add scale factor in GeometryDict

.github/scripts/sync-wiki.py

@@ -1,153 +0,0 @@
-#!/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

@@ -1,60 +0,0 @@
-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

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

@@ -66,13 +66,12 @@ 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, requireRVel);
+		return wordvCtorSelector_[demSystemName] (demSystemName, domains, argc, argv);
 	}
 	else
 	{

DEMSystems/DEMSystem/DEMSystem.hpp

@@ -71,15 +71,13 @@ 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
@@ -98,7 +96,7 @@ public:
 		return Control_();
 	}
 
-	auto inline constexpr usingDouble()const
+	auto inline constexpr usingDoulle()const
 	{
 		return pFlow::usingDouble__;
 	}
@@ -123,9 +121,6 @@ public:
 	virtual
 	span<real> diameter() = 0; 
 
-	virtual 
-	span<uint32> particleId() = 0;
-
 	virtual 
 	span<real> courseGrainFactor() = 0;
 
@@ -181,8 +176,7 @@ public:
 			word  demSystemName,
 			const std::vector<box>& domains, 
 			int argc, 
-			char* argv[],
+			char* argv[]);
-			bool requireRVel=false);
 
 };
 

DEMSystems/grainDEMSystem/grainDEMSystem.cpp

@@ -163,12 +163,6 @@ 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());
@@ -239,7 +233,6 @@ 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

@@ -63,8 +63,6 @@ protected:
 
 	ViewType1D<real, HostSpace> 	diameterHost_;
 
-	ViewType1D<uint32, HostSpace> 	particleIdHost_;
-
 	bool 							requireRVel_ = false;
 
 	ViewType1D<realx3, HostSpace> 	rVelocityHost_;
@@ -124,8 +122,6 @@ 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

@@ -165,11 +165,6 @@ 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());
@@ -240,7 +235,6 @@ 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

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

benchmarks/helicalMixer/helicalMixer_1m/caseSetup/interaction

@@ -1,53 +0,0 @@
-/* -------------------------------*- 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_1m/caseSetup/particleInsertion

@@ -1,72 +0,0 @@
-/* -------------------------------*- 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

@@ -1,12 +0,0 @@
-/* -------------------------------*- C++ -*--------------------------------- *\ 
-|  phasicFlow File                                                            | 
-|  copyright: www.cemf.ir                                                     | 
-\* ------------------------------------------------------------------------- */ 
-objectName  shapes;
-objectType  dictionary;
-fileFormat  ASCII;
-/*---------------------------------------------------------------------------*/
-
-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

@@ -1,7 +0,0 @@
-#!/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

@@ -1,32 +0,0 @@
-#!/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

@@ -1,49 +0,0 @@
-/* -------------------------------*- 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

@@ -1,60 +0,0 @@
-/* -------------------------------*- 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

@@ -1,27 +0,0 @@
-/* -------------------------------*- 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

@@ -1,37 +0,0 @@
-/* -------------------------------*- 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_250K/caseSetup/interaction

@@ -1,53 +0,0 @@
-/* -------------------------------*- 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

@@ -1,72 +0,0 @@
-/* -------------------------------*- 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/cleanThisCase

@@ -1,8 +0,0 @@
-#!/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

@@ -1,30 +0,0 @@
-#!/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

@@ -1,49 +0,0 @@
-/* -------------------------------*- 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

@@ -1,60 +0,0 @@
-/* -------------------------------*- 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

@@ -1,27 +0,0 @@
-/* -------------------------------*- 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

@@ -1,37 +0,0 @@
-/* -------------------------------*- 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/particleInsertion

@@ -1,72 +0,0 @@
-/* -------------------------------*- 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/cleanThisCase

@@ -1,7 +0,0 @@
-#!/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

@@ -1,32 +0,0 @@
-#!/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

@@ -1,49 +0,0 @@
-/* -------------------------------*- 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

@@ -1,60 +0,0 @@
-/* -------------------------------*- 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

@@ -1,27 +0,0 @@
-/* -------------------------------*- 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

@@ -1,37 +0,0 @@
-/* -------------------------------*- 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_4m/caseSetup/interaction

@@ -1,53 +0,0 @@
-/* -------------------------------*- 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

@@ -1,72 +0,0 @@
-/* -------------------------------*- 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/cleanThisCase

@@ -1,7 +0,0 @@
-#!/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

@@ -1,32 +0,0 @@
-#!/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

@@ -1,49 +0,0 @@
-/* -------------------------------*- 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

@@ -1,60 +0,0 @@
-/* -------------------------------*- 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

@@ -1,27 +0,0 @@
-/* -------------------------------*- 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

