postprocess for segregation

Update helicalMixer benchmarks

.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, "doc/mdDocs/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/sync-wiki.yml

@@ -0,0 +1,60 @@
+name: Sync-Wiki
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "**/*.md"
+      - ".github/workflows/sync-wiki.yml"
+      - "doc/mdDocs/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

.gitignore

@@ -37,11 +37,15 @@
 *.out
 *.app
 
-# directories
+# Exclude specific directories wherever they appear
 build/**
 include/**
 bin/**
 lib/**
+**/build/
+**/include/
+**/bin/
+**/lib/
 test*/**
 **/**notnow
 doc/code-documentation/
@@ -61,3 +65,5 @@ doc/DTAGS
 **/[0-9]*.[0-9][0-9][0-9][0-9][0-9][0-9][0-9]
 **/[0-9]*.[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]
 **/VTK
+
+

DEMSystems/DEMSystem/DEMSystem.cpp

@@ -66,12 +66,13 @@ pFlow::uniquePtr<pFlow::DEMSystem>
 		word  demSystemName,
 		const std::vector<box>& domains, 
 		int argc, 
-		char* argv[]
+		char* argv[],
+		bool requireRVel
 		)
 {
 	if( wordvCtorSelector_.search(demSystemName) )
 	{
-		return wordvCtorSelector_[demSystemName] (demSystemName, domains, argc, argv);
+		return wordvCtorSelector_[demSystemName] (demSystemName, domains, argc, argv, requireRVel);
 	}
 	else
 	{

DEMSystems/DEMSystem/DEMSystem.hpp

@@ -71,13 +71,15 @@ public:
 			word  demSystemName,
 			const std::vector<box>& domains, 
 			int argc, 
-			char* argv[]
+			char* argv[],
+			bool requireRVel
 		),
 		(
 			demSystemName,
 			domains, 
 			argc, 
-			argv
+			argv,
+			requireRVel
 		));
 
 	realx3 g()const
@@ -96,7 +98,7 @@ public:
 		return Control_();
 	}
 
-	auto inline constexpr usingDoulle()const
+	auto inline constexpr usingDouble()const
 	{
 		return pFlow::usingDouble__;
 	}
@@ -119,7 +121,10 @@ public:
 	span<const int32> parIndexInDomain(int32 domIndx)const = 0;
 
 	virtual
-	span<real> diameter() = 0; 
+	span<real> diameter() = 0;
+	
+	virtual 
+	span<uint32> particleId() = 0;
 
 	virtual 
 	span<real> courseGrainFactor() = 0;
@@ -176,7 +181,8 @@ public:
 			word  demSystemName,
 			const std::vector<box>& domains, 
 			int argc, 
-			char* argv[]);
+			char* argv[],
+			bool requireRVel=false);
 
 };
 

DEMSystems/grainDEMSystem/grainDEMSystem.cpp

@@ -163,6 +163,12 @@ pFlow::grainDEMSystem::parIndexInDomain(int32 di)const
 	return particleDistribution_->particlesInDomain(di);
 }
 
+pFlow::span<pFlow::uint32> pFlow::grainDEMSystem::particleId()
+{
+	return span<uint32>(particleIdHost_.data(), particleIdHost_.size());
+}
+
+
 pFlow::span<pFlow::real> pFlow::grainDEMSystem::diameter() 
 {	
 	return span<real>(diameterHost_.data(), diameterHost_.size());
@@ -233,6 +239,7 @@ bool pFlow::grainDEMSystem::beforeIteration()
 	velocityHost_ = std::as_const(particles_()).velocity().hostView();
 	positionHost_ = std::as_const(particles_()).pointPosition().hostView();
 	diameterHost_ = particles_->diameter().hostView();
+	particleIdHost_ = particles_->particleId().hostView();
 
 	if(requireRVel_)
 		rVelocityHost_ = std::as_const(particles_()).rVelocity().hostView();

DEMSystems/grainDEMSystem/grainDEMSystem.hpp

@@ -63,6 +63,8 @@ protected:
 
 	ViewType1D<real, HostSpace> 	diameterHost_;
 
+	ViewType1D<uint32, HostSpace> 	particleIdHost_;
+
 	bool 							requireRVel_ = false;
 
 	ViewType1D<realx3, HostSpace> 	rVelocityHost_;
@@ -122,6 +124,8 @@ public:
 
 	span<const int32> parIndexInDomain(int32 di)const override;
 
+	span<uint32> particleId() override;
+
 	span<real> diameter() override;
 
 	span<real> courseGrainFactor() override;

