phasicFlow v-0.1 (copyright(C): www.cemf.ir)
-  In this build, double is used for floating point operations.
-
-
-Finalizing host/device execution space ....
-```

doc/mdDocs/phasicFlowFeatures.md

@@ -1,64 +1,116 @@
-# PhasicFlow Features {#phasicFlowFeatures}
+# PhasicFlow Features (v-1.0)
+
+The features of PhasicFlow described here are the main features that are implemented in the code for version 1.0. This document is not a complete list of all the features of PhasicFlow. The features are being added to the code continuously and this document may be behind the latest updates. Of course, the code review will give you the complete list.
+
+## Table of Contents
+
+- [1. Building options](#1-building-options)
+- [2. Preprocessing tools](#2-preprocessing-tools)
+- [3. Solvers for simulations](#3-solvers-for-simulations)
+- [4. Postprocessing tools](#4-postprocessing-tools)
+- [5. Models and features for simulations](#5-models-and-features-for-simulations)
+  - [5.1. General representation of walls](#51-general-representation-of-walls)
+  - [5.2. High precision integeration methods](#52-high-precision-integeration-methods)
+  - [5.3. Contact force models](#53-contact-force-models-needs-improvement)
+  - [5.4. Particle insertion](#54-particle-insertion)
+  - [5.5. Restarting/resuming a simulation](#55-restartingresuming-a-simulation)
+  - [5.6. Postprocessing data during simulation](#56-postprocessing-data-during-simulation)
+
+## 1. Building options
 
-## Building options
 You can build PhasicFlow to be executed on multi-core CPUs or GPUs. It is also possible to select the type of floating point variables in PhasicFlow: double or float. float type requires less memory and mostly consumes less time of a processor to complete a mathematical operation. So, there is a benefit for using floats in DEM simulation specially when GPU is targeted for computations.
+
 Build options for PhasicFlow:
-* **serial (double or float type)**: execution on one cpu core
-* **OpenMp (double or float type)**: execution on multiple cores of a CPU
-* **cuda (double or float type)**: execution on cuda-enabled GPUs
 
+- **serial (double or float type)**: execution on one cpu core
+- **OpenMp (double or float type)**: execution on multiple cores of a CPU
+- **cuda (double or float type)**: execution on cuda-enabled GPUs
 
+for more information on building PhasicFlow, please refer to the [installation guide](./howToBuild-V1.0.md).
 
-## Preprocessing tools
-Preprocessing tools are used to facilitate the process of case setup. They include tools for defining initial state of particles and geometry conversion. 
-* **particlesPhasicFlow** tool can be used to define the initial position of particles (for example at t = 0 s) and to set the initial field values for particles (like velocity, orientation, acceleration and etc).
-* **geometryPhasicFlow** converts user inputs for walls into a data structures that is used by PhasicFlow.
+## 2. Preprocessing tools
 
+PhasicFlow provides a set of tools for preprocessing the simulation case. These tools are used to define the initial state of particles, walls and other parameters that are required for running a simulation.
 
+- [**particlesPhasicFlow**](./../../utilities/particlesPhasicFlow/) tool can be used to define the initial position of particles (for example at t = 0 s) and to set the initial field values for particles (like velocity, orientation, acceleration, etc.).
 
-## Models and features for simulations
+- [**geometryPhasicFlow**](./../../utilities/geometryPhasicFlow/) converts user inputs for walls into a data structure that is used by PhasicFlow.
 
