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

README.md

@@ -17,27 +17,36 @@ Ongoing development includes the integration of MPI-based parallelization with d
 5.  **Hybrid Parallelism:** MPI + OpenMP.
 6.  **Multi-GPU Parallelism:** MPI + CUDA.
 
-# **Build and Installation**
+## **Build and Installation**
 
 PhasicFlow can be compiled for both CPU and GPU execution.
 
 * **Current Development (v-1.0):** Comprehensive build instructions are available [here](https://github.com/PhasicFlow/phasicFlow/wiki/How-to-build-PhasicFlow%E2%80%90v%E2%80%901.0).
 * **Latest Release (v-0.1):** Detailed build instructions are available [here](https://github.com/PhasicFlow/phasicFlow/wiki/How-to-Build-PhasicFlow).
 
-# **Comprehensive Documentation**
+## **Comprehensive Documentation**
 
 In-depth documentation, including code structure, features, and usage guidelines, is accessible via the [online documentation portal](https://phasicflow.github.io/phasicFlow/).
 
-## **Tutorials and Examples**
+### **Tutorials and Examples**
 
 Practical examples and simulation setups are provided in the [tutorials directory](./tutorials). For detailed explanations and step-by-step guides, please refer to the [tutorial section on the PhasicFlow Wiki](https://github.com/PhasicFlow/phasicFlow/wiki/Tutorials).
 
-# **PhasicFlowPlus: Coupled CFD-DEM Simulations**
+## Contributing to PhasicFlow
+We welcome contributions to PhasicFlow! Whether you're a developer or a new user, there are many ways to get involved. Here's how you can help:
+1. Bug Reports
+2. Suggestions for better user experience
+3. Feature request and algorithm improvements
+4. Tutorials, Simulation Case Setups and documentation
+5. Direct Code Contributions
+
+For more details on how you can contribute to PhasicFlow see [this page](https://github.com/PhasicFlow/phasicFlow/wiki/How-to-contribute-to-PhasicFlow). 
+
+## **PhasicFlowPlus: Coupled CFD-DEM Simulations**
 
 PhasicFlowPlus is an extension of PhasicFlow that facilitates the simulation of particle-fluid systems using resolved and unresolved CFD-DEM methods. The repository for PhasicFlowPlus can be found [here](https://github.com/PhasicFlow/PhasicFlowPlus).
 
-
-# How to cite PhasicFlow?
+## How to cite PhasicFlow?
 
 If you are using PhasicFlow in your research or industrial work, cite the following [article](https://www.sciencedirect.com/science/article/pii/S0010465523001662):
 
@@ -58,9 +67,10 @@ If you are using PhasicFlow in your research or industrial work, cite the follow
 }
 ```
 
-# **Dependencies**
+
+## **Dependencies**
 
 PhasicFlow relies on the following external libraries:
 
-* **Kokkos:** A performance portability ecosystem developed by National Technology & Engineering Solutions of Sandia, LLC (NTESS). ([https://github.com/kokkos/kokkos](https://github.com/kokkos/kokkos))
+* **Kokkos:** A community-led performance portability ecosystem within the Linux Foundation's High-Performance Software Foundation (HPSF). ([https://github.com/kokkos/kokkos](https://github.com/kokkos/kokkos))
 * **CLI11 1.8:** A command-line interface parser developed by the University of Cincinnati. ([https://github.com/CLIUtils/CLI11](https://github.com/CLIUtils/CLI11))

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/caseSetup/interaction

@@ -19,7 +19,7 @@ contactSearch
 {
     method         NBS;
 
-    updateInterval   10;
+    updateInterval   20;
 
     sizeRatio       1.1;
 

benchmarks/rotatingDrum/rotatingDrum_1mParticles/caseSetup/shapes

@@ -2,12 +2,14 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
-objectType dicrionary;
-fileFormat  ASCII;
+
+objectName     shapes;
+objectType     dictionary;
+fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
-active         No;                               // is insertion active -> Yes or No
 
-collisionCheck No;                               // is checked          -> Yes or No
+names          (glassBead);    // names of shapes 
 
+diameters      (0.004);        // diameter of shapes 
 
+materials      (glassMat);     // material names for shapes 

benchmarks/rotatingDrum/rotatingDrum_1mParticles/settings/domainDict

@@ -0,0 +1,50 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     domainDict;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+{
+    min (-0.2 -0.2  0.0);
+    max ( 0.2  0.2  0.8);
+}
+
+boundaries
+{
+    neighborListUpdateInterval 200;
+    
+    updateInterval              20;
+    
+    left
+    {
+        type    exit;                            // other options: periodic, reflective 
+    }
+
+    right
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    bottom
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    top
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    rear
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    front
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_1mParticles/settings/geometryDict

@@ -0,0 +1,86 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     geometryDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+motionModel rotatingAxis;         // motion model: rotating object around an axis
+
+rotatingAxisInfo                  // information for rotatingAxisMotion motion model 
+{
+    rotAxis 
+    {
+        p1    (0.0 0.0 0.0);      // first point for the axis of rotation    
+        
+        p2    (0.0 0.0 1.0);      // second point for the axis of rotation    
+        
+        omega 1.256;              // rotation speed (rad/s) => 12 rpm
+    }
+}
+
+surfaces
+{
+    cylinder
+    {
+        type        cylinderWall;          // type of the wall
+        
+        p1          (0.0 0.0 0.0);         // begin point of cylinder axis
+           
+        p2          (0.0 0.0 0.8);         // end point of cylinder axis
+        
+        radius1     0.2;                   // radius at p1
+        
+        radius2     0.2;                   // radius at p2
+        
+        resolution  60;                    // number of divisions
+        
+        material    wallMat;               // material name of this wall
+        
+        motion      rotAxis;               // motion component name 
+    }
+
+    /*
+        This is a plane wall at the rear end of cylinder
+    */
+    
+    wall1
+    {
+        type      planeWall;               // type of the wall  
+        
+        p1        (-0.2 -0.2 0.0);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.0);         // second point
+        
+        p3        ( 0.2  0.2 0.0);         // third point
+        
+        p4        (-0.2  0.2 0.0);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+
+    /*
+        This is a plane wall at the front end of cylinder
+    */
+    
+    wall2
+    {
+        type      planeWall;               // type of the wall
+        
+        p1        (-0.2 -0.2 0.8);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.8);         // second point
+        
+        p3        ( 0.2  0.2 0.8);         // third point
+        
+        p4        (-0.2  0.2 0.8);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_1mParticles/settings/particlesDict

@@ -0,0 +1,47 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     particlesDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+setFields
+{
+    defaultValue 
+    {
+        velocity         realx3     (0 0 0);     // linear velocity (m/s)
+        acceleration     realx3     (0 0 0);     // linear acceleration (m/s2)
+        rotVelocity      realx3     (0 0 0);     // rotational velocity (rad/s)
+        shapeName        word       glassBead;   // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method ordered;
+
+    orderedInfo
+    {
+        distance   0.004;           // minimum space between centers of particles
+        
+        numPoints  1000000;          // number of particles in the simulation 
+        
+        axisOrder  (z x y);         // axis order for filling the space with particles
+    }
+
+    regionType cylinder;            // other options: box and sphere    
+
+    cylinderInfo                    // cylinder for positioning particles 
+    {
+        p1     (0.0  0.0  0.01);    // lower corner point of the box 
+        
+        p2     (0.0  0.0  0.79);    // upper corner point of the box 
+        
+        radius 0.195;               // radius of cylinder 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_1mParticles/settings/settingsDict

@@ -6,13 +6,13 @@ objectName    settingsDict;
 objectType    dictionary;
 fileFormat    ASCII;
 /*---------------------------------------------------------------------------*/
-run             rotatingDrum_4MParticles;
+run             rotatingDrum_1mParticles;
 
 dt              0.00001;      // time step for integration (s)
 
 startTime       0;            // start time for simulation 
 
-endTime         10;           // end time for simulation 
+endTime         4;           // end time for simulation 
 
 saveInterval    0.2;          // time interval for saving the simulation
 
@@ -31,4 +31,4 @@ writeFormat               binary;              // data writting format (ascii or
 
 timersReport              Yes;      
 
-timersReportInterval      0.05;    
+timersReportInterval      0.01;    

benchmarks/rotatingDrum/rotatingDrum_250kParticles/caseSetup/interaction

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+objectName     interaction;
+objectType     dictionary;
+fileFormat     ASCII;
+
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+contactSearch
+{
+    method         NBS;
+
+    updateInterval   20;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;
+}
+
+model
+{
+    contactForceModel    nonLinearLimited;
+
+    rollingFrictionModel normal;
+    
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
+
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);                                    // Young modulus [Pa]
+   
+    Geff (0.8e6  0.8e6  
+                 0.8e6);                                    // Shear modulus [Pa]
+
+    nu   (0.25   0.25  
+                 0.25);                                     // Poisson's ratio [-]
+
+    en   (0.97   0.85   
+                 1.00);                                     // coefficient of normal restitution
+
+    mu   (0.65   0.65   
+                 0.65);                                     // dynamic friction 
+
+    mur  (0.1    0.1    
+                 0.1);                                      // rolling friction 
+}
+

benchmarks/rotatingDrum/rotatingDrum_250kParticles/caseSetup/shapes

@@ -2,9 +2,14 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
-objectType dicrionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-active         No;                                      // is checked          -> Yes or No
 
+objectName     shapes;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+
+names          (glassBead);    // names of shapes 
+
+diameters      (0.006);        // diameter of shapes 
+
+materials      (glassMat);     // material names for shapes 

benchmarks/rotatingDrum/rotatingDrum_250kParticles/cleanThisCase

@@ -0,0 +1,7 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+ls | grep -P "^(([0-9]+\.?[0-9]*)|(\.[0-9]+))$" | xargs -d"\n" rm -rf
+rm -rf VTK 
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_250kParticles/runThisCase

@@ -0,0 +1,21 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+echo "\n<--------------------------------------------------------------------->"
+echo "1) Creating particles"
+echo "<--------------------------------------------------------------------->\n"
+particlesPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "2) Creating geometry"
+echo "<--------------------------------------------------------------------->\n"
+geometryPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "3) Running the case"
+echo "<--------------------------------------------------------------------->\n"
+sphereGranFlow
+
+
+
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_250kParticles/settings/domainDict

@@ -0,0 +1,50 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     domainDict;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+{
+    min (-0.2 -0.2  0.0);
+    max ( 0.2  0.2  0.8);
+}
+
+boundaries
+{
+    neighborListUpdateInterval 200;
+    
+    updateInterval              20;
+    
+    left
+    {
+        type    exit;                            // other options: periodic, reflective 
+    }
+
+    right
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    bottom
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    top
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    rear
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    front
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_250kParticles/settings/geometryDict

@@ -0,0 +1,86 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     geometryDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+motionModel rotatingAxis;         // motion model: rotating object around an axis
+
+rotatingAxisInfo                  // information for rotatingAxisMotion motion model 
+{
+    rotAxis 
+    {
+        p1    (0.0 0.0 0.0);      // first point for the axis of rotation    
+        
+        p2    (0.0 0.0 1.0);      // second point for the axis of rotation    
+        