DEMSystems/sphereDEMSystem/sphereDEMSystem.cpp

@@ -165,6 +165,11 @@ pFlow::sphereDEMSystem::parIndexInDomain(int32 di)const
 	return particleDistribution_->particlesInDomain(di);
 }
 
+pFlow::span<pFlow::uint32> pFlow::sphereDEMSystem::particleId()
+{
+    return span<uint32>();
+}
+
 pFlow::span<pFlow::real> pFlow::sphereDEMSystem::diameter() 
 {	
 	return span<real>(diameterHost_.data(), diameterHost_.size());
@@ -235,6 +240,7 @@ bool pFlow::sphereDEMSystem::beforeIteration()
 	velocityHost_ = std::as_const(particles_()).velocity().hostView();
 	positionHost_ = std::as_const(particles_()).pointPosition().hostView();
 	diameterHost_ = particles_->diameter().hostView();
+	particleIdHost_ = particles_->particleId().hostView();
 
 	if(requireRVel_)
 		rVelocityHost_ = std::as_const(particles_()).rVelocity().hostView();

DEMSystems/sphereDEMSystem/sphereDEMSystem.hpp

@@ -63,6 +63,8 @@ protected:
 
 	ViewType1D<real, HostSpace> 	diameterHost_;
 
+	ViewType1D<uint32, HostSpace> 	particleIdHost_;
+
 	bool 							requireRVel_ = false;
 
 	ViewType1D<realx3, HostSpace> 	rVelocityHost_;
@@ -122,6 +124,8 @@ public:
 
 	span<const int32> parIndexInDomain(int32 di)const override;
 
+	span<uint32> particleId() override;
+
 	span<real> diameter() override;
 
 	span<real> courseGrainFactor() override;

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/helicalMixer_1m/caseSetup/interaction

@@ -2,18 +2,21 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-
 objectName interaction;
 objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
 
 materials   (glassMat wallMat); // a list of materials names
+
 densities   (2500.0 2500);      // density of materials [kg/m3]
 
 contactListType   sortedContactList;
 
 model
 {
-   contactForceModel nonLinearLimited;
+   contactForceModel    nonLinearLimited;
+   
    rollingFrictionModel normal;
 
    Yeff (1.0e6 1.0e6  // Young modulus [Pa]
@@ -28,9 +31,6 @@ model
    en (0.97  0.85   // coefficient of normal restitution
              1.00);
 
-   et (1.0   1.0    // coefficient of tangential restitution 
-             1.0);
-
    mu (0.65  0.65   // dynamic friction 
              0.65);
 
@@ -41,19 +41,13 @@ model
 
 contactSearch
 {
-   method         NBS;           
+    method         NBS;  
-   wallMapping    cellMapping;   
 
-   NBSInfo
+    updateInterval   10;
-   {
-      updateFrequency 10;        // each 20 timesteps, update neighbor list 
-      sizeRatio      1.1;       // bounding box size to particle diameter (max)
-   }
 
-   cellMappingInfo
+    sizeRatio       1.1;
-   {
-      updateFrequency 10;        // each 20 timesteps, update neighbor list  
-      cellExtent     0.6;        // bounding box for particle-wall search (> 0.5)
-   }
 
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
 }

benchmarks/helicalMixer/helicalMixer_1m/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           250000;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           250000;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_1m/caseSetup/shapes

@@ -2,9 +2,11 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
+objectName  shapes;
-objectType dicrionary;
+objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-active         No;                                      // is checked          -> Yes or No
 
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.004 0.00401);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_1m/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 
+rm -rf stl
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_1m/runThisCase

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+
+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
+
+echo "\n<--------------------------------------------------------------------->"
+echo "4) Converting to VtK"
+echo "<--------------------------------------------------------------------->\n"
+pFlowToVTK -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_1m/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+boundaries
+{
+    
+    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/helicalMixer/helicalMixer_1m/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_1m/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- 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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_1m/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             2;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/helicalMixer_250K/caseSetup/interaction

@@ -0,0 +1,53 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+model
+{
+   contactForceModel    nonLinearLimited;
+   
+   rollingFrictionModel normal;
+
+   Yeff (1.0e6 1.0e6  // Young modulus [Pa]
+               1.0e6);
+   
+   Geff (0.8e6 0.8e6  // Shear modulus [Pa]
+               0.8e6);
+
+   nu    (0.25 0.25  // Poisson's ratio [-]
+               0.25);
+
+   en (0.97  0.85   // coefficient of normal restitution
+             1.00);
+
+   mu (0.65  0.65   // dynamic friction 
+             0.65);
+
+   mur (0.1  0.1    // rolling friction 
+             0.1);
+        
+}
+
+contactSearch
+{
+    method         NBS;  
+
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
+}

benchmarks/helicalMixer/helicalMixer_250K/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           62500;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           62500;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_250K/caseSetup/shapes