+## 3. Solvers for simulations
 
-### General representation of walls
+- [**sphereGranFlow**](./../../solvers/sphereGranFlow/) is a solver for simulating the flow of spherical particles with particle insertion mechanism. A full set of tutorial on various possible simulations can be found here: [sphereGranFlow tutorial](./../../tutorials/sphereGranFlow/).
+- [**grainGranFlow**](./../../solvers/grainGranFlow/) is a solver for simulating the flow of course-grained particles with particle insertion mechanism. A full set of tutorial on various possible simulations can be found here: [grainGranFlow tutorial](./../../tutorials/grainGranFlow/).
+- [**iterateGeometry**](./../../solvers/iterateGeometry/) is a  solver testing motion of walls without simulating particles. Since simulating with particles may take a long time and we may want to check the motion of geometry to be correct before actual simulation, we created this utility to test the motion of walls. A set of tutorial on various possible simulations can be found here: [iterateGeometry tutorial](./../../tutorials/iterateGeometry/).
+
+## 4. Postprocessing tools
+
+- [**pFlowToVTK**](./../../utilities/pFlowToVTK) is used to convert simulation results into vtk file format. vtk file format can be read by Paraview for visualizing the results.
+- [**postprocessPhasicFlow**](./../../utilities/postprocessPhasicFlow/) is a tool for performing various averaging and summation on the fields. Particle probing is also possible.
+
+## 5. Models and features for simulations
+
+### 5.1. General representation of walls
 
 Walls can be defined in three ways in PhasicFlow:
-* **Builtin walls** in PhasicFlow that include plane wall, cylinder/cone wall, cuboid, circle.
-* **stl wall**  that reads the data of the wall from an ASCII stl file.
-* **foamPatch wall** that reads the OpenFOAM mesh and converts the boundary patches into PhasicFlow walls (this feature is only available when performing CFD-DEM simulation using OpenFOAM).
 
-Walls can be fixed or in motion during simulations. Various motion models are implemented to cover most of the wall motions in phasicFlow ([see the source code] (./../../../src/MotionModel/)):
-* **fixedWall**  model, in which all walls are fixed. This model is mostly useful for granular flow under gravity or gas-solid flows (CFD-DEM). 
-* **rotatingAxisMotion**  model, in which walls are rotating around an axis of rotation with specified rotation speed. This model covers a wide range of granular flows in which the whole or a part of geometry is rotating, like mixers. 
-* **multiRotatingAxisMotion** model, in which a combination of rotations can be specified. One axis of rotation can itself have another axis of rotation, and so on. This creates the possibility of defining very complex motion pattern for walls, like what we see in Nauta blenders.
-* **vibratingMotion** model, in which walls vibrates based on a sinusoidal model with specified frequency and amplitude.
+- **Builtin walls** in PhasicFlow that include plane wall, cylinder/cone wall, cuboid, circle.
+- **stl wall**  that reads the data of the wall from an ASCII stl file.
+- **foamPatch wall** that reads the OpenFOAM mesh and converts the boundary patches into PhasicFlow walls (this feature is only available when performing CFD-DEM simulation using OpenFOAM).
+
+Walls can be fixed or in motion during simulations. Various motion models are implemented to cover most of the wall motions in phasicFlow ([see the source code](./../../src/MotionModel/)):
+
+- **stationay**  model, in which all walls are fixed. This model is mostly useful for granular flow under gravity or gas-solid flows (CFD-DEM).
+- **rotatingAxis**  model, in which walls are rotating around an axis of rotation with specified rotation speed. This model covers a wide range of granular flows in which the whole or a part of geometry is rotating, like mixers.
+- **multiRotatingAxis** model, in which a combination of rotations can be specified. One axis of rotation can itself have another axis of rotation, and so on. This creates the possibility of defining very complex motion pattern for walls, like what we see in Nauta blenders.
+- **vibrating** model, in which walls vibrates based on a sinusoidal model with specified frequency and amplitude.
 In addition to these models, the user can add other motion models to the code based on their need.
 
+### 5.2. High precision integeration methods
 
-### High precision integeration methods
 The precision of integration in a DEM simulation is very important. Since sudden changes in the interaction forces occur during simulations (when objects contact or when they rebound). High precision integration methods makes it possible to accurately track position and velocity of objects (specially when they are in contact). When using these methods, it is possible to choose larger time steps for integration without loosing accuracy and causing instability in the simulation. Although  a high-precision integration requires more computations, but the benefits of choosing larger time steps in simulation can totally compensate it.
+
 Various integration methods are implemented in PhasicFlow:
 