+        omega 1.256;              // rotation speed (rad/s) => 12 rpm
+    }
+}
+
+surfaces
+{
+    cylinder
+    {
+        type        cylinderWall;          // type of the wall
+        
+        p1          (0.0 0.0 0.0);         // begin point of cylinder axis
+           
+        p2          (0.0 0.0 0.8);         // end point of cylinder axis
+        
+        radius1     0.2;                   // radius at p1
+        
+        radius2     0.2;                   // radius at p2
+        
+        resolution  60;                    // number of divisions
+        
+        material    wallMat;               // material name of this wall
+        
+        motion      rotAxis;               // motion component name 
+    }
+
+    /*
+        This is a plane wall at the rear end of cylinder
+    */
+    
+    wall1
+    {
+        type      planeWall;               // type of the wall  
+        
+        p1        (-0.2 -0.2 0.0);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.0);         // second point
+        
+        p3        ( 0.2  0.2 0.0);         // third point
+        
+        p4        (-0.2  0.2 0.0);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+
+    /*
+        This is a plane wall at the front end of cylinder
+    */
+    
+    wall2
+    {
+        type      planeWall;               // type of the wall
+        
+        p1        (-0.2 -0.2 0.8);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.8);         // second point
+        
+        p3        ( 0.2  0.2 0.8);         // third point
+        
+        p4        (-0.2  0.2 0.8);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_250kParticles/settings/particlesDict

@@ -0,0 +1,47 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     particlesDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+setFields
+{
+    defaultValue 
+    {
+        velocity         realx3     (0 0 0);     // linear velocity (m/s)
+        acceleration     realx3     (0 0 0);     // linear acceleration (m/s2)
+        rotVelocity      realx3     (0 0 0);     // rotational velocity (rad/s)
+        shapeName        word       glassBead;   // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method ordered;
+
+    orderedInfo
+    {
+        distance   0.006;           // minimum space between centers of particles
+        
+        numPoints  250000;          // number of particles in the simulation 
+        
+        axisOrder  (z x y);         // axis order for filling the space with particles
+    }
+
+    regionType cylinder;            // other options: box and sphere    
+
+    cylinderInfo                    // cylinder for positioning particles 
+    {
+        p1     (0.0  0.0  0.01);    // lower corner point of the box 
+        
+        p2     (0.0  0.0  0.79);    // upper corner point of the box 
+        
+        radius 0.195;               // radius of cylinder 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_250kParticles/settings/settingsDict

@@ -0,0 +1,34 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName    settingsDict;
+objectType    dictionary;
+fileFormat    ASCII;
+/*---------------------------------------------------------------------------*/
+run             rotatingDrum_250KParticles;
+
+dt              0.00001;      // time step for integration (s)
+
+startTime       0;            // start time for simulation 
+
+endTime         4;           // end time for simulation 
+
+saveInterval    0.2;          // time interval for saving the simulation
+
+timePrecision   5;            // maximum number of digits for time folder 
+
+g               (0 -9.8 0);   // gravity vector (m/s2) 
+
+includeObjects (diameter);                     // save necessary (i.e., required) data on disk
+
+// exclude unnecessary data from saving on disk
+excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+
+integrationMethod         AdamsBashforth2;     // integration method 
+
+writeFormat               binary;              // data writting format (ascii or binary)
+
+timersReport              Yes;      
+
+timersReportInterval      0.01;    

benchmarks/rotatingDrum/rotatingDrum_2mParticles/caseSetup/interaction

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+objectName     interaction;
+objectType     dictionary;
+fileFormat     ASCII;
+
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+contactSearch
+{
+    method         NBS;
+
+    updateInterval   20;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;
+}
+
+model
+{
+    contactForceModel    nonLinearLimited;
+
+    rollingFrictionModel normal;
+    
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
+
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);                                    // Young modulus [Pa]
+   
+    Geff (0.8e6  0.8e6  
+                 0.8e6);                                    // Shear modulus [Pa]
+
+    nu   (0.25   0.25  
+                 0.25);                                     // Poisson's ratio [-]
+
+    en   (0.97   0.85   
+                 1.00);                                     // coefficient of normal restitution
+
+    mu   (0.65   0.65   
+                 0.65);                                     // dynamic friction 
+
+    mur  (0.1    0.1    
+                 0.1);                                      // rolling friction 
+}
+

benchmarks/rotatingDrum/rotatingDrum_2mParticles/cleanThisCase

@@ -0,0 +1,7 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+ls | grep -P "^(([0-9]+\.?[0-9]*)|(\.[0-9]+))$" | xargs -d"\n" rm -rf
+rm -rf VTK 
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_2mParticles/runThisCase

@@ -0,0 +1,21 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+echo "\n<--------------------------------------------------------------------->"
+echo "1) Creating particles"
+echo "<--------------------------------------------------------------------->\n"
+particlesPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "2) Creating geometry"
+echo "<--------------------------------------------------------------------->\n"
+geometryPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "3) Running the case"
+echo "<--------------------------------------------------------------------->\n"
+sphereGranFlow
+
+
+
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_2mParticles/settings/domainDict

@@ -0,0 +1,50 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     domainDict;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+{
+    min (-0.2 -0.2  0.0);
+    max ( 0.2  0.2  1.2);
+}
+
+boundaries
+{
+    neighborListUpdateInterval 200;
+    
+    updateInterval              20;
+    
+    left
+    {
+        type    exit;                            // other options: periodic, reflective 
+    }
+
+    right
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    bottom
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    top
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    rear
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    front
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_2mParticles/settings/geometryDict

@@ -0,0 +1,86 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     geometryDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+motionModel rotatingAxis;         // motion model: rotating object around an axis
+
+rotatingAxisInfo                  // information for rotatingAxisMotion motion model 
+{
+    rotAxis 
+    {
+        p1    (0.0 0.0 0.0);      // first point for the axis of rotation    
+        
+        p2    (0.0 0.0 1.0);      // second point for the axis of rotation    
+        
+        omega 1.256;              // rotation speed (rad/s) => 12 rpm
+    }
+}
+
+surfaces
+{
+    cylinder
+    {
+        type        cylinderWall;          // type of the wall
+        
+        p1          (0.0 0.0 0.0);         // begin point of cylinder axis
+           
+        p2          (0.0 0.0 1.2);         // end point of cylinder axis
+        
+        radius1     0.2;                   // radius at p1
+        
+        radius2     0.2;                   // radius at p2
+        
+        resolution  60;                    // number of divisions
+        
+        material    wallMat;               // material name of this wall
+        
+        motion      rotAxis;               // motion component name 
+    }
+
+    /*
+        This is a plane wall at the rear end of cylinder
+    */
+    
+    wall1
+    {
+        type      planeWall;               // type of the wall  
+        
+        p1        (-0.2 -0.2 0.0);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.0);         // second point
+        
+        p3        ( 0.2  0.2 0.0);         // third point
+        
+        p4        (-0.2  0.2 0.0);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+
+    /*
+        This is a plane wall at the front end of cylinder
+    */
+    
+    wall2
+    {
+        type      planeWall;               // type of the wall
+        
+        p1        (-0.2 -0.2 1.2);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 1.2);         // second point
+        
+        p3        ( 0.2  0.2 1.2);         // third point
+        
+        p4        (-0.2  0.2 1.2);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_2mParticles/settings/particlesDict

@@ -0,0 +1,47 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     particlesDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+setFields
+{
+    defaultValue 
+    {
+        velocity         realx3     (0 0 0);     // linear velocity (m/s)
+        acceleration     realx3     (0 0 0);     // linear acceleration (m/s2)
+        rotVelocity      realx3     (0 0 0);     // rotational velocity (rad/s)
+        shapeName        word       glassBead;   // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method ordered;
+
+    orderedInfo
+    {
+        distance   0.003;           // minimum space between centers of particles
+        
+        numPoints  2000000;          // number of particles in the simulation 
+        
+        axisOrder  (z x y);         // axis order for filling the space with particles
+    }
+
+    regionType cylinder;            // other options: box and sphere    
+
+    cylinderInfo                    // cylinder for positioning particles 
+    {
+        p1     (0.0  0.0  0.01);    // lower corner point of the box 
+        
+        p2     (0.0  0.0  1.19);    // upper corner point of the box 
+        
+        radius 0.195;               // radius of cylinder 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_2mParticles/settings/settingsDict

@@ -0,0 +1,34 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName    settingsDict;
+objectType    dictionary;
+fileFormat    ASCII;
+/*---------------------------------------------------------------------------*/
+run             rotatingDrum_2mParticles;
+
+dt              0.00001;      // time step for integration (s)
+
+startTime       0;            // start time for simulation 
+
+endTime         4;           // end time for simulation 
+
+saveInterval    0.2;          // time interval for saving the simulation
+
+timePrecision   5;            // maximum number of digits for time folder 
+
+g               (0 -9.8 0);   // gravity vector (m/s2) 
+
+includeObjects (diameter);                     // save necessary (i.e., required) data on disk
+
+// exclude unnecessary data from saving on disk
+excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+
+integrationMethod         AdamsBashforth2;     // integration method 
+
+writeFormat               binary;              // data writting format (ascii or binary)
+
+timersReport              Yes;      
+
+timersReportInterval      0.01;    

benchmarks/rotatingDrum/rotatingDrum_4mParticles/caseSetup/interaction

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+objectName     interaction;
+objectType     dictionary;
+fileFormat     ASCII;
+
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+contactSearch
+{
+    method         NBS;
+
+    updateInterval   20;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;
+}
+
+model
+{
+    contactForceModel    nonLinearLimited;
+
+    rollingFrictionModel normal;
+    
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
+
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);                                    // Young modulus [Pa]
+   
+    Geff (0.8e6  0.8e6  
+                 0.8e6);                                    // Shear modulus [Pa]
+
+    nu   (0.25   0.25  
+                 0.25);                                     // Poisson's ratio [-]
+
+    en   (0.97   0.85   
+                 1.00);                                     // coefficient of normal restitution
+
+    mu   (0.65   0.65   
+                 0.65);                                     // dynamic friction 
+
+    mur  (0.1    0.1    
+                 0.1);                                      // rolling friction 
+}
+

benchmarks/rotatingDrum/rotatingDrum_4mParticles/caseSetup/shapes

@@ -3,10 +3,13 @@
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
 
-objectName     particleInsertion;
-objectType     dicrionary;
+objectName     shapes;
+objectType     dictionary;
 fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
 
-active  No;          // is insertion active?