@@ -2,12 +2,11 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
+objectName  shapes;
-objectType dicrionary;
+objectType  dictionary;
 fileFormat  ASCII;
 /*---------------------------------------------------------------------------*/
-active         No;                               // is insertion active -> Yes or No
-
-collisionCheck No;                               // is checked          -> Yes or No
-
 
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.006 0.00601);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_250K/cleanThisCase

@@ -0,0 +1,8 @@
+#!/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
+rm -rf stl 
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_250K/runThisCase

@@ -0,0 +1,30 @@
+#!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+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
+
+echo "\n<--------------------------------------------------------------------->"
+echo "4) Converting to VtK"
+echo "<--------------------------------------------------------------------->\n"
+pFlowToVTK -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_250K/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+boundaries
+{
+    
+    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/helicalMixer/helicalMixer_250K/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_250K/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- 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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_250K/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             7.5;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/helicalMixer_2m/caseSetup/interaction

@@ -0,0 +1,53 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+model
+{
+   contactForceModel    nonLinearLimited;
+   
+   rollingFrictionModel normal;
+
+   Yeff (1.0e6 1.0e6  // Young modulus [Pa]
+               1.0e6);
+   
+   Geff (0.8e6 0.8e6  // Shear modulus [Pa]
+               0.8e6);
+
+   nu    (0.25 0.25  // Poisson's ratio [-]
+               0.25);
+
+   en (0.97  0.85   // coefficient of normal restitution
+             1.00);
+
+   mu (0.65  0.65   // dynamic friction 
+             0.65);
+
+   mur (0.1  0.1    // rolling friction 
+             0.1);
+        
+}
+
+contactSearch
+{
+    method         NBS;  
+
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
+}

benchmarks/helicalMixer/helicalMixer_2m/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           500000;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           500000;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_2m/caseSetup/shapes

@@ -0,0 +1,12 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  shapes;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.003 0.00301);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_2m/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 
+rm -rf stl
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_2m/runThisCase

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+
+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
+
+echo "\n<--------------------------------------------------------------------->"
+echo "4) Converting to VtK"
+echo "<--------------------------------------------------------------------->\n"
+pFlowToVTK -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_2m/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+boundaries
+{
+    
+    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/helicalMixer/helicalMixer_2m/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_2m/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- 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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_2m/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             2;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/helicalMixer_4m/caseSetup/interaction

@@ -0,0 +1,53 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+model
+{
+   contactForceModel    nonLinearLimited;
+   
+   rollingFrictionModel normal;
+
+   Yeff (1.0e6 1.0e6  // Young modulus [Pa]
+               1.0e6);
+   
+   Geff (0.8e6 0.8e6  // Shear modulus [Pa]
+               0.8e6);
+
+   nu    (0.25 0.25  // Poisson's ratio [-]
+               0.25);
+
+   en (0.97  0.85   // coefficient of normal restitution
+             1.00);
+
+   mu (0.65  0.65   // dynamic friction 
+             0.65);
+
+   mur (0.1  0.1    // rolling friction 
+             0.1);
+        
+}
+
+contactSearch
+{
+    method         NBS;  
+
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
+}

benchmarks/helicalMixer/helicalMixer_4m/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           1000000;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           1000000;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_4m/caseSetup/shapes

@@ -0,0 +1,12 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  shapes;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.002 0.00201);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_4m/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 
+rm -rf stl
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_4m/runThisCase

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+
+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
+
+echo "\n<--------------------------------------------------------------------->"
+echo "4) Converting to VtK"
+echo "<--------------------------------------------------------------------->\n"
+pFlowToVTK -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_4m/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+boundaries
+{
+    
+    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/helicalMixer/helicalMixer_4m/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_4m/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- 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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_4m/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             2;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/helicalMixer_500k/caseSetup/interaction