-| Integration Method | Order | Type|
+|Integration Method | Order | Type|
 | :--- | :---: | :---: |
 | AdamsBashforth2 | 2 | one-step |
 | AdamsBashforth3 | 3 | one-step |
 | AdamsBashforth4 | 4 | one-step |
 | AdamsBashforth5 | 5 | one-step |
-| AdamsMoulton3 | 3 | predictor-corrector |
-| AdamsMoulton4 | 4 | predictor-corrector |
-| AdamsMoulton5 | 5 | predictor-corrector |
+| AdamsMoulton3 | 3 | predictor-corrector (not active)|
+| AdamsMoulton4 | 4 | predictor-corrector (not active)|
+| AdamsMoulton5 | 5 | predictor-corrector (not active)|
 
+### 5.3. Contact force models (needs improvement)
 
-### Contact force models
 Linear and non-linear visco-elastic contact force models are considered in the simulation. In addition to these, limited and non-limited Coulomb's friction model can be used to account for the friction between objects. For spherical objects, rolling friction can also be specified between bodies in contact.
+In addition, for course-grained particles simulation, we developed a speciall set of***
 
-### Particle insertion
-Particles can be inserted during simulation from specified region at specified rate and time interval. Any number of insertion regions can be defined in a simulation. Various region types are considered here: box, cylinder and sphere. Particles are inserted into the simulation through the specified region.
+### 5.4. Particle insertion
 
-### restarting/resuming a simulation
-It is possible to resume a simulation fron any time-folder that is avaiable in the simulation case setup directory. PhasicFlow restart the simulation from that time folder.
+Particles can be inserted during simulation from specified region at specified rate and time interval. Any number of insertion regions can be defined in a simulation. Various region types are considered here: `box`, `cylinder` and `sphere`. Particles are inserted into the simulation through the specified region.
 
-## Postprocessing tools
+### 5.5. restarting/resuming a simulation
 
-* **pFlowToVTK** is used to convert simulation results into vtk file format. vtk file format can be read by Paraview for visualizing the results.
-* **postprocessPhasicFlow** is a tool for performing various cell-based averaging on the fields. 
+It is possible to resume a simulation from any time-folder that is available in the simulation case setup directory. PhasicFlow restarts the simulation from that time folder.
+
+### 5.6. Postprocessing data during simulation
+
+PhasicFlow provides a powerful in-simulation postprocessing module that allows users to analyze particle data in real-time while the simulation is running. This feature enables:
+
+- **Real-time data analysis** without waiting for simulation completion
+- **Region-based processing** in spheres, along lines, or at specific points
+- **Various statistical operations** including weighted averages and sums of particle properties
+- **Individual particle tracking** to monitor specific particles throughout simulation
+- **Multiple processing methods** including arithmetic mean, uniform distribution, and Gaussian distribution
+- **Particle filtering** based on properties like diameter, mass, etc.
+- **Flexible time control** options for when postprocessing should be executed
+
+To activate in-simulation postprocessing, users need to:
+
+1. Create a `postprocessDataDict` file in the `settings` directory with appropriate configurations
+2. Add `libs ("libPostprocessData.so")` and `auxFunctions postprocessData` to the `settings/settingsDict` file
+
+Results are written to output files in the case directory with timestamps, allowing users to monitor simulation behavior as it progresses without interrupting the simulation. for more information on how to use this feature, please refer to the [PostprocessData](./../../src/PostprocessData/) module.
+
+The same postprocessing module can also be used after simulation completion through the [`postprocessPhasicFlow`](./../../utilities/postprocessPhasicFlow/) utility.

src/phasicFlow/structuredData/pointStructure/selectors/selectorStridedRange/selectorStridedRange.cpp

@@ -59,7 +59,7 @@ pFlow::selectorStridedRange::selectorStridedRange(
     end_(dict.getValOrSet<uint32>("end", pStruct.size())),
     stride_(dict.getValOrSet<uint32>("stride", 1u))
 {
-	begin_  = max(begin_, 1u);
+	begin_  = max(begin_, 0u);
 	end_    = min(end_, static_cast<uint32>(pStruct.size()));
 	stride_ = max(stride_, 1u);
 

utilities/Utilities/geometryPhasicFlow/stlWall/stlFile.cpp

@@ -52,13 +52,12 @@ bool pFlow::stlFile::readSolid
 (
 	iIstream& is,
 	realx3x3Vector & vertecies,
-	word & name,
-	real scaleFactor
+	word & name
 )
 {
 
 	token tok;
-	is>> tok;
+	is >> tok;
 	if(!checkWordToken(is, tok, "solid")) return false;
 