+names          (glassBead);    // names of shapes 
 
+diameters      (0.003);        // diameter of shapes 
 
+materials      (glassMat);     // material names for shapes 

benchmarks/rotatingDrum/rotatingDrum_4mParticles/cleanThisCase

@@ -0,0 +1,7 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+ls | grep -P "^(([0-9]+\.?[0-9]*)|(\.[0-9]+))$" | xargs -d"\n" rm -rf
+rm -rf VTK 
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_4mParticles/runThisCase

@@ -0,0 +1,21 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+echo "\n<--------------------------------------------------------------------->"
+echo "1) Creating particles"
+echo "<--------------------------------------------------------------------->\n"
+particlesPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "2) Creating geometry"
+echo "<--------------------------------------------------------------------->\n"
+geometryPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "3) Running the case"
+echo "<--------------------------------------------------------------------->\n"
+sphereGranFlow
+
+
+
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_4mParticles/settings/domainDict

@@ -8,12 +8,16 @@ fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
 globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
 {
-    min (-0.2 -0.2 -0.0);
+    min (-0.2 -0.2  0.0);
     max ( 0.2  0.2  1.6);
 }
 
 boundaries
 {
+    neighborListUpdateInterval 200;
+    
+    updateInterval              20;
+    
     left
     {
         type    exit;                            // other options: periodic, reflective 

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

@@ -27,9 +27,9 @@ 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 
+        numPoints  4000000;          // number of particles in the simulation 
         
         axisOrder  (z x y);         // axis order for filling the space with particles
     }

benchmarks/rotatingDrum/rotatingDrum_4mParticles/settings/settingsDict

@@ -0,0 +1,34 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName    settingsDict;
+objectType    dictionary;
+fileFormat    ASCII;
+/*---------------------------------------------------------------------------*/
+run             rotatingDrum_4mParticles;
+
+dt              0.00001;      // time step for integration (s)
+
+startTime       0;            // start time for simulation 
+
+endTime         4;           // end time for simulation 
+
+saveInterval    0.2;          // time interval for saving the simulation
+
+timePrecision   5;            // maximum number of digits for time folder 
+
+g               (0 -9.8 0);   // gravity vector (m/s2) 
+
+includeObjects (diameter);                     // save necessary (i.e., required) data on disk
+
+// exclude unnecessary data from saving on disk
+excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+
+integrationMethod         AdamsBashforth2;     // integration method 
+
+writeFormat               binary;              // data writting format (ascii or binary)
+
+timersReport              Yes;      
+
+timersReportInterval      0.01;    

benchmarks/rotatingDrum/rotatingDrum_500kParticles/caseSetup/interaction

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+objectName     interaction;
+objectType     dictionary;
+fileFormat     ASCII;
+
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+contactSearch
+{
+    method         NBS;
+
+    updateInterval   20;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;
+}
+
+model
+{
+    contactForceModel    nonLinearLimited;
+
+    rollingFrictionModel normal;
+    
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
+
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);                                    // Young modulus [Pa]
+   
+    Geff (0.8e6  0.8e6  
+                 0.8e6);                                    // Shear modulus [Pa]
+
+    nu   (0.25   0.25  
+                 0.25);                                     // Poisson's ratio [-]
+
+    en   (0.97   0.85   
+                 1.00);                                     // coefficient of normal restitution
+
+    mu   (0.65   0.65   
+                 0.65);                                     // dynamic friction 
+
+    mur  (0.1    0.1    
+                 0.1);                                      // rolling friction 
+}
+

benchmarks/rotatingDrum/rotatingDrum_500kParticles/caseSetup/shapes

@@ -0,0 +1,15 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+objectName     shapes;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+
+names          (glassBead);    // names of shapes 
+
+diameters      (0.005);        // diameter of shapes 
+
+materials      (glassMat);     // material names for shapes 

benchmarks/rotatingDrum/rotatingDrum_500kParticles/cleanThisCase

@@ -0,0 +1,7 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+ls | grep -P "^(([0-9]+\.?[0-9]*)|(\.[0-9]+))$" | xargs -d"\n" rm -rf
+rm -rf VTK 
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_500kParticles/runThisCase

@@ -0,0 +1,21 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+echo "\n<--------------------------------------------------------------------->"
+echo "1) Creating particles"
+echo "<--------------------------------------------------------------------->\n"
+particlesPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "2) Creating geometry"
+echo "<--------------------------------------------------------------------->\n"
+geometryPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "3) Running the case"
+echo "<--------------------------------------------------------------------->\n"
+sphereGranFlow
+
+
+
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_500kParticles/settings/domainDict

@@ -0,0 +1,50 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     domainDict;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+{
+    min (-0.2 -0.2  0.0);
+    max ( 0.2  0.2  0.8);
+}
+
+boundaries
+{
+    neighborListUpdateInterval 200;
+    
+    updateInterval              20;
+    
+    left
+    {
+        type    exit;                            // other options: periodic, reflective 
+    }
+
+    right
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    bottom
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    top
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    rear
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    front
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_500kParticles/settings/geometryDict

@@ -0,0 +1,86 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     geometryDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+motionModel rotatingAxis;         // motion model: rotating object around an axis
+
+rotatingAxisInfo                  // information for rotatingAxisMotion motion model 
+{
+    rotAxis 
+    {
+        p1    (0.0 0.0 0.0);      // first point for the axis of rotation    
+        
+        p2    (0.0 0.0 1.0);      // second point for the axis of rotation    
+        
+        omega 1.256;              // rotation speed (rad/s) => 12 rpm
+    }
+}
+
+surfaces
+{
+    cylinder
+    {
+        type        cylinderWall;          // type of the wall
+        
+        p1          (0.0 0.0 0.0);         // begin point of cylinder axis
+           
+        p2          (0.0 0.0 0.8);         // end point of cylinder axis
+        
+        radius1     0.2;                   // radius at p1
+        
+        radius2     0.2;                   // radius at p2
+        
+        resolution  60;                    // number of divisions
+        
+        material    wallMat;               // material name of this wall
+        
+        motion      rotAxis;               // motion component name 
+    }
+
+    /*
+        This is a plane wall at the rear end of cylinder
+    */
+    
+    wall1
+    {
+        type      planeWall;               // type of the wall  
+        
+        p1        (-0.2 -0.2 0.0);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.0);         // second point
+        
+        p3        ( 0.2  0.2 0.0);         // third point
+        
+        p4        (-0.2  0.2 0.0);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+
+    /*
+        This is a plane wall at the front end of cylinder
+    */
+    
+    wall2
+    {
+        type      planeWall;               // type of the wall
+        
+        p1        (-0.2 -0.2 0.8);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.8);         // second point
+        
+        p3        ( 0.2  0.2 0.8);         // third point
+        
+        p4        (-0.2  0.2 0.8);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_500kParticles/settings/particlesDict

@@ -0,0 +1,47 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     particlesDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+setFields
+{
+    defaultValue 
+    {
+        velocity         realx3     (0 0 0);     // linear velocity (m/s)
+        acceleration     realx3     (0 0 0);     // linear acceleration (m/s2)
+        rotVelocity      realx3     (0 0 0);     // rotational velocity (rad/s)
+        shapeName        word       glassBead;   // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method ordered;
+
+    orderedInfo
+    {
+        distance   0.005;           // minimum space between centers of particles
+        
+        numPoints  500000;          // number of particles in the simulation 
+        
+        axisOrder  (z x y);         // axis order for filling the space with particles
+    }
+
+    regionType cylinder;            // other options: box and sphere    
+
+    cylinderInfo                    // cylinder for positioning particles 
+    {
+        p1     (0.0  0.0  0.01);    // lower corner point of the box 
+        
+        p2     (0.0  0.0  0.79);    // upper corner point of the box 
+        
+        radius 0.195;               // radius of cylinder 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_500kParticles/settings/settingsDict

@@ -0,0 +1,34 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName    settingsDict;
+objectType    dictionary;
+fileFormat    ASCII;
+/*---------------------------------------------------------------------------*/
+run             rotatingDrum_500KParticles;
+
+dt              0.00001;      // time step for integration (s)
+
+startTime       0;            // start time for simulation 
+
+endTime         4;           // end time for simulation 
+
+saveInterval    0.2;          // time interval for saving the simulation
+
+timePrecision   5;            // maximum number of digits for time folder 
+
+g               (0 -9.8 0);   // gravity vector (m/s2) 
+
+includeObjects (diameter);                     // save necessary (i.e., required) data on disk
+
+// exclude unnecessary data from saving on disk
+excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+
+integrationMethod         AdamsBashforth2;     // integration method 
+
+writeFormat               binary;              // data writting format (ascii or binary)
+
+timersReport              Yes;      
+
+timersReportInterval      0.01;    

benchmarks/rotatingDrum/rotatingDrum_8mParticles/caseSetup/interaction

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+objectName     interaction;
+objectType     dictionary;
+fileFormat     ASCII;
+
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+contactSearch
+{
+    method         NBS;
+
+    updateInterval   20;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;
+}
+
+model
+{
+    contactForceModel    nonLinearLimited;
+
+    rollingFrictionModel normal;
+    
+    /*
+       Property (glassMat-glassMat      glassMat-wallMat
+                                        wallMat-wallMat);
+    */
+
+    Yeff (1.0e6  1.0e6  
+                 1.0e6);                                    // Young modulus [Pa]
+   
+    Geff (0.8e6  0.8e6  
+                 0.8e6);                                    // Shear modulus [Pa]
+
+    nu   (0.25   0.25  
+                 0.25);                                     // Poisson's ratio [-]
+
+    en   (0.97   0.85   
+                 1.00);                                     // coefficient of normal restitution
+
+    mu   (0.65   0.65   
+                 0.65);                                     // dynamic friction 
+
+    mur  (0.1    0.1    
+                 0.1);                                      // rolling friction 
+}
+

benchmarks/rotatingDrum/rotatingDrum_8mParticles/caseSetup/shapes

@@ -0,0 +1,15 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+objectName     shapes;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+
+names          (glassBead);    // names of shapes 
+
+diameters      (0.002);        // diameter of shapes 
+
+materials      (glassMat);     // material names for shapes 

benchmarks/rotatingDrum/rotatingDrum_8mParticles/cleanThisCase

@@ -0,0 +1,7 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+ls | grep -P "^(([0-9]+\.?[0-9]*)|(\.[0-9]+))$" | xargs -d"\n" rm -rf
+rm -rf VTK 
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_8mParticles/runThisCase

@@ -0,0 +1,21 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+echo "\n<--------------------------------------------------------------------->"
+echo "1) Creating particles"
+echo "<--------------------------------------------------------------------->\n"
+particlesPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "2) Creating geometry"
+echo "<--------------------------------------------------------------------->\n"
+geometryPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "3) Running the case"
+echo "<--------------------------------------------------------------------->\n"
+sphereGranFlow
+
+
+
+
+#------------------------------------------------------------------------------

benchmarks/rotatingDrum/rotatingDrum_8mParticles/settings/domainDict

@@ -0,0 +1,50 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName     domainDict;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+globalBox                                        // Simulation domain: every particles that goes outside this domain will be deleted
+{
+    min (-0.2 -0.2  0.0);