@@ -0,0 +1,53 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+materials   (glassMat wallMat); // a list of materials names
+
+densities   (2500.0 2500);      // density of materials [kg/m3]
+
+contactListType   sortedContactList;
+
+model
+{
+   contactForceModel    nonLinearLimited;
+   
+   rollingFrictionModel normal;
+
+   Yeff (1.0e6 1.0e6  // Young modulus [Pa]
+               1.0e6);
+   
+   Geff (0.8e6 0.8e6  // Shear modulus [Pa]
+               0.8e6);
+
+   nu    (0.25 0.25  // Poisson's ratio [-]
+               0.25);
+
+   en (0.97  0.85   // coefficient of normal restitution
+             1.00);
+
+   mu (0.65  0.65   // dynamic friction 
+             0.65);
+
+   mur (0.1  0.1    // rolling friction 
+             0.1);
+        
+}
+
+contactSearch
+{
+    method         NBS;  
+
+    updateInterval   10;
+
+    sizeRatio       1.1;
+
+    cellExtent     0.55;
+
+    adjustableBox   Yes;     
+}

benchmarks/helicalMixer/helicalMixer_500k/caseSetup/particleInsertion

@@ -0,0 +1,72 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  particleInsertion;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+active  yes;          // is insertion active?
+
+particleInlet1
+{
+   regionType     box; // type of insertion region
+   
+   rate           125000;  // insertion rate (particles/s)
+   
+   timeControl    simulationTime;
+   
+   startTime      0;      // (s)
+   
+   endTime        2.0;    // (s)
+   
+   insertionInterval    0.05;  //s  
+
+   boxInfo 
+   {
+        min (-0.17 0.23 0.46); // (m,m,m)
+        max ( 0.17 0.24 0.88); // (m,m,m)
+   }
+   
+   setFields
+   {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+        smallParticle 1; // mixture composition of inserted particles 
+   }
+}
+
+particleInlet2
+{
+    regionType     box; // type of insertion region
+
+    rate           125000;  // insertion rate (particles/s)
+
+    timeControl    simulationTime;
+
+    startTime      0;      // (s)
+
+    endTime        2.0;    // (s)
+
+    insertionInterval    0.05;  //s  
+
+    boxInfo 
+    {
+        min ( -0.17 0.23 0.02); // (m,m,m)
+        max (  0.17 0.24 0.44); // (m,m,m)
+    }
+
+    setFields
+    {
+        velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
+    }
+   
+   mixture
+   {
+        largeParticle 1; // mixture composition of inserted particles 
+   }
+}

benchmarks/helicalMixer/helicalMixer_500k/caseSetup/shapes

@@ -0,0 +1,12 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName  shapes;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+names       (smallParticle largeParticle);  // names of shapes 
+diameters   (0.005 0.00501);                // diameter of shapes 
+materials   (glassMat glassMat);            // material names for shapes 

benchmarks/helicalMixer/helicalMixer_500k/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 
+rm -rf stl
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_500k/runThisCase

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -e  # Exit immediately if a command exits with a non-zero status
+cd ${0%/*} || exit 1    # Run from this directory
+
+echo "\n<--------------------------------------------------------------------->"
+echo "0) Copying stl files"
+echo "\n<--------------------------------------------------------------------->"
+mkdir -p stl
+cp -rfv $pFlow_PROJECT_DIR/resources/stls/helicalMixer/* ./stl/
+
+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
+
+echo "\n<--------------------------------------------------------------------->"
+echo "4) Converting to VtK"
+echo "<--------------------------------------------------------------------->\n"
+pFlowToVTK -f diameter id velocity --binary
+
+#------------------------------------------------------------------------------

benchmarks/helicalMixer/helicalMixer_500k/settings/domainDict

@@ -0,0 +1,49 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  domainDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// Simulation domain
+globalBox                                        
+{
+    min (-0.19  -0.19 -0.02);
+    max ( 0.19   0.26  0.92);
+}
+
+boundaries
+{
+    
+    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/helicalMixer/helicalMixer_500k/settings/geometryDict

@@ -0,0 +1,60 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName  geometryDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxis; 
+
+rotatingAxisInfo
+{
+    rotAxis 
+    {
+        // end points of axis
+        p1          (0 0 0);
+        p2          (0 0 1);
+        
+        // rotation speed (rad/s) => 30 rpm
+        omega       3.1428;      
+
+        // interval for rotation of axis 
+        startTime   2.5;
+        endTime     100;
+    }
+}
+
+surfaces
+{
+    
+    helix
+    {
+        type     stlWall;       // type of the wall
+        file     helix2.stl;    // file name in stl folder
+        material wallMat;       // material name of this wall
+        motion   rotAxis;       // motion component name 
+    }
+
+    shell
+    {
+        type     stlWall;       // type of the wall
+        file     shell2.stl;    // file name in stl folder      
+        material wallMat;       // material name of this wall
+        motion   none;          // motion component name 
+    }
+        
+    plug
+    {
+        type    planeWall;
+        p1      (-0.075 -0.185 0.375);
+        p2      ( 0.075 -0.185 0.375);
+        p3      ( 0.075 -0.185 0.525);
+        p4      (-0.075 -0.185 0.525);
+        material wallMat;
+        motion   none; 
+    }
+     
+}