 	// check if there is a name associated with solid 
@@ -72,7 +71,6 @@ bool pFlow::stlFile::readSolid
 	while (nWords < 20 )
 	{
 		if( badInput(is, tok) ) return false;
-		//if(!tok.isWord()) return false;
 		nWords++;	
 		if(tok.isWord() && tok.wordToken() != "facet" )	
 		{
@@ -105,16 +103,58 @@ bool pFlow::stlFile::readSolid
 	vertecies.clear();
 	while(true )
 	{
-		is>>tok;
+		is >> tok;
 		if( badInput(is,tok) || !tok.isWord() )return false;
 		word wTok = tok.wordToken();
-		if( wTok == "endsolid" ) return true; // end of solid 
+		if( wTok == "endsolid" )// end of solid
+		{
+			// check if there is a name associated with endsolid
+			is >> tok;
+			if( !badInput(is, tok) && !is.eof())
+			{
+				word endName = "";
+				int32 nWords =0;
+
+				while (nWords < 20 )
+				{
+					if( badInput(is, tok) ) return false;
+					nWords++;	
+					if(tok.isWord())	
+					{
+						endName += tok.wordToken();	
+					}
+					else if( tok.isNumber())
+					{
+						auto val = tok.number();
+						endName += real2Word(val);
+					}
+					else if( tok.isPunctuation())
+					{
+						endName += tok.pToken();
+					}
+					else if (tok.isWord())
+					{
+						is.putBack(tok);
+						break;
+					}
+					else
+					{
+						return false;
+					}
+					is >> tok;
+
+					if(is.eof())return true;
+				}
+			}
+			return true;
+		}
+
 		if( wTok != "facet" ) return false;
 		
 		// read facet 
 		is.putBack(tok);
 		realx3x3 tri;
-		if( !readFacet(is, tri, scaleFactor) ) return false;
+		if( !readFacet(is, tri) ) return false;
 
 		vertecies.push_back(tri);
 		
@@ -127,8 +167,7 @@ bool pFlow::stlFile::readSolid
 bool pFlow::stlFile::readFacet
 (
 	iIstream& is,
-	realx3x3& tri,
-	real scaleFactor
+	realx3x3& tri
 )
 {
 	token tok;
@@ -164,9 +203,9 @@ bool pFlow::stlFile::readFacet
 		if(!checkNumberToken(is, tok, v.y()))return false;
 		is>>tok;
 		if(!checkNumberToken(is, tok, v.z()))return false;
-		if( i==0 ) tri.x() = v * scaleFactor;
-		if( i==1 ) tri.y() = v * scaleFactor;
-		if( i==2)  tri.z() = v * scaleFactor;
+		if( i==0 ) tri.x() = v;
+		if( i==1 ) tri.y() = v;
+		if( i==2)  tri.z() = v;
 	}
 	is>> tok;
 	if(!checkWordToken(is, tok, "endloop")) return false;
@@ -291,7 +330,7 @@ void pFlow::stlFile::addSolid
 
 
 
-bool pFlow::stlFile::read(real scaleFactor)
+bool pFlow::stlFile::read()
 {
 	solids_.clear();
 	solidNames_.clear();
@@ -305,7 +344,7 @@ bool pFlow::stlFile::read(real scaleFactor)
 		
 		realx3x3Vector vertecies;
 		word name;
-		if(!readSolid(is, vertecies, name, scaleFactor))
+		if(!readSolid(is, vertecies, name))
 		{
 			ioErrorInFile(is.name(), is.lineNumber());
 		 	return false;

utilities/Utilities/geometryPhasicFlow/stlWall/stlFile.hpp

@@ -52,9 +52,9 @@ protected:
 
 	// - protected members
 
-		bool readSolid(iIstream& is, realx3x3Vector & vertecies, word & name, real scaleFactor);
+		bool readSolid(iIstream& is, realx3x3Vector & vertecies, word & name);
 