@@ -1,37 +0,0 @@
-/* -------------------------------*- 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_500k/caseSetup/interaction

@@ -1,53 +0,0 @@
-/* -------------------------------*- 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

@@ -1,72 +0,0 @@
-/* -------------------------------*- 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

@@ -1,12 +0,0 @@
-/* -------------------------------*- 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

@@ -1,7 +0,0 @@
-#!/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

@@ -1,32 +0,0 @@
-#!/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

@@ -1,49 +0,0 @@
-/* -------------------------------*- 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

@@ -1,60 +0,0 @@
-/* -------------------------------*- 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

@@ -1,27 +0,0 @@
-/* -------------------------------*- 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

@@ -1,37 +0,0 @@
-/* -------------------------------*- 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/readme.md

@@ -1,101 +0,0 @@
-# Helical Mixer Benchmark (phasicFlow v-1.0)
-
-## Overview
-
-This benchmark compares the performance of phasicFlow with a well-stablished commercial DEM software for simulating a helical mixer with varying particle counts (250k to 4M particles). The benchmark measures both computational efficiency and memory usage across different hardware configurations.
-
-**Summary of Results:**
-
-- phasicFlow achieves similar performance to the commercial DEM software on the same hardware.
-- phasicFlow shows a 30% performance improvement when using the NVIDIA RTX A4000 compared to the RTX 4050Ti.
-- Memory usage is approximately 50% lower in phasicFlow compared to the commercial software, with phasicFlow using about 0.7 GB of memory per million particles, while the commercial software uses about 1.5 GB per million particles.
-
-## 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 helical mixer simulations.
-</div>
-
-| Case     | Particle Diameter | Particle Count | 
-| :-------: | :---------------: | :--------------: | 
-| 250k     | 6 mm              | 250,000        | 
-| 500k     | 5 mm              | 500,000        | 
-| 1M       | 4 mm              | 1,000,000      | 
-| 2M       | 3 mm              | 2,000,000      | 
-| 4M       | 2 mm              | 4,000,000      |
-
-The time step for all simulations was set to 1.0e-5 seconds and the simulation ran for 7.5 seconds.
-
-## Performance Comparison
-
-### Execution Time
-
-<div align="center">
-    Table 3. Total calculation time (minutes) for different configurations.
-</div>
-
-|     Software      | 250k   | 500k   | 1M     | 2M     | 4M     | 
-| :---------------: | :----: | :-----: | :-----: | :-----: | :-----: |
-| phasicFlow-4050Ti | 110 min | 215 min | 413 min | - | -       | 
-| Commercial DEM-4050Ti | 111 min | 210 min | 415 min | - | -       | 
-| phasicFlow-A4000  | 82 min | 150 min  | 300 min | 613 min | 1236 min |
-
-The execution time scales linearly with particle count. phasicFlow demonstrates approximately:
-
-- the computing speed is basically the same as 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/performance.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      | 
-| :---------------: | :-----: | :-----: | :-----: | :-----: | :-----: | 
-| phasicFlow-4050Ti | 260 MB  | 404 MB  | 710 MB  | - | -       | 
-| Commercial DEM-4050Ti | 460 MB | 920 MB | 1574 MB | - | -       | 
-| phasicFlow-A4000  | 352 MB  | 496 MB  | 802 MB  | 1376 MB | 2310 MB |
-
-Memory efficiency comparison:
-
-- phasicFlow uses approximately 0.7 GB of memory per million particles
-- Commercial DEM software uses approximately 1.5 GB of memory per million particles
-- phasicFlow shows ~50% 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/helicalMixer_4MParticles/caseSetup/interaction

@@ -2,21 +2,18 @@
 |  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]
@@ -31,6 +28,9 @@ 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);
 
@@ -41,13 +41,19 @@ model
 
 contactSearch
 {
-    method         NBS;  
+   method         NBS;           
+   wallMapping    cellMapping;   
 
-    updateInterval   10;
+   NBSInfo
+   {
+      updateFrequency 10;        // each 20 timesteps, update neighbor list 
+      sizeRatio      1.1;       // bounding box size to particle diameter (max)
+   }
 
-    sizeRatio       1.1;
+   cellMappingInfo
+   {
+      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_4MParticles/caseSetup/particleInsertion

@@ -0,0 +1,67 @@
+/* -------------------------------*- 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

@@ -0,0 +1,11 @@
+/* -------------------------------*- 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/runThisCase

@@ -1,5 +1,4 @@
 #!/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"
@@ -16,7 +15,9 @@ echo "3) Running the case"
 echo "<--------------------------------------------------------------------->\n"
 sphereGranFlow
 