benchmarks/helicalMixer/helicalMixer_500k/settings/particlesDict

@@ -0,0 +1,27 @@
+/* -------------------------------*- 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)
+        rVelocity       realx3  (0 0 0);        // rotational velocity (rad/s)
+        shapeName       word    smallParticle;  // name of the particle shape 
+    }
+
+    selectors
+    {}
+}
+
+positionParticles
+{
+    method empty;     // creates the required fields with zero particles (empty). 
+}

benchmarks/helicalMixer/helicalMixer_500k/settings/settingsDict

@@ -0,0 +1,37 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName  settingsDict;
+objectType  dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+run         		helicalMixer;
+
+dt                  0.00001;      // time step for integration (s)
+
+startTime           0;            // start time for simulation
+
+endTime             2;          // end time for simulation
+
+saveInterval        0.05;         // time interval for saving the simulation
+
+timePrecision       4;            // maximum number of digits for time folder
+
+g                 	(0 -9.8 0);   // gravity vector (m/s2)
+
+// save necessary (i.e., required) data on disk
+includeObjects 		(diameter);                       
+
+// exclude unnecessary data from saving on disk
+excludeObjects 		(); 
+
+integrationMethod   	AdamsBashforth2; // integration method
+
+integrationHistory      off;             // Do not save integration history on the disk 
+
+writeFormat             binary;          // data writting format (ascii or binary)
+
+timersReport            Yes;             // report timers (Yes or No)
+
+timersReportInterval    0.05;            // time interval for reporting timers

benchmarks/helicalMixer/readme.md

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

benchmarks/helicalMixer_4MParticles/caseSetup/particleInsertion

@@ -1,67 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-
-objectName particleInsertion;
-objectType dicrionary;
-
-
-active  yes;          // is insertion active?
-
-collisionCheck No;   // not implemented for yes
-
-
-
-particleInlet1
-{
-   type		      boxRegion; // type of insertion region
-   rate 	         1000000;  // insertion rate (particles/s)
-   startTime 	   0;      // (s)
-   endTime   	   2.0;    // (s)
-   interval       0.05;  //s  
-
-   boxRegionInfo 
-   {
-   	min ( -0.17 0.23 0.46); // (m,m,m)
-   	max (  0.17 0.24 0.88); // (m,m,m)
-   }
-   
-   setFields
-   {
-     velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
-   }
-   
-   mixture
-   {
-      smallParticle 1; // mixture composition of inserted particles 
-      
-   }
-}
-
-particleInlet2
-{
-   type           boxRegion; // type of insertion region
-   rate           1000000;  // insertion rate (particles/s)
-   startTime      0;      // (s)
-   endTime        2.0;    // (s)
-   interval       0.05;  //s  
-
-   boxRegionInfo 
-   {
-      min ( -0.17 0.23 0.02); // (m,m,m)
-      max (  0.17 0.24 0.44); // (m,m,m)
-   }
-   
-   setFields
-   {
-     velocity    realx3 (0.0 -0.3 0.0); // initial velocity of inserted particles 
-   }
-   
-   mixture
-   {
-      largeParticle 1; // mixture composition of inserted particles 
-      
-   }
-}
-

benchmarks/helicalMixer_4MParticles/caseSetup/sphereShape

@@ -1,11 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-
-objectName 	sphereDict;
-objectType 	sphereShape;
-
-names 		(smallParticle largeParticle); 	// names of shapes 
-diameters 	(0.002 0.00201);				// diameter of shapes 
-materials	(glassMat glassMat);		// material names for shapes 