-		bool readFacet(iIstream& is, realx3x3& tri, real scaleFactor);
+		bool readFacet(iIstream& is, realx3x3& tri);
 
 		bool writeSolid(iOstream& os, const realx3x3Vector& vertecies, const word& name)const;
 
@@ -91,7 +91,7 @@ public:
 		void addSolid(const word& name, realx3x3Vector&& vertecies);
 
 		// - clear current content and read from file
-		bool read(real scaleFactor);
+		bool read();
 
 		// - write the current contnet to file
 		bool write()const;

utilities/Utilities/geometryPhasicFlow/stlWall/stlWall.cpp

@@ -26,33 +26,61 @@ Licence:
 
 bool pFlow::stlWall::readSTLWall
 (
-	const dictionary& dict
+    const dictionary& dict
 )
 {
-	auto fileName = dict.getVal<word>("file");
+    auto fileName = dict.getVal<word>("file");
 
-	real scale = dict.getValOrSet("scale", static_cast<real>(1.0));
+    real scale = dict.getValOrSet("scale", static_cast<real>(1.0));
+
+    realx3 transform = dict.getValOrSet<realx3>("transform", realx3(0));
+
+    auto scaleFirst = dict.getValOrSet("scaleFirst", Logical("Yes"));
+    
+    fileSystem file("./stl",fileName);
+
+    stlFile stl(file);
+    if(!stl.read())
+    {
+        fatalErrorInFunction <<
+        "  error in reading stl file "<< file <<endl;
+        return false;
+    }
+
+    // Scale and transform the stl vertex
+    realx3x3Vector newStlVertx;
+    for(uint64 i = 0; i < stl.size(); i++)
+    {
+        for(uint64 j = 0; j < stl.solid(i).size(); j++)
+        {
+            realx3x3 tri;
+
+            if(scaleFirst)
+            {
+                tri.x() = stl.solid(i)[j].x() * scale + transform.x();
+                tri.y() = stl.solid(i)[j].y() * scale + transform.y();
+                tri.z() = stl.solid(i)[j].z() * scale + transform.z();
+            }
+            else
+            {
+                tri.x() = (stl.solid(i)[j].x() + transform.x()) * scale;
+                tri.y() = (stl.solid(i)[j].y() + transform.y()) * scale;
+                tri.z() = (stl.solid(i)[j].z() + transform.z()) * scale;
+            }
+
+            newStlVertx.push_back(tri);
+        }
+    }
+
+    // Insert the new vertex to the triangles_
+    for(uint64 i = 0; i < stl.size(); i++)
+    {
+        auto it = triangles_.end();
+        triangles_.insert(it, newStlVertx.begin(), newStlVertx.end());
+    }
     
 
-	fileSystem file("./stl",fileName);
-
-	stlFile stl(file);
-	if(!stl.read(scale))
-	{
-		fatalErrorInFunction <<
-		"  error in reading stl file "<< file <<endl;
-		return false;
-	}
-
-	for(uint64 i=0; i<stl.size(); i++)
-	{
-		auto it = triangles_.end();
-		triangles_.insert(it, stl.solid(i).begin(), stl.solid(i).end());
-	}
-
-	
-
-	return true;
+    return true;
     
 }
 
@@ -61,13 +89,13 @@ pFlow::stlWall::stlWall()
 
 pFlow::stlWall::stlWall
 (
-	const dictionary& dict
+    const dictionary& dict
 )
 :
-	Wall(dict)
+    Wall(dict)
 {
-	if(!readSTLWall(dict))
-	{
-		fatalExit;
-	}
+    if(!readSTLWall(dict))
+    {
+        fatalExit;
+    }
 }