+    max ( 0.2  0.2  1.6);
+}
+
+boundaries
+{
+    neighborListUpdateInterval 200;
+    
+    updateInterval              20;
+    
+    left
+    {
+        type    exit;                            // other options: periodic, reflective 
+    }
+
+    right
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    bottom
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    top
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    rear
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+
+    front
+    {
+        type     exit;                           // other options: periodic, reflective 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_8mParticles/settings/geometryDict

@@ -0,0 +1,86 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     geometryDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+motionModel rotatingAxis;         // motion model: rotating object around an axis
+
+rotatingAxisInfo                  // information for rotatingAxisMotion motion model 
+{
+    rotAxis 
+    {
+        p1    (0.0 0.0 0.0);      // first point for the axis of rotation    
+        
+        p2    (0.0 0.0 1.0);      // second point for the axis of rotation    
+        
+        omega 1.256;              // rotation speed (rad/s) => 12 rpm
+    }
+}
+
+surfaces
+{
+    cylinder
+    {
+        type        cylinderWall;          // type of the wall
+        
+        p1          (0.0 0.0 0.0);         // begin point of cylinder axis
+           
+        p2          (0.0 0.0 1.6);         // end point of cylinder axis
+        
+        radius1     0.2;                   // radius at p1
+        
+        radius2     0.2;                   // radius at p2
+        
+        resolution  60;                    // number of divisions
+        
+        material    wallMat;               // material name of this wall
+        
+        motion      rotAxis;               // motion component name 
+    }
+
+    /*
+        This is a plane wall at the rear end of cylinder
+    */
+    
+    wall1
+    {
+        type      planeWall;               // type of the wall  
+        
+        p1        (-0.2 -0.2 0.0);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 0.0);         // second point
+        
+        p3        ( 0.2  0.2 0.0);         // third point
+        
+        p4        (-0.2  0.2 0.0);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+
+    /*
+        This is a plane wall at the front end of cylinder
+    */
+    
+    wall2
+    {
+        type      planeWall;               // type of the wall
+        
+        p1        (-0.2 -0.2 1.6);         // first point of the wall
+        
+        p2        ( 0.2 -0.2 1.6);         // second point
+        
+        p3        ( 0.2  0.2 1.6);         // third point
+        
+        p4        (-0.2  0.2 1.6);         // fourth point 
+        
+        material  wallMat;                 // material name of the wall  
+        
+        motion    rotAxis;                 // motion component name 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_8mParticles/settings/particlesDict

@@ -0,0 +1,47 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+
+objectName     particlesDict;
+objectType     dictionary;
+fileFormat     ASCII;
+
+setFields
+{
+    defaultValue 
+    {
+        velocity         realx3     (0 0 0);     // linear velocity (m/s)
+        acceleration     realx3     (0 0 0);     // linear acceleration (m/s2)
+        rotVelocity      realx3     (0 0 0);     // rotational velocity (rad/s)
+        shapeName        word       glassBead;   // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method ordered;
+
+    orderedInfo
+    {
+        distance   0.003;           // minimum space between centers of particles
+        
+        numPoints  6000000;          // number of particles in the simulation 
+        
+        axisOrder  (z x y);         // axis order for filling the space with particles
+    }
+
+    regionType cylinder;            // other options: box and sphere    
+
+    cylinderInfo                    // cylinder for positioning particles 
+    {
+        p1     (0.0  0.0  0.01);    // lower corner point of the box 
+        
+        p2     (0.0  0.0  1.59);    // upper corner point of the box 
+        
+        radius 0.195;               // radius of cylinder 
+    }
+}

benchmarks/rotatingDrum/rotatingDrum_8mParticles/settings/settingsDict

@@ -0,0 +1,34 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName    settingsDict;
+objectType    dictionary;
+fileFormat    ASCII;
+/*---------------------------------------------------------------------------*/
+run             rotatingDrum_4mParticles;
+
+dt              0.00001;      // time step for integration (s)
+
+startTime       0;            // start time for simulation 
+
+endTime         4;           // end time for simulation 
+
+saveInterval    0.2;          // time interval for saving the simulation
+
+timePrecision   5;            // maximum number of digits for time folder 
+
+g               (0 -9.8 0);   // gravity vector (m/s2) 
+
+includeObjects (diameter);                     // save necessary (i.e., required) data on disk
+
+// exclude unnecessary data from saving on disk
+excludeObjects (rVelocity.dy1 pStructPosition.dy1 pStructVelocity.dy1); 
+
+integrationMethod         AdamsBashforth2;     // integration method 
+
+writeFormat               binary;              // data writting format (ascii or binary)
+
+timersReport              Yes;      
+
+timersReportInterval      0.01;    

cmake/autoComplete

@@ -1,48 +1,89 @@
 PF_cFlags="--description --help --version"
 AllTimeFolders=
 __getAllTime(){
-	files=( $(ls) )
-	deleteFiles=(settings caseSetup cleanThisCase VTK runThisCase stl postprocess postProcess) 
-	declare -A delk
-	for del in "${deleteFiles[@]}" ; do delk[$del]=1 ; done
-		# Tag items to remove, based on
-	for k in "${!files[@]}" ; do
-		[ "${delk[${files[$k]}]-}" ] && unset 'files[k]'
-	done
-		# Compaction
-	COMPREPLY=("${files[@]}")
-	AllTimeFolders="${files[@]}"
+    # Initialize empty array for time folders
+    local time_folders=()
+    
+    # Loop through all directories in current folder
+    for dir in */; do
+        # Remove trailing slash
+        dir=${dir%/}
+        
+        # Check if directory name is a valid floating point number
+        # This pattern matches integers and floating point numbers
+        if [[ $dir =~ ^[0-9]+(\.[0-9]+)?$ ]]; then
+            time_folders+=("$dir")
+        fi
+    done
+    
+    # Set completion reply to the time folders
+    COMPREPLY=("${time_folders[@]}")
+    AllTimeFolders="${time_folders[@]}"
 }
 
 __getFields(){
-	__getAllTime
-	local -A unique_files=()
+    __getAllTime
+    local -A unique_files=()
+    # Files to exclude from suggestions
+    local exclude_files=("shapeHash" "pStructure" "particleInsertion" "p" "alpha" "U" "Sp" "Su" "phi")
+    declare -A exclude_dict
+    
+    # Build exclude dictionary for faster lookups
+    for file in "${exclude_files[@]}"; do
+        exclude_dict["$file"]=1
+    done
 
-	for dir in $AllTimeFolders; do
-	  # Check if the directory exists
-	  if [ ! -d "$dir" ]; then
-		continue  # Skip to the next directory
-	  fi
-		  
-	  files_in_dir=$(find "$dir" -maxdepth 1 -type f -printf '%f\n' | sort -u)
-	  
-	# Add filenames to the associative array (duplicates will be overwritten)
-	  while IFS= read -r filename; do
-		unique_files["$filename"]=1 # Just the key is important, value can be anything
-	  done <<< "$files_in_dir"
-	  
-	done
-	COMPREPLY=("${!unique_files[@]}")
-	AllTimeFolders=
+    for dir in $AllTimeFolders; do
+        # Skip if not a directory
+        [ ! -d "$dir" ] && continue
+        
+        # Find all files in this time directory
+        while IFS= read -r filename; do
+            # Skip empty lines and excluded files
+            [ -z "$filename" ] || [ "${exclude_dict[$filename]+exists}" ] && continue
+            
+            # Add to unique files
+            unique_files["$filename"]=1
+        done < <(find "$dir" -maxdepth 1 -type f -printf '%f\n')
+    done
+    
+    # Set completion reply to the unique filenames
+    COMPREPLY=(${!unique_files[@]})
+    
+    # Clear global variable
+    AllTimeFolders=
 }
 
 _pFlowToVTK(){
-    if [ "$3" == "--time" ]  ; then
+    local cur="${COMP_WORDS[COMP_CWORD]}"
+    local prev="${COMP_WORDS[COMP_CWORD-1]}"
+    
+    # Check if we're completing a field
+    local is_field=0
+    for ((i=1; i<COMP_CWORD; i++)); do
+        if [[ "${COMP_WORDS[i]}" == "--fields" ]]; then
+            is_field=1
+            break
+        fi
+    done
+    
+    if [ "$prev" == "--time" ]; then
         __getAllTime
-    elif [ "$3" == "--fields" ]; then 
-    	__getFields
+    elif [ "$prev" == "--fields" ] || [ $is_field -eq 1 ]; then 
+        # We're completing field names
+        __getFields
+        # Filter the results based on the current word prefix
+        if [ -n "$cur" ]; then
+            local filtered=()
+            for item in "${COMPREPLY[@]}"; do
+                if [[ "$item" == "$cur"* ]]; then
+                    filtered+=("$item")
+                fi
+            done
+            COMPREPLY=("${filtered[@]}")
+        fi
     else
-        COMPREPLY=( $(compgen -W "$PF_cFlags --binary --no-geometry --no-particles --out-folder --time --separate-surfaces --fields" -- "$2") )
+        COMPREPLY=( $(compgen -W "$PF_cFlags --binary --no-geometry --no-particles --out-folder --time --separate-surfaces --fields" -- "$cur") )
     fi
 }
 complete -F _pFlowToVTK pFlowToVTK

doc/mdDocs/codingStyle.md

@@ -0,0 +1,231 @@
+# PhasicFlow Coding Style Guidelines
+This document outlines the coding style guidelines for the PhasicFlow codebase. 
+Adhering to these guidelines ensures consistency, readability, and maintainability of the project.
+## 1. FormattingIndentation: 
+* Use 4 spaces for every logical level and block.
+* Line Spacing: Leave two empty lines between sections (e.g., between functions in a .cpp file, between class members).
+
+## 2. Naming ConventionsGeneral Naming: 
+* All names should start with lowercase letters, except for special names (e.g., Ergun, Hertz).
+* Macro names start with Upper case or all the letters are in UPPER case.
+* Compound Names: For compound names, the first word starts with a lowercase letter, and subsequent words start with an uppercase letter (e.g., boundaryBase, motionModel).
+
+## 3. File Structure 
+* Header Files: Use the .hpp extension for header files.
+* Source Files: Use the .cpp extension for source files.
+* Header and Source File Headers: All header and source files must include a standardized header that describes the project's intention and licensing information.
+* File Naming: Header and source file names should correspond to the class they contain. Aim for one class per file.
+* Inline Functions: Place inline functions in a separate classNameI.hpp file to avoid cluttering the main header file.
+
+## 4. Class DesignClass Member Order:
+* Private members and methods
+* Private static members and methods
+* Public methods
+* Public static methods
+* Enumerations and Nested Classes: Declare enumerations and nested classes before all class members and methods.
+* Special Functions: Each class must explicitly define all special functions:Constructor, Copy constructor and assignment operator, Move constructor and assignment operator
+* Destructor: Each class must have an explicit destructor declaration:`~className() = default`; or `~className();`
+* Interface classes or classes with virtual methods must have a virtual destructor.
+* Virtual Method Overrides: When implementing a `virtual` method from a base class in a derived class, use the `override` keyword. The same applies to derived class destructors.
+## 5. NamespacesOfficial Namespace: 
+The official namespace for the codebase is pFlow. All entities should be defined within this namespace.
+
+### Example File Structure
+```
+src/
+├── componentName1/
+│   ├── componentName1.hpp
+│   ├── componentName1.cpp
+│   ├── componentName1I.hpp
+│   └── ...
+└── componentName2/
+    ├── componentName2.hpp
+    ├── componentName2.cpp
+    └── ...
+```
+### Example Class Structure
+```C++
+namespace pFlow 
+{
+
+class MyClass 
+{
+public:
+    enum class MyEnum 
+    {
+        Value1,
+        Value2
+    };
+
+    class NestedClass 
+    {
+        // ...
+    };
+
+private:
+    int privateMember_;
+    
+    void privateMethod();
+
+    
+    static int privateStaticMember_;
+    
+    static void privateStaticMethod();
+
+public:
+    
+    MyClass();
+
+    MyClass(const MyClass& other);
+    
+    MyClass(MyClass&& other);
+    
+    MyClass& operator=(const MyClass& other);
+    
+    MyClass& operator=(MyClass&& other);
+    
+    ~MyClass();
+
+    
+    void publicMethod();
+    
+    static void publicStaticMethod();
+
+};
+
+// assuming base class has virtual methods 
+class DerivedClass 
+: 
+    public BaseClass 
+{
+public:
+     
+     ...
+
+    ~DerivedClass() override;
+    
+     void virtualMethod() override;
+};
+
+} // namespace pFlow
+``` 
+
+## 6. Doxygen Documentation
+
+### 6.1. Ruls
+provide the documentations in the header files only. In rare cases where you are generating documentations for executables, the doxygen documentation can be supplied in the .cpp file.  
+
+* **General Doxygen Style:**
+
+    * Use `///` for short documentations for methods and members.
+
+    * Use `/** */` for classes and main methods which play a significant role in the class or code.
+
+    * Place Doxygen comments *before* the declaration of the entity being documented (e.g., class, function, variable).
+
+    * Use `@param` to document function parameters, `@return` for return values, `@brief` for a short description, and `@details` for a more in-depth explanation.
+
+    * Use Markdown syntax within Doxygen comments for formatting.
+
+* **File Headers:** Each file should contain a Doxygen comment at the top, including:
+
+    * `@file` : The name of the file.
+
+    * `@brief`: A brief description of the file's purpose.
+
+    * `@author`: The author(s) of the file.