-
+echo "\n<--------------------------------------------------------------------->"
-
+echo "4) Converting to VtK"
+echo "<--------------------------------------------------------------------->\n"
+pFlowToVTK -f diameter id velocity
 
 #------------------------------------------------------------------------------

benchmarks/helicalMixer_4MParticles/settings/geometryDict

@@ -0,0 +1,56 @@
+/* -------------------------------*- 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

@@ -0,0 +1,31 @@
+/* -------------------------------*- 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

@@ -0,0 +1,36 @@
+/* -------------------------------*- 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

@@ -1,9 +0,0 @@
-
-# Benchmarks
-
-Benchmakrs has been done on two different simulations: simulation with simple geometry (rotating drum) and a simulation with complex geometry (helical mixer). These benchmarks are used to show how PhasicFlow performs in different scenarios.
-
-- [rotating drum](./rotatingDrum/)
-- [helical mixer](./helicalMixer/)
-
-**Note:** If you have performed benchmarks with PhasicFlow using other hardware or software other than PhasicFlow, we would be happy to include them in this section. Please open an issue for more arrangements or send a pull request with the benchmarks results.

benchmarks/rotatingDrum/readme.md

@@ -1,102 +0,0 @@
-# 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.
-
-**Summary of Results:**
-
-- phasicFlow achieves approximately 20% faster calculation than the commercial DEM software on the same hardware.
-- phasicFlow shows a 30% performance improvement when using the NVIDIA RTX A4000 compared to the RTX 4050Ti.
-- Memory usage is approximately 42% lower in phasicFlow compared to the commercial software, with phasicFlow using about 0.7 GB of memory per million particles, while the commercial software uses about 1.2 GB per million particles
-
-## 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/runThisCase

@@ -1,5 +1,4 @@
 #!/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"

benchmarks/rotatingDrum/rotatingDrum_1mParticles/settings/geometryDict

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

benchmarks/rotatingDrum/rotatingDrum_1mParticles/settings/particlesDict

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

benchmarks/rotatingDrum/rotatingDrum_250kParticles/runThisCase

@@ -1,5 +1,4 @@
 #!/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"

benchmarks/rotatingDrum/rotatingDrum_250kParticles/settings/geometryDict

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

benchmarks/rotatingDrum/rotatingDrum_250kParticles/settings/particlesDict

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

benchmarks/rotatingDrum/rotatingDrum_2mParticles/runThisCase

@@ -1,5 +1,4 @@
 #!/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"

benchmarks/rotatingDrum/rotatingDrum_2mParticles/settings/geometryDict

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

benchmarks/rotatingDrum/rotatingDrum_2mParticles/settings/particlesDict

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

benchmarks/rotatingDrum/rotatingDrum_4mParticles/runThisCase

@@ -1,5 +1,4 @@
 #!/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"

benchmarks/rotatingDrum/rotatingDrum_4mParticles/settings/geometryDict

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

benchmarks/rotatingDrum/rotatingDrum_4mParticles/settings/particlesDict

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

benchmarks/rotatingDrum/rotatingDrum_500kParticles/settings/geometryDict

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

benchmarks/rotatingDrum/rotatingDrum_500kParticles/settings/particlesDict

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

benchmarks/rotatingDrum/rotatingDrum_8mParticles/runThisCase

@@ -1,5 +1,4 @@
 #!/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"

benchmarks/rotatingDrum/rotatingDrum_8mParticles/settings/geometryDict

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

benchmarks/rotatingDrum/rotatingDrum_8mParticles/settings/particlesDict

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

cmake/bashrc

@@ -19,7 +19,7 @@ export pFlow_SRC_DIR="$pFlow_PROJECT_DIR/src"
 
 export Kokkos_DIR="$kokkosDir"
 
-#export Zoltan_DIR="$projectDir/Zoltan"
+export Zoltan_DIR="$projectDir/Zoltan"
 