utilities/geometryPhasicFlow/README.md

@@ -0,0 +1,149 @@
+# geometryPhasicFlow Utility
+
+## Overview
+
+`geometryPhasicFlow` is a preprocessing utility for Discrete Element Method (DEM) simulations in phasicFlow. It converts wall geometry definitions from the `geometryDict` file into the internal geometry data structures used by the phasicFlow simulation engine.
+
+This utility reads geometry definitions including wall types, material properties, and motion models from the `geometryDict` file located in the `settings` folder of your simulation case directory. It then processes these definitions to create the necessary triangulated surfaces and motion models that will be used during the simulation.
+
+## Usage
+
+Run the utility from your case directory containing the `settings` folder:
+
+```bash
+geometryPhasicFlow
+```
+
+For fluid-particle coupling simulations:
+
+```bash
+geometryPhasicFlow -c
+```
+
+## Wall Types
+
+phasicFlow supports several built-in wall types that can be defined in the `geometryDict`:
+
+1. **planeWall** - Flat wall defined by four points (p1, p2, p3, p4)
+2. **cylinderWall** - Cylindrical wall defined by two axis points and radius
+3. **cuboidWall** - Box-shaped wall defined by center point and dimensions
+4. **stlWall** - Complex geometry imported from an STL file
+
+## Motion Models
+
+Walls can be associated with different motion models:
+
+1. **stationary** - Fixed walls (no movement)
+2. **rotatingAxis** - Rotation around a specified axis
+3. **multiRotatingAxis** - Multiple rotations (for complex motions)
+4. **vibrating** - Oscillating motion with specified frequency and amplitude
+5. **conveyorBelt** - Creates a conveyor belt effect with constant tangential velocity
+
+## geometryDict File Structure
+
+The geometryDict file requires the following structure:
+
+```C++
+
+// Motion model selection
+motionModel <motionModelName>;
+
+// Motion model specific information
+<motionModelName>Info
+{
+    // Motion model parameters
+    // ...
+}
+
+// Wall surfaces definitions
+surfaces
+{
+    <wallName1>
+    {
+        type        <wallType>;      // Wall type (planeWall, cylinderWall, etc.)
+        // Wall type specific parameters
+        // ...
+        material    <materialName>;  // Material name for this wall
+        motion      <motionName>;    // Motion component name
+    }
+    
+    <wallName2>
+    {
+        // Another wall definition
+        // ...
+    }
+    
+    // Additional walls as needed
+}
+```
+
+## Example
+
+Here's a simple example of a `geometryDict` file for a rotating drum:
+
+```C++
+
+// Rotation around an axis
+motionModel rotatingAxis;
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        p1        (0.0 0.0 0.0);    // First point for axis of rotation
+        p2        (0.0 0.0 1.0);    // Second point for axis of rotation
+        omega     1.214;            // Rotation speed (rad/s)
+    }
+}
+
+surfaces
+{
+    cylinder
+    {
+        type        cylinderWall;    // Type of wall
+        p1          (0.0 0.0 0.0);   // Begin point of cylinder axis
+        p2          (0.0 0.0 0.1);   // End point of cylinder axis
+        radius1     0.12;            // Radius at p1
+        radius2     0.12;            // Radius at p2
+        resolution  24;              // Number of divisions
+        material    prop1;           // Material name
+        motion      rotAxis;         // Motion component name
+    }
+    
+    wall1
+    {
+        type        planeWall;       // Type of wall
+        p1          (-0.12 -0.12 0.0); // First point
+        p2          ( 0.12 -0.12 0.0); // Second point
+        p3          ( 0.12  0.12 0.0); // Third point
+        p4          (-0.12  0.12 0.0); // Fourth point
+        material    prop1;           // Material name
+        motion      rotAxis;         // Motion component name
+    }
+}
+```
+
+## STL File Support
+
+For complex geometries, you can use STL files:
+
+```C++
+wallName
+{
+    type        stlWall;         // Type is STL wall
+    file        filename.stl;    // File name in ./stl folder
+    scale       1.0;             // Optional scale for changing the size of surface
+    transform   (0 0 0);         // Optional translation vector
+    scaleFirst  Yes;             // Scale first or translate first
+    material    wallMat;         // Material name
+    motion      rotAxis;         // Motion component name
+}
+```
+
+STL files should be placed in an `stl` folder in your case directory.
+
+## See Also
+
+- [particlesPhasicFlow](../particlesPhasicFlow) - Utility for creating initial particle configurations
+- [pFlowToVTK](../pFlowToVTK) - Utility for converting simulation results to VTK format
+- [Tutorials](../../tutorials) - Example cases demonstrating phasicFlow capabilities