+
+    * `@date` : The date of creation or last modification.
+
+* **Class Documentation:**
+
+    * Use `/** */` for class documentation.
+
+    * Provide a `@brief` description of the class.
+
+    * Use `@tparam` to document template parameters.
+
+    * Document the purpose of the class, its invariants, and how it should be used.
+
+* **Function/Method Documentation:**
+
+    * Use `///` for short documentations.
+
+    * Use `/** */` for main methods which play a significant role.
+
+    * Provide a `@brief` description of the function.
+
+    * Use `@param` to describe each parameter, including its purpose and whether it is an input, output, or input/output parameter.
+
+    * Use `@return` to describe the return value, including its meaning and possible values.
+
+    * Use `@pre` to document any preconditions that must be met before calling the function.
+
+    * Use `@post` to document any postconditions that will be true after the function returns.
+
+    * Use `@throws` to document any exceptions that the function may throw.
+
+    * Use `@details` for a more detailed explanation of the function's behavior, algorithms, or any other relevant information.
+
+* **Variable Documentation:**
+
+    * Use `///<` for single-line documentation of variables.
+
+### 6.2. Doxygen Documentation Examples
+
+* **Class example**
+
+```cpp
+/**
+ * @brief Represents a particle in the simulation.
+ * @details This class stores the position, velocity, and other physical
+ * properties of a particle.
+ */
+class Particle
+{
+private:
+
+    Point     position_;   ///< The current position of the particle.
+
+    Vector    velocity_;   ///< The current velocity of the particle.
+
+    double     mass_;      ///< The mass of the particle.
+
+public:
+
+    /// Constructs a particle with default values.
+    Particle();
+
+    /**
+     * @brief Updates the position of the particle based on its velocity
+     * and the given time step.
+     * @param deltaTime The time elapsed since the last update, in seconds.
+     */
+    void updatePosition(const timeInfo& ti );
+
+    /// Gets the current position of the particle.
+    Point getPosition() const;
+};
+```
+
+* **Function Example**
+
+```cpp
+/**
+ * @brief Calculates the distance between two points.
+ * @param p1 The first point.
+ * @param p2 The second point.
+ * @return The distance between the two points.
+ */
+double calculateDistance(const Point& p1, const Point& p2)
+{
+    // Implementation
+    return 0.0;
+}
+
+/// Returns the velocity of the particle.
+Vector getVelocity() const
+{
+    return velocity_;
+}
+``` 

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
+
+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.
 
-## 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.
-In addition to these models, the user can add other motion models to the code based on their need. 
+- **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
+
+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.
 
-### 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. 
+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/CMakeLists.txt

@@ -13,3 +13,5 @@ add_subdirectory(Interaction)
 
 add_subdirectory(MotionModel)
 
+add_subdirectory(PostprocessData)
+

src/Geometry/geometryMotion/geometryMotion.cpp

@@ -21,7 +21,6 @@ Licence:
 template<typename MotionModel>
 bool pFlow::geometryMotion<MotionModel>::findMotionIndex()
 {
-	
 	if(motionComponentName().size() != numSurfaces() )
 	{
 		fatalErrorInFunction<<

src/Geometry/geometryMotion/geometryMotions.cpp

@@ -28,4 +28,4 @@ template class pFlow::geometryMotion<pFlow::stationaryWall>;
 
 template class pFlow::geometryMotion<pFlow::conveyorBeltMotion>;
 
-//template class pFlow::geometryMotion<pFlow::multiRotatingAxisMotion>;
+template class pFlow::geometryMotion<pFlow::multiRotatingAxisMotion>;

src/Geometry/geometryMotion/geometryMotions.hpp

@@ -25,7 +25,7 @@ Licence:
 #include "stationaryWall.hpp"
 #include "rotatingAxisMotion.hpp"
 #include "conveyorBeltMotion.hpp"
-//#include "multiRotatingAxisMotion.hpp"
+#include "multiRotatingAxisMotion.hpp"
 #include "vibratingMotion.hpp"
 
 
@@ -40,10 +40,7 @@ using stationaryGeometry = geometryMotion<stationaryWall>;
 
 using conveyorBeltMotionGeometry = geometryMotion<conveyorBeltMotion>;
 
-//typedef geometryMotion<multiRotatingAxisMotion> multiRotationAxisMotionGeometry;
-
-
-
+using multiRotationAxisMotionGeometry = geometryMotion<multiRotatingAxisMotion>;
 
 }
 

src/Integration/AdamsBashforth2/AdamsBashforth2.cpp

@@ -97,10 +97,11 @@ pFlow::AdamsBashforth2::AdamsBashforth2
 	const word& baseName,
 	pointStructure& pStruct,
 	const word& method,
-	const realx3Field_D& initialValField
+	const realx3Field_D& initialValField,
+	bool  keepHistory
 )
 :
-	integration(baseName, pStruct, method, initialValField),
+	integration(baseName, pStruct, method, initialValField, keepHistory),
 	realx3PointField_D
 	(
 		objectFile
@@ -108,7 +109,7 @@ pFlow::AdamsBashforth2::AdamsBashforth2
 			groupNames(baseName,"dy1"),
 			pStruct.time().integrationFolder(),
 			objectFile::READ_IF_PRESENT,
-			objectFile::WRITE_ALWAYS
+			keepHistory?objectFile::WRITE_ALWAYS:objectFile::WRITE_NEVER
 		),
 		pStruct,
 		zero3,

src/Integration/AdamsBashforth2/AdamsBashforth2.hpp

@@ -81,7 +81,8 @@ public:
 			const word& baseName,
 			pointStructure& pStruct,
 			const word& method,
-			const realx3Field_D& initialValField);
+			const realx3Field_D& initialValField,
+			bool  keepHistory);
 
 		/// Destructor 
 		~AdamsBashforth2()override = default;

src/Integration/AdamsBashforth3/AdamsBashforth3.cpp

@@ -109,10 +109,11 @@ pFlow::AdamsBashforth3::AdamsBashforth3
 	const word& baseName,
 	pointStructure& pStruct,
 	const word& method,
-	const realx3Field_D& initialValField
+	const realx3Field_D& initialValField,
+	bool  keepHistory
 )
 :
-	AdamsBashforth2(baseName, pStruct, method, initialValField),
+	AdamsBashforth2(baseName, pStruct, method, initialValField, keepHistory),
 	dy2_
 	(
 		objectFile
@@ -120,7 +121,7 @@ pFlow::AdamsBashforth3::AdamsBashforth3
 			groupNames(baseName,"dy2"),
 			pStruct.time().integrationFolder(),
 			objectFile::READ_IF_PRESENT,
-			objectFile::WRITE_ALWAYS
+			keepHistory ? objectFile::WRITE_ALWAYS : objectFile::WRITE_NEVER
 		),
 		pStruct,
 		zero3,

src/Integration/AdamsBashforth3/AdamsBashforth3.hpp

@@ -71,7 +71,8 @@ public:
 			const word& baseName,
 			pointStructure& pStruct,
 			const word& method,
-			const realx3Field_D& initialValField);
+			const realx3Field_D& initialValField,
+			bool  keepHistory);
 		
 
 		/// Destructor 

src/Integration/AdamsBashforth4/AdamsBashforth4.cpp

@@ -115,10 +115,11 @@ pFlow::AdamsBashforth4::AdamsBashforth4
 	const word& baseName,
 	pointStructure& pStruct,
 	const word& method,
-	const realx3Field_D& initialValField
+	const realx3Field_D& initialValField,
+	bool keepHistory
 )
 :
-	AdamsBashforth3(baseName, pStruct, method, initialValField),
+	AdamsBashforth3(baseName, pStruct, method, initialValField, keepHistory),
 	dy3_
 	(
 		objectFile
@@ -126,7 +127,7 @@ pFlow::AdamsBashforth4::AdamsBashforth4
 			groupNames(baseName,"dy3"),
 			pStruct.time().integrationFolder(),
 			objectFile::READ_IF_PRESENT,
-			objectFile::WRITE_ALWAYS
+			keepHistory?objectFile::WRITE_ALWAYS:objectFile::WRITE_NEVER
 		),
 		pStruct,
 		zero3,

src/Integration/AdamsBashforth4/AdamsBashforth4.hpp

@@ -69,7 +69,8 @@ public:
 			const word& baseName,
 			pointStructure& pStruct,
 			const word& method,
-			const realx3Field_D& initialValField);
+			const realx3Field_D& initialValField,
+			bool  keepHistory);
 		
 		
 

src/Integration/AdamsBashforth5/AdamsBashforth5.cpp

@@ -123,10 +123,11 @@ pFlow::AdamsBashforth5::AdamsBashforth5
 	const word &baseName, 
 	pointStructure &pStruct, 
 	const word &method, 
-	const realx3Field_D &initialValField
+	const realx3Field_D &initialValField,
+	bool  keepHistory
 )
 :
-	AdamsBashforth4(baseName, pStruct, method, initialValField),
+	AdamsBashforth4(baseName, pStruct, method, initialValField, keepHistory),
 	dy4_
 	(
 		objectFile
@@ -134,7 +135,7 @@ pFlow::AdamsBashforth5::AdamsBashforth5
 			groupNames(baseName,"dy4"),
 			pStruct.time().integrationFolder(),
 			objectFile::READ_IF_PRESENT,
-			objectFile::WRITE_ALWAYS
+			keepHistory?objectFile::WRITE_ALWAYS:objectFile::WRITE_NEVER
 		),
 		pStruct,
 		zero3,

src/Integration/AdamsBashforth5/AdamsBashforth5.hpp

@@ -68,7 +68,8 @@ public:
 			const word& baseName,
 			pointStructure& pStruct,
 			const word& method,
-			const realx3Field_D& initialValField);
+			const realx3Field_D& initialValField,
+			bool  keepHistory);
 		
 		
 

src/Integration/integration/integration.cpp

@@ -51,10 +51,12 @@ pFlow::integration::integration(
     const word &baseName,
     pointStructure &pStruct,
     const word &,
-    const realx3Field_D &)