 # Cleanup variables (done as final statement for a clean exit code)
 unset projectDir

cmake/zoltanInstallCheck.cmake

@@ -1,44 +0,0 @@
-# Macro to check for Zoltan installation and build it if needed
-# Usage: zoltan_find_or_build(ZOLTAN_DIR)
-# Returns: ZOLTAN_INCLUDE_DIR, ZOLTAN_LIBRARY
-
-macro(zoltan_find_or_build ZOLTAN_DIR)
-    # Set the Zoltan directory
-    set(ZOLTAN_PREFIX "${ZOLTAN_DIR}" CACHE STRING "Zoltan install directory")
-    message(STATUS "Zoltan install directory is ${ZOLTAN_PREFIX}")
-
-    # Check if the Zoltan library is already built
-    find_path(ZOLTAN_INCLUDE_DIR zoltan.h PATHS "${ZOLTAN_PREFIX}/include")
-    message(STATUS "Zoltan include path: ${ZOLTAN_INCLUDE_DIR}")
-
-    find_library(ZOLTAN_LIBRARY zoltan PATHS "${ZOLTAN_PREFIX}/lib")
-    message(STATUS "Zoltan lib path: ${ZOLTAN_LIBRARY}")
-    
-    # Check if Zoltan library exists, if not compile it using buildlib script
-    if(NOT ZOLTAN_LIBRARY)
-        message(STATUS "Zoltan library not found. Compiling from source using buildlib script...")
-
-        # Execute the buildlib bash script
-        execute_process(
-            COMMAND bash ${ZOLTAN_PREFIX}/buildlib
-            WORKING_DIRECTORY ${ZOLTAN_PREFIX}
-            RESULT_VARIABLE ZOLTAN_BUILD_RESULT
-            OUTPUT_VARIABLE ZOLTAN_BUILD_OUTPUT
-            ERROR_VARIABLE ZOLTAN_BUILD_ERROR
-        )
-
-        if(NOT ZOLTAN_BUILD_RESULT EQUAL 0)
-            message(FATAL_ERROR "Failed to build Zoltan library using buildlib script. Error: ${ZOLTAN_BUILD_ERROR}")
-        endif()
-
-        # Try to find the library again after building
-        find_library(ZOLTAN_LIBRARY zoltan PATHS "${ZOLTAN_PREFIX}/lib" NO_DEFAULT_PATH)
-        find_path(ZOLTAN_INCLUDE_DIR zoltan.h PATHS "${ZOLTAN_PREFIX}/include" NO_DEFAULT_PATH)
-
-        if(NOT ZOLTAN_LIBRARY)
-            message(FATAL_ERROR "Failed to locate Zoltan library after building")
-        endif()
-
-        message(STATUS "Successfully built Zoltan library at ${ZOLTAN_LIBRARY}")
-    endif()
-endmacro()

doc/mdDocs/howToBuild-V1.0.md

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

doc/mdDocs/howToBuild.md

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

doc/mdDocs/markdownList.yml

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

doc/mdDocs/phasicFlowFeatures.md

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

src/Integration/AdamsBashforth2/processorAB2BoundaryIntegration.cpp

@@ -1,71 +0,0 @@
-#include "processorAB2BoundaryIntegration.hpp"
-#include "AdamsBashforth2.hpp"
-#include "AB2Kernels.hpp"
-#include "boundaryConfigs.hpp"
-
-pFlow::processorAB2BoundaryIntegration::processorAB2BoundaryIntegration(
-    const boundaryBase &boundary, 
-    const pointStructure &pStruct,  
-    const word &method,
-    integration& intgrtn
-)
-:
-    boundaryIntegration(boundary, pStruct, method, intgrtn)
-{}
-
-bool pFlow::processorAB2BoundaryIntegration::correct(
-    real dt, 
-	const realx3PointField_D& y, 
-	const realx3PointField_D& dy
-)
-{
-
-#ifndef BoundaryModel1
-    if(this->isBoundaryMaster())
-    {
-        const uint32 thisIndex = thisBoundaryIndex();
-		const auto&  AB2 =  static_cast<const AdamsBashforth2&>(Integration());
-        const auto& dy1View = AB2.BoundaryField(thisIndex).neighborProcField().deviceView();
-		const auto& dyView = dy.BoundaryField(thisIndex).neighborProcField().deviceView();
-		const auto& yView = y.BoundaryField(thisIndex).neighborProcField().deviceView();        
-        const rangeU32 aRange(0u, dy1View.size());
-        return  AB2Kernels::intAllActive(
-			"AB2Integration::correct."+this->boundaryName(), 
-			dt,
-            aRange, 
-			yView, 
-			dyView, 
-			dy1View
-		); 
-    }
-#endif //BoundaryModel1
-    
-    
-    return true;
-}
-
-bool pFlow::processorAB2BoundaryIntegration::correctPStruct(real dt, const realx3PointField_D &vel)
-{
-
-	#ifndef BoundaryModel1
-    if(this->isBoundaryMaster())
-    {
-		const uint32 thisIndex = thisBoundaryIndex();
-		const auto&  AB2 =  static_cast<const AdamsBashforth2&>(Integration());
-		const auto& dy1View = AB2.BoundaryField(thisIndex).neighborProcField().deviceView();
-		const auto& velView = vel.BoundaryField(thisIndex).neighborProcField().deviceView();
-		const auto& xposView = boundary().neighborProcPoints().deviceView();        
-		const rangeU32 aRange(0u, dy1View.size());
-		return  AB2Kernels::intAllActive(
-			"AB2Integration::correctPStruct."+this->boundaryName(), 
-			dt,
-			aRange, 
-			xposView, 
-			velView, 
-			dy1View
-		); 
-    }
-#endif //BoundaryModel1
-    
-    return true;
-}