benchmarks/helicalMixer_4MParticles/settings/geometryDict

@@ -1,56 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-
-objectName 	geometryDict;
-objectType 	dictionary;
-
-// motion model: rotating object around an axis
-motionModel rotatingAxisMotion; 
-
-surfaces
-{
-	
-	helix
-	{
-		type 	 stlWall;   // type of the wall
-		file 	 helix2.stl;	// file name in stl folder
-		material wallMat;   // material name of this wall
-		motion 	 rotAxis;	// motion component name 
-	}
-
-	
-	shell
-	{
-		type 	 stlWall;  	// type of the wall
-		file 	 shell2.stl;	// file name in stl folder		
-		material wallMat;   // material name of this wall
-		motion 	 none;		// motion component name 
-	}
-
-		
-	plug
-	{
-		type 	planeWall;
-		p1 (-0.075 -0.185 0.375);
-		p2 ( 0.075 -0.185 0.375);
-		p3 ( 0.075 -0.185 0.525);
-		p4 (-0.075 -0.185 0.525);
-		material wallMat;   // material name of this wall
-		motion 	 none;		// motion component name 
-	}
-	
-	
-}
-
-// information for rotatingAxisMotion motion model 
-rotatingAxisMotionInfo
-{
-	rotAxis 
-	{
-		p1 ( 0 0 0);
-		p2 ( 0 0 1);
-		omega 0; //3.1428; 		// rotation speed (rad/s) => 30 rpm
-	}
-}

benchmarks/helicalMixer_4MParticles/settings/particlesDict

@@ -1,31 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-
-objectName 	particlesDict;
-objectType 	dictionary;
-
-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	smallParticle; 	// name of the particle shape 
-	}
-
-	selectors
-	{}
-}
-
-// positions particles 
-positionParticles
-{
-	method empty;     		// creates the required fields with zero particles (empty). 
-
-	maxNumberOfParticles 	4100000; // maximum number of particles in the simulation
-	mortonSorting 			Yes;    // perform initial sorting based on morton code?   
-
-}

benchmarks/helicalMixer_4MParticles/settings/settingsDict

@@ -1,36 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */  
-objectName 	settingsDict;
-objectType 	dictionary;;
-
-run 			inclinedScrewConveyor;
-
-dt 				0.00001; 	// time step for integration (s)
-
-startTime 		2.9; 			// start time for simulation 
-
-endTime 		7;			// end time for simulation 
-
-saveInterval 	0.05; 		// time interval for saving the simulation
-
-timePrecision   3;			// maximum number of digits for time folder 
-
-g 				(0 -9.8 0); // gravity vector (m/s2) 
-
-/*
-	Simulation domain 
-	every particles that goes outside this domain is deleted.
-*/
-domain 
-{
-	min (-0.19  -0.19 -0.02);
-	max ( 0.19   0.26  0.92);
-}
-
-integrationMethod 		AdamsBashforth2; 	// integration method 
-
-timersReport 			Yes;  	// report timers?
-
-timersReportInterval   	0.01;	// time interval for reporting timers

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

@@ -2,13 +2,14 @@
 |  phasicFlow File                                                            | 
 |  copyright: www.cemf.ir                                                     | 
 \* ------------------------------------------------------------------------- */ 
-objectName particleInsertion;
+
-objectType dicrionary;
+objectName     shapes;
-fileFormat  ASCII;
+objectType     dictionary;
+fileFormat     ASCII;
 /*---------------------------------------------------------------------------*/
 
-active  no;          // is insertion active?
+names          (glassBead);    // names of shapes 
-
-collisionCheck No;   // not implemented for yes
 
+diameters      (0.004);        // diameter of shapes 
 
+materials      (glassMat);     // material names for shapes 

benchmarks/rotatingDrum/rotatingDrum_1mParticles/runThisCase

@@ -1,4 +1,5 @@
 #!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
 cd ${0%/*} || exit 1    # Run from this directory
 echo "\n<--------------------------------------------------------------------->"
 echo "1) Creating particles"
@@ -15,9 +16,7 @@ echo "3) Running the case"
 echo "<--------------------------------------------------------------------->\n"
 sphereGranFlow
 
-echo "\n<--------------------------------------------------------------------->"
+
-echo "4) Converting to VtK"
+
-echo "<--------------------------------------------------------------------->\n"
-pFlowToVTK -f diameter id velocity
 
 #------------------------------------------------------------------------------

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

@@ -0,0 +1,15 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+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/runThisCase

@@ -0,0 +1,22 @@
+#!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
+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 +1,22 @@
+#!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
+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

@@ -0,0 +1,15 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+
+objectName     shapes;
+objectType     dictionary;
+fileFormat     ASCII;
+/*---------------------------------------------------------------------------*/
+
+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 +1,22 @@
+#!/bin/sh
+set -e  # Exit immediately if a command exits with a non-zero status
+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