+    const realx3Field_D &,
+	bool keepHistory)
     : owner_(*pStruct.owner()),
       pStruct_(pStruct),
-      baseName_(baseName)
+      baseName_(baseName),
+      keepHistory_(keepHistory)
 {}
 
 
@@ -64,12 +66,13 @@ pFlow::uniquePtr<pFlow::integration>
 		const word& baseName,
 		pointStructure& pStruct,
 		const word& method,
-		const realx3Field_D& initialValField
+		const realx3Field_D& initialValField,
+		bool  keepHistory
 )
 {
 	if( wordvCtorSelector_.search(method) )
 	{
-		return wordvCtorSelector_[method] (baseName, pStruct, method, initialValField);
+		return wordvCtorSelector_[method] (baseName, pStruct, method, initialValField, keepHistory);
 	}
 	else
 	{

src/Integration/integration/integration.hpp

@@ -24,6 +24,7 @@ Licence:
 
 #include "virtualConstructor.hpp"
 #include "pointFields.hpp"
+#include "Logical.hpp"
 
 
 namespace pFlow
@@ -63,6 +64,8 @@ private:
 		/// The base name for integration 
 		const word baseName_;
 
+		bool 	keepHistory_;
+
 protected:
 
 	bool insertValues(
@@ -83,7 +86,8 @@ public:
 			const word& baseName,
 			pointStructure& pStruct,
 			const word& method,
-			const realx3Field_D& initialValField);
+			const realx3Field_D& initialValField,
+			bool  keepHistory);
 
 		/// Copy constructor 
 		integration(const integration&) = default;
@@ -109,9 +113,10 @@ public:
 				const word& baseName,
 				pointStructure& pStruct,
 				const word& method,
-				const realx3Field_D& initialValField
+				const realx3Field_D& initialValField,
+				bool keepHistory
 			),
-			(baseName, pStruct, method, initialValField)
+			(baseName, pStruct, method, initialValField, keepHistory)
 		);
 
 
@@ -138,6 +143,11 @@ public:
 			return owner_;
 		}
 
+		bool keepHistory()const
+		{
+			return keepHistory_;
+		}
+
 		virtual 
 		void updateBoundariesSlaveToMasterIfRequested() = 0;
 		/// return integration method 
@@ -164,7 +174,8 @@ public:
 			const word& baseName,
 			pointStructure& pStruct,
 			const word& method,
-			const realx3Field_D& initialValField);
+			const realx3Field_D& initialValField,
+			bool  keepHistory);
 
 }; // integration
 

src/Interaction/contactLists/sortedPairs.hpp

@@ -193,7 +193,7 @@ public:
 
 		if( capacity+1 > flags_.size() )
 		{
-			reallocNoInit(flags_, capacity+1);
+			reallocInit(flags_, capacity+1);
 		}
 
 		// fill the flags
@@ -219,7 +219,7 @@ public:
 		{
 			// get more space to prevent reallocations in next iterations
 			uint32 len = size_*1.1+1; 
-			reallocNoInit(sortedPairs_, len);
+			reallocInit(sortedPairs_, len);
 		}
 		
 		Kokkos::parallel_for(
@@ -231,6 +231,7 @@ public:
 		// - sort paris based on the first and second
 		sort(sortedPairs_, 0, size_ );
 		
+		
 
 	}
 

src/Interaction/sphereInteraction/sphereInteractionsNonLinearModModels.cpp

@@ -58,5 +58,5 @@ createInteraction(pFlow::cfModels::limitedNonLinearModNormalRolling, pFlow::conv
 createInteraction(pFlow::cfModels::nonLimitedNonLinearModNormalRolling,pFlow::conveyorBeltMotionGeometry);
 
 // multiRotationAxisMotionGeometry
-//createInteraction(pFlow::cfModels::limitedNonLinearModNormalRolling, pFlow::multiRotationAxisMotionGeometry);
-//createInteraction(pFlow::cfModels::nonLimitedNonLinearModNormalRolling,pFlow::multiRotationAxisMotionGeometry);
+createInteraction(pFlow::cfModels::limitedNonLinearModNormalRolling, pFlow::multiRotationAxisMotionGeometry);
+createInteraction(pFlow::cfModels::nonLimitedNonLinearModNormalRolling,pFlow::multiRotationAxisMotionGeometry);

src/MotionModel/CMakeLists.txt

@@ -14,8 +14,8 @@ entities/stationary/stationary.cpp
 conveyorBeltMotion/conveyorBeltMotion.cpp
 entities/conveyorBelt/conveyorBelt.cpp
 
-#entities/multiRotatingAxis/multiRotatingAxis.cpp
-#multiRotatingAxisMotion/multiRotatingAxisMotion.cpp
+entities/multiRotatingAxis/multiRotatingAxis.cpp
+multiRotatingAxisMotion/multiRotatingAxisMotion.cpp
 
 )
 

src/MotionModel/MotionModel/MotionModel.cpp

@@ -32,7 +32,6 @@ bool pFlow::MotionModel<Model, Component>::impl_nameToIndex(const word& name, ui
 		indx = static_cast<uint32>(i);
 		return true;
 	}
-	
 }
 
 template<typename Model, typename Component>

src/MotionModel/entities/multiRotatingAxis/multiRotatingAxis.cpp

@@ -22,31 +22,32 @@ Licence:
 #include "multiRotatingAxisMotion.hpp"
 #include "dictionary.hpp"
 
+/// Construct from dictionary
 FUNCTION_H
-pFlow::multiRotatingAxis::multiRotatingAxis
-(
-	multiRotatingAxisMotion* axisMotion
-)
-{
-	//axisList_ = axisMotion->getAxisListPtr();	
-}
+pFlow::multiRotatingAxis::multiRotatingAxis(const dictionary& dict)
+:
+	rotatingAxis(dict)
+{}
+
 
 FUNCTION_H
 pFlow::multiRotatingAxis::multiRotatingAxis
 (
-	multiRotatingAxisMotion* axisMotion,
+	multiRotatingAxis* axisListPtr,
+	const wordList& componentsNames,
 	const dictionary& dict
 )
+:
+	rotatingAxis(dict),
+	axisList_(axisListPtr)
 {
 
-	if(!read(axisMotion, dict))
+	if(!read(dict, componentsNames))
 	{
 		fatalErrorInFunction<<
 		"  error in reading rotatingAxis from dictionary "<< dict.globalName()<<endl;
 		fatalExit;
 	}
-
-	//axisList_ = axisMotion->getAxisListPtr();
 }
 
 
@@ -54,22 +55,29 @@ pFlow::multiRotatingAxis::multiRotatingAxis
 FUNCTION_H
 bool pFlow::multiRotatingAxis::read
 (
-	multiRotatingAxisMotion* axisMotion,
-	const dictionary& dict
+	const dictionary& dict,
+	const wordList& componentNames
 )
 {
-
-	if(!rotatingAxis::read(dict))return false;
 			
 	word rotAxis = dict.getValOrSet<word>("rotationAxis", "none");
 
 	if(rotAxis == "none")
 	{
-		parentAxisIndex_ = -1;
+		parentAxisIndex_ = static_cast<uint32>(-1);
 	}
 	else
 	{
-		parentAxisIndex_ = axisMotion-> nameToIndex(rotAxis);
+		if( auto i = componentNames.findi(rotAxis); i != -1 )
+		{
+			parentAxisIndex_ = i;
+		}
+		else
+		{
+			fatalErrorInFunction<<"crotationAxis "<< rotAxis<<" in dictionary "<<
+			dict.globalName()<<" is not found in list of axis names "<< componentNames<<endl;
+			return false;
+		}
 	}
 
 	return true;
@@ -78,8 +86,8 @@ bool pFlow::multiRotatingAxis::read
 FUNCTION_H
 bool pFlow::multiRotatingAxis::write
 (
-	const multiRotatingAxisMotion* axisMotion,
-	dictionary& dict
+	dictionary& dict, 
+	const wordList& componentNames
 ) const
 {
 	if( !rotatingAxis::write(dict) ) return false;
@@ -90,10 +98,8 @@ bool pFlow::multiRotatingAxis::write
 	}
 	else
 	{
-		auto rotAxis  = axisMotion->indexToName(parentAxisIndex_);
-		dict.add("rotationAxis", rotAxis);	
+		dict.add("rotationAxis", componentNames[parentAxisIndex_]);	
 	}
 	
 	return true;
 }
-

src/MotionModel/entities/multiRotatingAxis/multiRotatingAxis.hpp

@@ -24,7 +24,7 @@ Licence:
 
 #include "rotatingAxis.hpp"
 #include "KokkosTypes.hpp"
-
+#include "List.hpp"
 
 namespace pFlow
 {
@@ -79,26 +79,31 @@ class multiRotatingAxis
 protected:
 
 	/// This is device pointer to all axes
-	multiRotatingAxis*		axisList_;
+	multiRotatingAxis*		axisList_ = nullptr;
 
 	/// Index of parent axis
-	int32 					parentAxisIndex_ = -1;
+	uint32 					parentAxisIndex_ = static_cast<uint32>(-1);
 
 public:
 
+	TypeInfoNV("multiRotatingAxis");
+
 	// - Constructors
 
 		/// Empty Constructor
-		INLINE_FUNCTION_HD
-		multiRotatingAxis(){}
+		FUNCTION_HD
+		multiRotatingAxis() = default;
 
-		/// Empty with list of axes
+		/// Construct from dictionary
 		FUNCTION_H
-		multiRotatingAxis(multiRotatingAxisMotion* axisMotion);
+		explicit multiRotatingAxis(const dictionary& dict);
 
 		/// Construct from dictionary and list of axes
 		FUNCTION_H
-		multiRotatingAxis(multiRotatingAxisMotion* axisMotion, const dictionary& dict);
+		multiRotatingAxis(
+			multiRotatingAxis* axisListPtr, 
+			const wordList& componentsNames,
+			const dictionary& dict);
 		
 		/// Copy constructor 
 		FUNCTION_HD
@@ -123,11 +128,11 @@ public:
 			while(parIndex != -1)
 			{
 				auto& ax = axisList_[parIndex];
-				parentVel += ax.linTangentialVelocityPoint(p);
+				parentVel += ax.linVelocityPoint(p);
 				parIndex = ax.parentAxisIndex();
 			}
 
-			return parentVel + rotatingAxis::linTangentialVelocityPoint(p);
+			return parentVel + rotatingAxis::linVelocityPoint(p);
 		}
 
 		/// Translate point p for dt seconds based on the axis information
@@ -143,7 +148,7 @@ public:
 			}
 
 			auto parIndex = parentAxisIndex_;
-			while(parIndex != -1)
+			while(parIndex != static_cast<uint32>(-1))
 			{
 				auto& ax = axisList_[parIndex];
 				newP = pFlow::rotate(newP, ax, dt);
@@ -157,12 +162,12 @@ public:
 		INLINE_FUNCTION_HD
 		bool hasParent()const
 		{
-			return parentAxisIndex_ > -1;
+			return parentAxisIndex_ != static_cast<uint32>(-1);
 		}
 
 		/// Return the index of parent axis
 		INLINE_FUNCTION_HD
-		int32 parentAxisIndex()const
+		uint32 parentAxisIndex()const
 		{
 			return parentAxisIndex_;
 		}
@@ -182,6 +187,7 @@ public:
 		 * It is assumed that the axis with deepest level (with more parrents) is
 		 * moved first and then the axis with lower levels.