src/Integration/AdamsBashforth2/processorAB2BoundaryIntegration.hpp

@@ -1,51 +0,0 @@
-
-
-#ifndef __processorAB2BoundaryIntegration_hpp__
-#define __processorAB2BoundaryIntegration_hpp__
-
-#include "boundaryIntegration.hpp"
-
-namespace pFlow
-{
-
-class processorAB2BoundaryIntegration
-:
-    public boundaryIntegration
-{   
-public:
-
-    TypeInfo("boundaryIntegration<processor,AdamsBashforth2>");
-
-    processorAB2BoundaryIntegration(
-        const boundaryBase& boundary,
-        const pointStructure& pStruct, 
-        const word& method,
-        integration& intgrtn
-    );
-
-    ~processorAB2BoundaryIntegration()override=default;
-
-    
-	bool correct(
-        real dt, 
-        const realx3PointField_D& y, 
-        const realx3PointField_D& dy)override;
-	
-
-    
-    bool correctPStruct(real dt, const realx3PointField_D& vel)override;
-    
-    
-    add_vCtor(
-        boundaryIntegration,
-        processorAB2BoundaryIntegration,
-        boundaryBase
-    );
-
-    
-
-};
-
-}
-
-#endif

src/Interaction/contactSearch/boundaries/processorBoundaryContactSearch/processorBoundaryContactSearch.cpp

@@ -1,111 +0,0 @@
-/*------------------------------- phasicFlow ---------------------------------
-      O        C enter of
-     O O       E ngineering and
-    O   O      M ultiscale modeling of
-   OOOOOOO     F luid flow
-------------------------------------------------------------------------------
-  Copyright (C): www.cemf.ir
-  email: hamid.r.norouzi AT gmail.com
-------------------------------------------------------------------------------
-Licence:
-  This file is part of phasicFlow code. It is a free software for simulating
-  granular and multiphase flows. You can redistribute it and/or modify it under
-  the terms of GNU General Public License v3 or any other later versions.
-
-  phasicFlow is distributed to help others in their research in the field of
-  granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
-  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
------------------------------------------------------------------------------*/
-
-#include "processorBoundaryContactSearch.hpp"
-#include "contactSearch.hpp"
-#include "particles.hpp"
-//#include "pointStructure.hpp"
-//#include "geometry.hpp"
-
-
-void pFlow::processorBoundaryContactSearch::setSearchBox()
-{
-       
-    auto l = boundary().neighborLength();
-    auto n = boundary().boundaryPlane().normal();
-    auto pp1 = boundary().boundaryPlane().parallelPlane(l);
-    auto pp2 = boundary().boundaryPlane().parallelPlane(-l);
-
-    realx3 minP1 = min(min(min(pp1.p1(), pp1.p2()), pp1.p3()), pp1.p4());
-    realx3 maxP1 = max(max(max(pp1.p1(), pp1.p2()), pp1.p3()), pp1.p4());
-
-    realx3 minP2 = min(min(min(pp2.p1(), pp2.p2()), pp2.p3()), pp2.p4());
-    realx3 maxP2 = max(max(max(pp2.p1(), pp2.p2()), pp2.p3()), pp2.p4());
-
-    auto minP = min(minP1, minP2) - l*(realx3(1.0)-abs(n));
-    auto maxP = max(maxP1, maxP2) + l*(realx3(1.0)-abs(n));
-    
-    searchBox_={minP, maxP};
-}
-
-pFlow::processorBoundaryContactSearch::processorBoundaryContactSearch(
-    const dictionary &dict,
-    const boundaryBase &boundary,
-    const contactSearch &cSearch)
-: 
-    boundaryContactSearch(dict, boundary, cSearch),
-    diameter_(cSearch.Particles().boundingSphere()),
-    masterSearch_(this->isBoundaryMaster()),
-    sizeRatio_(dict.getVal<real>("sizeRatio"))
-{
-    
-    if(masterSearch_)
-    {        
-        setSearchBox();
-        
-        real minD;
-        real maxD;
-        cSearch.Particles().boundingSphereMinMax(minD, maxD);
-        
-        ppContactSearch_ = makeUnique<twoPartContactSearch>(
-            searchBox_,
-            maxD,
-            sizeRatio_);
-    }
-    else
-    {
-        searchBox_={{0,0,0},{0,0,0}};
-    }
-}
-
-bool pFlow::processorBoundaryContactSearch::broadSearch
-(
-    uint32 iter, 
-    real t, 
-    real dt, 
-    csPairContainerType &ppPairs, 
-    csPairContainerType &pwPairs, 
-    bool force
-)
-{
-    if(masterSearch_)
-    {
-        const auto thisPoints = boundary().thisPoints();
-        const auto& neighborProcPoints = boundary().neighborProcPoints();
-        const auto& bDiams = diameter_.BoundaryField(thisBoundaryIndex());
-        const auto thisDiams = bDiams.thisField();
-        const auto& neighborProcDiams = bDiams.neighborProcField();
-        
-        ppContactSearch_().broadSearchPP(
-            ppPairs, 
-            thisPoints, 
-            thisDiams,
-            neighborProcPoints,
-            neighborProcDiams,
-            boundaryName()
-        );
-        //pOutput<<"ppSize "<< ppPairs.size()<<endl;
-        return true;
-
-    }else
-    {
-        return true;
-    }
-}

src/Interaction/contactSearch/boundaries/processorBoundaryContactSearch/processorBoundaryContactSearch.hpp

@@ -1,76 +0,0 @@
-/*------------------------------- phasicFlow ---------------------------------
-      O        C enter of
-     O O       E ngineering and
-    O   O      M ultiscale modeling of
-   OOOOOOO     F luid flow
-------------------------------------------------------------------------------
-  Copyright (C): www.cemf.ir
-  email: hamid.r.norouzi AT gmail.com
-------------------------------------------------------------------------------
-Licence:
-  This file is part of phasicFlow code. It is a free software for simulating
-  granular and multiphase flows. You can redistribute it and/or modify it under
-  the terms of GNU General Public License v3 or any other later versions.
-
-  phasicFlow is distributed to help others in their research in the field of
-  granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
-  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
------------------------------------------------------------------------------*/
-#ifndef __processorBoundaryContactSearch_hpp__
-#define __processorBoundaryContactSearch_hpp__
-
-#include "boundaryContactSearch.hpp"
-#include "pointFields.hpp"
-#include "twoPartContactSearch.hpp"
-
-namespace pFlow
-{
-
-class processorBoundaryContactSearch : public boundaryContactSearch
-{
-private:
-
-	box                             searchBox_;
-
-	uniquePtr<twoPartContactSearch> ppContactSearch_ = nullptr;
-
-	const realPointField_D&         diameter_;
-
-	bool                            masterSearch_;
-
-	real 							sizeRatio_;
-
-	void                            setSearchBox();
-
-public:
-
-	TypeInfo("boundaryContactSearch<MPI,processor>")
-
-	  processorBoundaryContactSearch(
-	    const dictionary&    dict,
-	    const boundaryBase&  boundary,
-	    const contactSearch& cSearch
-	  );
-
-	~processorBoundaryContactSearch() override = default;
-
-	add_vCtor(
-	  boundaryContactSearch,
-	  processorBoundaryContactSearch,
-	  boundaryBase
-	);
-
-	bool broadSearch(
-	  uint32               iter,
-	  real                 t,
-	  real                 dt,
-	  csPairContainerType& ppPairs,
-	  csPairContainerType& pwPairs,
-	  bool                 force = false
-	) override;
-};
-
-}
-
-#endif //__processorBoundaryContactSearch_hpp__

src/Interaction/contactSearch/boundaries/twoPartContactSearch/twoPartContactSearch.cpp