 		 */
+		INLINE_FUNCTION_HD
 		void move(real dt)
 		{
 			
@@ -201,11 +207,12 @@ public:
 
 		/// Read from dictionary
 		FUNCTION_H 
-		bool read(multiRotatingAxisMotion* axisMotion, const dictionary& dict);
+		bool read(const dictionary& dict, const wordList& componentNames);
 
 		/// Write to dictionary
 		FUNCTION_H
-		bool write(const multiRotatingAxisMotion* axisMotion, dictionary& dict) const;
+		bool write(dictionary& dict, const wordList& componentNames) const;
+
 
 };
 

src/MotionModel/multiRotatingAxisMotion/multiRotatingAxisMotion.cpp

@@ -19,40 +19,63 @@ Licence:
 -----------------------------------------------------------------------------*/
 
 #include "multiRotatingAxisMotion.hpp"
-#include "dictionary.hpp"
-#include "vocabs.hpp"
 
-
-bool pFlow::multiRotatingAxisMotion::readDictionary
+void pFlow::multiRotatingAxisMotion::impl_setTime
 (
-	const dictionary& dict
-)
+	uint32 iter, 
+	real t, 
+	real dt
+)const
 {
+	auto motion = motionComponents_.deviceViewAll();
+	Kokkos::parallel_for(
+		"multiRotatingAxisMotion::impl_setTime",
+		deviceRPolicyStatic(0, numComponents_),
+		LAMBDA_D(uint32 i){
+			motion[i].setTime(t);
+		});
+	Kokkos::fence();
+}
 
-	auto motionModel = dict.getVal<word>("motionModel");
+bool pFlow::multiRotatingAxisMotion::impl_move(uint32 iter, real t , real dt ) const
+{
+	auto motion = motionComponents_.deviceViewAll();
+	Kokkos::parallel_for(
+		"multiRotatingAxisMotion::impl_move",
+		deviceRPolicyStatic(0, numComponents_),
+		LAMBDA_D(uint32 i){
+			motion[i].move(dt);
+		});
+	Kokkos::fence();
+	return true;
+}
 
-	if(motionModel != "multiRotatingAxisMotion")
+bool pFlow::multiRotatingAxisMotion::impl_readDictionary(const dictionary &dict)
+{
+	auto modelName = dict.getVal<word>("motionModel");
+
+	if(modelName != getTypeName<ModelComponent>())
 	{
 		fatalErrorInFunction<<
-		"  motionModel should be multiRotatingAxisMotion, but found "
-		 << motionModel <<endl;
+		"  motionModel should be "<< Yellow_Text(getTypeName<ModelComponent>())<<
+		", but found "<< Yellow_Text(modelName)<<endl;
 		return false;
 	}
 
-	auto& motionInfo = dict.subDict("multiRotatingAxisMotionInfo");
-	auto axisNames = motionInfo.dictionaryKeywords();
-	wordList rotationAxis;
-
-	// first check if 
+	auto& motionInfo = dict.subDict(modelName+"Info");
+	auto compNames = motionInfo.dictionaryKeywords();
 	
-			
-	for(auto& aName: axisNames)
+	wordList rotationAxisNames;
+
+	
+	// in the first round read all dictionaries 			
+	for(auto& compName: compNames)
 	{
-		auto& axDict = motionInfo.subDict(aName);
+		auto& axDict = motionInfo.subDict(compName);
 		
 		if(auto axPtr = makeUnique<rotatingAxis>(axDict); axPtr)
 		{
-			rotationAxis.push_back(
+			rotationAxisNames.push_back(
 				axDict.getValOrSet<word>("rotationAxis", "none"));
 		}
 		else
@@ -63,26 +86,26 @@ bool pFlow::multiRotatingAxisMotion::readDictionary
 		}
 	}
 
-	if( !axisNames.search("none") )
+	if( !compNames.search("none") )
 	{
-		axisNames.push_back("none");
-		rotationAxis.push_back("none");
+		compNames.push_back("none");
+		rotationAxisNames.push_back("none");
 	}
 
 	using intPair = std::pair<int32, int32>;
 
 	std::vector<intPair> numRotAxis;
 
-	for(size_t i=0; i< axisNames.size(); i++)
+	for(size_t i=0; i< compNames.size(); i++)
 	{
-		word rotAxis = rotationAxis[i];
+		word rotAxis = rotationAxisNames[i];
 		int32 n=0;
 		while(rotAxis != "none")
 		{
 			n++;
-			if(int32 iAxis = axisNames.findi(rotAxis) ; iAxis != -1)
+			if(int32 iAxis = compNames.findi(rotAxis) ; iAxis != -1)
 			{
-				rotAxis = rotationAxis[iAxis];	
+				rotAxis = rotationAxisNames[iAxis];	
 			}else
 			{
 				fatalErrorInFunction<<
@@ -98,60 +121,73 @@ bool pFlow::multiRotatingAxisMotion::readDictionary
 	auto compareFunc = [](const intPair& a, const intPair& b) 
 		{ return a.first > b.first; };
 
-	algorithms::STD::sort(numRotAxis.data(), numRotAxis.size(), compareFunc);
+	std::sort(numRotAxis.begin(), numRotAxis.end(), compareFunc);
+	Vector<int> sortedIndex; 
+	componentNames_.clear();
 
-	sortedIndex_.clear();
-	axisName_.clear();
+	output<<compNames<<endl;
 	
-
 	for(auto ax:numRotAxis)
 	{
-		axisName_.push_back(axisNames[ax.second]);
-		sortedIndex_.push_back(ax.second);
+		componentNames_.push_back(compNames[ax.second]);
+		sortedIndex.push_back(ax.second);
 	}
 
-	numAxis_ = axisName_.size();
-	axis_.clear();
-	axis_.reserve(numAxis_);
+	numComponents_ = componentNames_.size();
+	motionComponents_.reserve(numComponents_);
+	sortedIndex_.assign(sortedIndex);
 
-
-	// create the actual axis vector 
-	for(auto& aName: axisName_)
+	Vector<ModelComponent> components("Read::modelComponent", 
+		compNames.size()+1, 
+		0, 
+		RESERVE());
+	
+		
+	for(auto& compName: componentNames_)
 	{
-		if(aName != "none")
+		
+		if(compName != "none")
 		{
-			auto& axDict = motionInfo.subDict(aName);
-			axis_.push_back(
-				multiRotatingAxis(this, axDict));	
+			auto& compDict = motionInfo.subDict(compName);
+			components.emplace_back(
+				motionComponents_.data(), 
+				componentNames_, 
+				compDict);
 		}
 		else
 		{
-			axis_.push_back(
-				multiRotatingAxis(this));
+			components.emplace_back(impl_noneComponent());
 		}
 		
 	}
 
-	return true;
+	motionComponents_.assign(components);
+    return true;
 }
 
-bool pFlow::multiRotatingAxisMotion::writeDictionary
+
+bool pFlow::multiRotatingAxisMotion::impl_writeDictionary
 (
 	dictionary& dict
 )const
 {
-	dict.add("motionModel", "multiRotatingAxisMotion");
+	word modelName = "multiRotatingAxis";
 
-	auto& motionInfo = dict.subDictOrCreate("multiRotatingAxisMotionInfo");
-	
-	ForAll(i, axis_)
+	dict.add("motionModel", modelName );
+
+	auto modelDictName = modelName+"Info";
+
+	auto& motionInfo = dict.subDictOrCreate(modelDictName);
+	auto hostComponents = motionComponents_.hostView();
+
+	ForAll(i, motionComponents_)
 	{
 		
-		auto& axDict = motionInfo.subDictOrCreate(axisName_[i]);
-		if( !axis_.hostVectorAll()[i].write(this,axDict))
+		auto& axDict = motionInfo.subDictOrCreate(componentNames_[i]);
+		if( !hostComponents[i].write(axDict, componentNames_))
 		{
 			fatalErrorInFunction<<
-			"  error in writing axis "<< axisName_[i] << " to dicrionary "
+			"  error in writing axis "<< componentNames_[i] << " to dicrionary "
 			<< motionInfo.globalName()<<endl;
 			return false;
 		}
@@ -160,79 +196,52 @@ bool pFlow::multiRotatingAxisMotion::writeDictionary
 	return true;
 }
 
-pFlow::multiRotatingAxisMotion::multiRotatingAxisMotion()
-{}
-
-pFlow::multiRotatingAxisMotion::multiRotatingAxisMotion
-(
-	const dictionary& dict
-)
+pFlow::multiRotatingAxisMotion::multiRotatingAxisMotion(
+    const objectFile &objf,
+    repository *owner)
+    : fileDictionary(objf, owner)
 {
-	if(! readDictionary(dict) )
+
+	if(! getModel().impl_readDictionary(*this) )
 	{
+		fatalErrorInFunction;
 		fatalExit;
 	}
 }
 
-FUNCTION_H
-bool pFlow::multiRotatingAxisMotion::move(real t, real dt)
-{
-
-	// every thing is done on host 
-	for(int32 i=0; i<numAxis_; i++)
-	{	
-		auto& ax = axis_[sortedIndex_[i]];
-		ax.setTime(t);
-		ax.setAxisList(getAxisListPtrHost());
-		ax.move(dt);
-	}
-
-	// transfer to device
-	axis_.modifyOnHost();
-	axis_.syncViews();
-
-	return true;
-}
-
-bool pFlow::multiRotatingAxisMotion::read
+pFlow::multiRotatingAxisMotion::multiRotatingAxisMotion
 (
-	iIstream& is
+	const objectFile &objf, 
+	const dictionary &dict, 
+	repository *owner
 )
+:
+fileDictionary(objf, dict, owner)
 {
-	// create an empty file dictionary
-	dictionary motionInfo(motionModelFile__, true);
-
-	// read dictionary from stream
-	if( !motionInfo.read(is) )
+	if(!getModel().impl_readDictionary(*this) )
 	{
-		ioErrorInFile(is.name(), is.lineNumber()) <<
-		"  error in reading dictionray " << motionModelFile__ <<" from file. \n";
-		return false;
+		fatalErrorInFunction;
+		fatalExit;
 	}
-
-	if( !readDictionary(motionInfo) ) return false;
-	
-	return true;
 }
 
 bool pFlow::multiRotatingAxisMotion::write
 (
-	iOstream& os
-)const
+	iOstream &os, 
+	const IOPattern &iop
+) const
 {
-	// create an empty file dictionary
-	dictionary motionInfo(motionModelFile__, true);
-
-	if( !writeDictionary(motionInfo))
+	// a global dictionary
+	dictionary newDict(fileDictionary::dictionary::name(), true);
+	if( iop.thisProcWriteData() )
 	{
-		return false;
+		if( !getModel().impl_writeDictionary(newDict) || 
+			!newDict.write(os))
+		{
+			fatalErrorInFunction<<
+			" error in writing to dictionary "<< newDict.globalName()<<endl;
+			return false;
+		}
 	}
-
-	if( !motionInfo.write(os) )
-	{
-		ioErrorInFile( os.name(), os.lineNumber() )<<
-		"  error in writing dictionray to file. \n";
-		return false;
-	}
-	return true;
+    return true;
 }

src/MotionModel/multiRotatingAxisMotion/multiRotatingAxisMotion.hpp

@@ -22,18 +22,16 @@ Licence:
 #define __multiRotatingAxisMotion_hpp__
 
 
-#include "types.hpp"
-#include "typeInfo.hpp"
-#include "VectorDual.hpp"
-#include "List.hpp"
+#include "MotionModel.hpp"
 #include "multiRotatingAxis.hpp"
+#include "fileDictionary.hpp"
 
 
 namespace pFlow
 {
 
 // forward
-class dictionary;
+// class dictionary;
 
 /**
  * Rotating axis motion model for walls
@@ -63,200 +61,55 @@ multiRotatingAxisMotionInfo
  *
  */
 class multiRotatingAxisMotion
+:
+    public fileDictionary,
+    public MotionModel<multiRotatingAxisMotion, multiRotatingAxis>
 {
-public:
-	
-	/** Motion model class to be passed to computational units/kernels for
-	 *  transfing points and returning velocities at various positions
-	 */
-	class Model
-	{
-	protected:
-		
-		deviceViewType1D<multiRotatingAxis> 	axis_;
-		int32 									numAxis_=0;
-
-	public:
-
-		INLINE_FUNCTION_HD
-		Model(deviceViewType1D<multiRotatingAxis> axis, int32 numAxis):
-			axis_(axis),
-			numAxis_(numAxis)
-		{}
-
-		INLINE_FUNCTION_HD
-		Model(const Model&) = default;