@@ -1,163 +0,0 @@
-
-#include "twoPartContactSearch.hpp"
-#include "twoPartContactSearchKernels.hpp"
-#include "phasicFlowKokkos.hpp"
-#include "streams.hpp"
-
-void pFlow::twoPartContactSearch::checkAllocateNext(uint32 n)
-{
-	if( nextCapacity_ < n)
-	{
-		nextCapacity_ = n;	
-		reallocNoInit(next_, n);
-	}
-}
-
-void pFlow::twoPartContactSearch::nullifyHead()
-{
-	fill(head_, static_cast<uint32>(-1));
-}
-
-void pFlow::twoPartContactSearch::nullifyNext(uint32 n)
-{
-	fill(next_, 0u, n, static_cast<uint32>(-1));
-}
-
-void pFlow::twoPartContactSearch::buildList(
-	const deviceScatteredFieldAccess<realx3> &points)
-{
-	if(points.empty())return;
-	uint32 n = points.size();
-	checkAllocateNext(n);
-	nullifyNext(n);
-	nullifyHead();
-	
-	pFlow::twoPartContactSearchKernels::buildNextHead(
-		points,
-		searchCells_,
-		head_,
-		next_
-	);
-}
-
-pFlow::twoPartContactSearch::twoPartContactSearch
-(
-    const box &domain,
-    real cellSize,
-	real sizeRatio
-)
-:
-	searchCells_(domain, cellSize),
-	head_("periodic:head",searchCells_.nx(), searchCells_.ny(), searchCells_.nz()),
-	sizeRatio_(sizeRatio)
-{
-
-}
-
-bool pFlow::twoPartContactSearch::broadSearchPP
-(
-	csPairContainerType &ppPairs, 
-	const deviceScatteredFieldAccess<realx3> &points1, 
-	const deviceScatteredFieldAccess<real>& diams1, 
-	const deviceScatteredFieldAccess<realx3> &points2, 
-	const deviceScatteredFieldAccess<real>& diams2, 
-	const realx3& transferVec
-)
-{
-	if(points1.empty())return true;
-	if(points2.empty()) return true;
-
-	buildList(points1);
-
-	uint32 nNotInserted = 1;
-
-	// loop until the container size fits the numebr of contact pairs
-	while (nNotInserted > 0)
-	{
-
-		nNotInserted = pFlow::twoPartContactSearchKernels::broadSearchPP
-		(
-			ppPairs,
-			points1,
-			diams1,
-			points2,
-			diams2,
-			transferVec,
-			head_,
-			next_,
-			searchCells_,
-			sizeRatio_
-		);
-		
-	
-		if(nNotInserted)
-		{
-			// - resize the container
-			//   note that getFull now shows the number of failed insertions.
-			uint32 len = max(nNotInserted,100u) ;
-			
-			auto oldCap = ppPairs.capacity();
-			
-			ppPairs.increaseCapacityBy(len);
-
-			INFORMATION<< "Particle-particle contact pair container capacity increased from "<<
-			oldCap << " to "<<ppPairs.capacity()<<" in contact search in boundary region."<<END_INFO;
-			
-		}
-
-	}	
-	
-    return true;
-}
-
-bool pFlow::twoPartContactSearch::broadSearchPP
-(
-	csPairContainerType &ppPairs,
-	const deviceScatteredFieldAccess<realx3> &points1,
-	const deviceScatteredFieldAccess<real> &diams1,
-	const realx3Vector_D& points2,
-	const realVector_D& diams2,
-	const word& name
-)
-{
-	buildList(points1);
-
-	uint32 nNotInserted = 1;
-
-	// loop until the container size fits the numebr of contact pairs
-	while (nNotInserted > 0)
-	{
-
-		nNotInserted = pFlow::twoPartContactSearchKernels::broadSearchPP
-		(
-			ppPairs,
-			points1,
-			diams1,
-			points2,
-			diams2,
-			head_,
-			next_,
-			searchCells_,
-			sizeRatio_
-		);
-		
-	
-		if(nNotInserted)
-		{
-			// - resize the container
-			//   note that getFull now shows the number of failed insertions.
-			uint32 len = max(nNotInserted,100u) ;
-			
-			auto oldCap = ppPairs.capacity();
-			
-			ppPairs.increaseCapacityBy(len);
-			
-			INFORMATION<< "Particle-particle contact pair container capacity increased from "<<
-			oldCap << " to "<<ppPairs.capacity()<<" in boundary contact search in "<< name <<END_INFO;
-			
-		}
-
-	}	
-	
-    return true;
-}

src/Interaction/contactSearch/boundaries/twoPartContactSearch/twoPartContactSearch.hpp