-		
-		
-		INLINE_FUNCTION_HD
-		Model& operator=(const Model&) = default;
-
-
-		INLINE_FUNCTION_HD
-		realx3 pointVelocity(int32 n, const realx3& p)const
-		{
-			return axis_[n].pointTangentialVel(p);
-		}
-
-		INLINE_FUNCTION_HD
-		realx3 operator()(int32 n, const realx3& p)const
-		{
-			return pointVelocity(n,p);
-		}
-
-		INLINE_FUNCTION_HD
-		realx3 transferPoint(int32 n, const realx3 p, real dt)const
-		{
-			return axis_[n].transferPoint(p, dt);	
-		}
-
-		INLINE_FUNCTION_HD int32 numComponents()const
-		{
-			return numAxis_;
-		}
-	};
-
 protected:
 
-	using axisVector_HD = VectorDual<multiRotatingAxis>;
+	VectorSingle<int32> 	sortedIndex_;
 
-	/// Vector of multiRotaingAxis axes
-	axisVector_HD 		axis_;
-	
-	/// Sorted index based on number of parrents each axis ha
-	VectorDual<int32> 	sortedIndex_;
+	friend MotionModel<multiRotatingAxisMotion, multiRotatingAxis>;
 
-	/// List of axes names
-	wordList  			axisName_;
+	/// is the geometry attached to this component moving
+	bool impl_isMoving()const
+	{
+		return true;
+	}
 
-	/// Number of axes
-	label  				numAxis_= 0;
 
-	/// Read from a dictionary
-	bool readDictionary(const dictionary& dict);
 
-	/// Write to a dictionary 
-	bool writeDictionary(dictionary& dict)const;
+	/// Read from dictionary 
+	bool impl_readDictionary(const dictionary& dict);
+
+	bool impl_writeDictionary(dictionary& dict)const;
 
 public:
 	
-	/// Type info
-	TypeInfoNV("multiRotatingAxisMotion");
+    TypeInfo("multiRotatingAxisMotion");
 
-	// - Constructor 
+	multiRotatingAxisMotion(const objectFile& objf, repository* owner);
 
-		/// Empty constructor 
-		FUNCTION_H
-		multiRotatingAxisMotion();
+	multiRotatingAxisMotion(
+		const objectFile& objf, 
+		const dictionary& dict, 
+		repository* owner);
 
-		/// Construct with dictionary 
-		FUNCTION_H
-		multiRotatingAxisMotion(const dictionary& dict);
+    using fileDictionary::write;
 
-		/// Copy constructor 
-		FUNCTION_H
-		multiRotatingAxisMotion(const multiRotatingAxisMotion&) = default;
+	bool write(iOstream& os, const IOPattern& iop)const override;
 
-		/// No Move 
-		multiRotatingAxisMotion(multiRotatingAxisMotion&&) = delete;
+	static
+    multiRotatingAxis noneComponent()
+    {
+        return multiRotatingAxis();
+    }
 
-		/// Copy assignment 
-		FUNCTION_H
-		multiRotatingAxisMotion& operator=(const multiRotatingAxisMotion&) = default;
+    // TODO: make this method protected
+    void impl_setTime(uint32 iter, real t, real dt)const;
 
-		/// No move assignment 
-		multiRotatingAxisMotion& operator=(multiRotatingAxisMotion&&) = delete;
-
-		/// Destructor 
-		FUNCTION_H
-		~multiRotatingAxisMotion() = default;
-
-	// - Methods 
-
-		/// Retrun motion model at time t 
-		Model getModel(real t)
-		{
-			for(int32 i= 0; i<numAxis_; i++ )
-			{
-				axis_[i].setTime(t);
-				axis_[i].setAxisList(getAxisListPtrDevice());
-			}
-			axis_.modifyOnHost();
-			axis_.syncViews();
-
-			return Model(axis_.deviceVector(), numAxis_);
-		}
-
-		/// Pointer to axis list on host side 
-		INLINE_FUNCTION_H
-		multiRotatingAxis* getAxisListPtrHost()
-		{
-			return axis_.hostVectorAll().data();
-		}
-
-		/// Pointer to axis list on device 
-		INLINE_FUNCTION_H
-		multiRotatingAxis* getAxisListPtrDevice()
-		{
-			return axis_.deviceVectorAll().data();
-		}
-
-		/// Name of motion component to index 
-		INLINE_FUNCTION_H
-		int32 nameToIndex(const word& name)const
-		{
-			if( auto i = axisName_.findi(name); i == -1)
-			{
-				fatalErrorInFunction<<
-				"axis name " << name << " does not exist. \n";
-				fatalExit;
-				return i;
-			}
-			else
-			{
-				return i;
-			}
-			
-		}
-
-		/// Index of motion component to component name 
-		INLINE_FUNCTION_H
-		word indexToName(label i)const
-		{
-			if(i < numAxis_ )
-				return axisName_[i];
-			else
-			{
-				fatalErrorInFunction<<
-				"out of range access to the list of axes " << i <<endl<<
-				" size of axes_ is "<<numAxis_<<endl;
-				fatalExit;
-				return "";
-			}
-		}
-
-		/// Is moving 
-		INLINE_FUNCTION_HD
-		bool isMoving()const
-		{
-			return true;
-		}
-
-		/// Move points 
-		FUNCTION_H
-		bool move(real t, real dt);
-		
-	// - IO operation 
-
-		/// Read from input stream is 
-		FUNCTION_H
-		bool read(iIstream& is);
-
-		/// Write to output stream os 
-		FUNCTION_H
-		bool write(iOstream& os)const;
-
-	
+	/// move the component itself
+	bool impl_move(uint32 iter, real t, real dt)const;
 };
 
 } // pFlow

src/Particles/GrainParticles/grainParticles/grainParticles.cpp

@@ -248,7 +248,8 @@ pFlow::grainParticles::grainParticles(
 			"rVelocity",
 			dynPointStruct(),
 			intMethod,
-			rAcceleration_.field()
+			rAcceleration_.field(),
+			control.keepIntegrationHistory()
 		);
 
 	if( !rVelIntegration_ )

src/Particles/GrainParticles/grainShape/grainShape.cpp

@@ -73,6 +73,18 @@ pFlow::grainShape::grainShape
 	}
 }
 
+pFlow::grainShape::grainShape
+(
+	const word &shapeType, 
+	const word &fileName, 
+	repository *owner, 
+	const property &prop
+)
+:
+	grainShape(fileName, owner, prop)
+{
+}
+
 pFlow::real pFlow::grainShape::maxBoundingSphere() const
 {
     return max(grainDiameters_);
@@ -99,9 +111,12 @@ pFlow::real pFlow::grainShape::boundingDiameter(uint32 index) const
 	{
 		return grainDiameters_[index];
 	}
-	fatalErrorInFunction<<"Invalid index for diameter "<<
-	index<<endl;
+
+	fatalErrorInFunction
+		<<"Invalid index for diameter "
+		<<index<<endl;
 	fatalExit;
+	
 	return 0.0;
 }
 
@@ -122,13 +137,17 @@ pFlow::real pFlow::grainShape::coarseGrainFactor(uint32 index) const
 	return 0.0;
 }
 
+pFlow::realVector pFlow::grainShape::volume() const
+{
+    return realVector("volume", Pi/6*pow(grainDiameters_,(real)3.0));
+}
 
 pFlow::realVector pFlow::grainShape::coarseGrainFactor() const
 {
     return coarseGrainFactor_;
 }
 
-pFlow::real pFlow::grainShape::orginalDiameter(uint32 index) const
+pFlow::real pFlow::grainShape::originalDiameter(uint32 index) const
 {
 	if(indexValid(index))
 	{
@@ -142,7 +161,7 @@ pFlow::real pFlow::grainShape::orginalDiameter(uint32 index) const
 
 
 
-pFlow::realVector pFlow::grainShape::orginalDiameter() const
+pFlow::realVector pFlow::grainShape::originalDiameter() const
 {
     return sphereDiameters_;
 }

src/Particles/GrainParticles/grainShape/grainShape.hpp

@@ -32,9 +32,13 @@ class grainShape
 {
 private:
 	
-	// - diameter of spheres
+	/// diameter of grains
 	realVector 			grainDiameters_;
+
+	/// diameter of spheres
 	realVector 			sphereDiameters_;
+	
+	/// course-grain factor 
 	realVector 			coarseGrainFactor_;
 
 	
@@ -54,9 +58,21 @@ public:
 		repository* owner,
 		const property& prop);
 
+	grainShape(
+		const word& shapeType,
+		const word& fileName,
+		repository* owner,
+		const property& prop);
+
 	
 	~grainShape() override = default;
 
+	add_vCtor
+	(
+		shape, 
+		grainShape,
+		word
+	);
 	//// - Methods
 
 	real maxBoundingSphere()const override;
@@ -68,14 +84,16 @@ public:
 	real boundingDiameter(uint32 index)const override;
 
 	realVector boundingDiameter()const override;
+	
+	realVector volume()const override;
 
-		real coarseGrainFactor(uint32 index)const ;
+	real coarseGrainFactor(uint32 index)const ;
 
 	realVector coarseGrainFactor()const ;
 
-	real orginalDiameter(uint32 index)const ;
+	real originalDiameter(uint32 index)const ;
 
-	realVector orginalDiameter()const ;
+	realVector originalDiameter()const ;
 
 	bool mass(uint32 index, real& m)const override;
 

src/Particles/SphereParticles/sphereParticles/sphereParticles.cpp

@@ -229,7 +229,8 @@ pFlow::sphereParticles::sphereParticles(
 			"rVelocity",
 			dynPointStruct(),
 			intMethod,
-			rAcceleration_.field()
+			rAcceleration_.field(),
+			control.keepIntegrationHistory()
 		);
 
 	if( !rVelIntegration_ )

src/Particles/SphereParticles/sphereShape/sphereShape.cpp

@@ -68,6 +68,18 @@ pFlow::sphereShape::sphereShape
 	}
 }
 
+pFlow::sphereShape::sphereShape
+(
+	const word &shapeType, 
+	const word &fileName, 
+	repository *owner, 
+	const property &prop
+)
+:
+	sphereShape(fileName, owner, prop)
+{
+}
+
 pFlow::real pFlow::sphereShape::maxBoundingSphere() const
 {
     return max(diameters_);
@@ -105,6 +117,11 @@ pFlow::realVector pFlow::sphereShape::boundingDiameter() const
     return diameters_;
 }
 
+pFlow::realVector pFlow::sphereShape::volume() const
+{
+    return realVector("volume", Pi/6*pow(diameters_,(real)3.0));
+}
+
 bool pFlow::sphereShape::mass(uint32 index, real &m) const
 {
     if( indexValid(index) )

src/Particles/SphereParticles/sphereShape/sphereShape.hpp

@@ -51,9 +51,22 @@ public:
 		repository* owner,
 		const property& prop);
 
+	sphereShape(
+		const word& shapeType,
+		const word& fileName,
+		repository* owner,
+		const property& prop);
+
 	
 	~sphereShape() override = default;
 
+	add_vCtor
+	(
+		shape,
+		sphereShape,
+		word
+	);
+
 	//// - Methods
 
 	real maxBoundingSphere()const override;
@@ -66,6 +79,8 @@ public:
 
 	realVector boundingDiameter()const override;
 
+	realVector volume()const override;
+
 	bool mass(uint32 index, real& m)const override;
 
 	real mass(uint32 index) const override;

src/Particles/dynamicPointStructure/dynamicPointStructure.cpp

@@ -58,13 +58,14 @@ pFlow::dynamicPointStructure::dynamicPointStructure
 {
 	REPORT(1)<< "Creating integration method "<<
 		Green_Text(integrationMethod_)<<" for dynamicPointStructure."<<END_REPORT;
-
+	
 	integrationPos_ = integration::create
 	(
 		"pStructPosition",
 		*this,
 		integrationMethod_,
-		velocity_.field()
+		velocity_.field(),
+		control.keepIntegrationHistory()
 	);
 
 	if( !integrationPos_ )
@@ -79,7 +80,8 @@ pFlow::dynamicPointStructure::dynamicPointStructure
 		"pStructVelocity",
 		*this,
 		integrationMethod_,
-		acceleration_.field()
+		acceleration_.field(),
+		control.keepIntegrationHistory()
 	);
 
 	if( !integrationVel_ )