@@ -1,104 +0,0 @@
-/*------------------------------- phasicFlow ---------------------------------
-	  O        C enter of
-	 O O       E ngineering and
-	O   O      M ultiscale modeling of
-   OOOOOOO     F luid flow
-------------------------------------------------------------------------------
-  Copyright (C): www.cemf.ir
-  email: hamid.r.norouzi AT gmail.com
-------------------------------------------------------------------------------
-Licence:
-  This file is part of phasicFlow code. It is a free software for simulating
-  granular and multiphase flows. You can redistribute it and/or modify it under
-  the terms of GNU General Public License v3 or any other later versions.
-
-  phasicFlow is distributed to help others in their research in the field of
-  granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
-  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
------------------------------------------------------------------------------*/
-
-#ifndef __twoPartContactSearch_hpp__
-#define __twoPartContactSearch_hpp__
-
-#include "contactSearchGlobals.hpp"
-#include "scatteredFieldAccess.hpp"
-#include "cells.hpp"
-#include "VectorSingles.hpp"
-
-namespace pFlow
-{
-
-class twoPartContactSearch
-{
-public:
-	using HeadType = deviceViewType3D<uint32>;
-
-	using NextType = deviceViewType1D<uint32>;
-
-private:
-
-	cells    searchCells_;
-
-	HeadType head_{ "periodic::head", 1, 1, 1 };
-
-	NextType next_{ "periodic::next", 1 };
-
-	real     sizeRatio_ = 1.0;
-
-	uint32   nextCapacity_ = 0;
-
-	void checkAllocateNext(uint32 n);
-
-	void nullifyHead();
-
-	void nullifyNext(uint32 n);
-
-	void buildList(
-		const deviceScatteredFieldAccess<realx3> &points);
-
-public:
-	twoPartContactSearch(
-		const box &domain,
-		real cellSize,
-		real sizeRatio = 1.0);
-
-	/// @brief Perform a broad-search for spheres in two adjacent regions.
-	/// Region 1 is considered as the master (primary) region and region 2 as slave 
-	/// @param ppPairs pairs container which holds i and j
-	/// @param points1 point positions in region 1
-	/// @param diams1  diameter of spheres in region 1
-	/// @param points2 point positions in region 2
-	/// @param diams2 diameter of spheres in region 2
-	/// @param transferVec a vector to transfer points from region 2 to region 1
-	/// @return true if it is successful 
-	bool broadSearchPP(
-		csPairContainerType &ppPairs,
-		const deviceScatteredFieldAccess<realx3> &points1,
-		const deviceScatteredFieldAccess<real> &diams1,
-		const deviceScatteredFieldAccess<realx3> &points2,
-		const deviceScatteredFieldAccess<real> &diams2,
-		const realx3 &transferVec);
-	
-	bool broadSearchPP(
-		csPairContainerType &ppPairs,
-		const deviceScatteredFieldAccess<realx3> &points1,
-		const deviceScatteredFieldAccess<real> &diams1,
-		const realx3Vector_D& points2,
-		const realVector_D& diams2,
-		const word& name);
-
-	const auto& searchCells()const
-	{
-		return searchCells_;
-	}
-
-	real sizeRatio()const
-	{
-		return sizeRatio_;
-	}
-};
-
-}
-
-#endif //__twoPartContactSearch_hpp__

src/Interaction/contactSearch/boundaries/twoPartContactSearch/twoPartContactSearchKernels.cpp

@@ -1,186 +0,0 @@
-#include "twoPartContactSearchKernels.hpp"
-
-INLINE_FUNCTION_HD
-bool
-sphereSphereCheckB(
-  const pFlow::realx3& p1,
-  const pFlow::realx3  p2,
-  pFlow::real          d1,
-  pFlow::real          d2
-)
-{
-	return pFlow::length(p2 - p1) < 0.5 * (d2 + d1);
-}
-
-void
-pFlow::twoPartContactSearchKernels::buildNextHead(
-  const deviceScatteredFieldAccess<realx3>& points,
-  const cells&                              searchCells,
-  deviceViewType3D<uint32>&                 head,
-  deviceViewType1D<uint32>&                 next
-)
-{
-	
-	uint32 n = points.size();
-
-	Kokkos::parallel_for(
-	  "pFlow::ppwBndryContactSearch::buildList",
-	  deviceRPolicyStatic(0, n),
-	  LAMBDA_HD(uint32 i) {
-		  int32x3 ind;
-		  if (searchCells.pointIndexInDomain(points[i], ind))
-		  {
-			  // discards points out of searchCell
-			  uint32 old =
-			    Kokkos::atomic_exchange(&head(ind.x(), ind.y(), ind.z()), i);
-			  next[i] = old;
-		  }
-	  }
-	);
-	Kokkos::fence();
-}
-
-pFlow::uint32
-pFlow::twoPartContactSearchKernels::broadSearchPP(
-  csPairContainerType&                      ppPairs,
-  const deviceScatteredFieldAccess<realx3>& points,
-  const deviceScatteredFieldAccess<real>&   diams,
-  const deviceScatteredFieldAccess<realx3>& mirrorPoints,
-  const deviceScatteredFieldAccess<real>&   mirrorDiams,
-  const realx3&                             transferVec,
-  const deviceViewType3D<uint32>&           head,
-  const deviceViewType1D<uint32>&           next,
-  const cells&                              searchCells,
-  const real                                sizeRatio
-)
-{
-	if (points.empty())
-		return 0;
-	if (mirrorPoints.empty())
-		return 0;
-
-	auto   nMirror = mirrorPoints.size();
-
-	uint32 getFull = 0;
-
-	Kokkos::parallel_reduce(
-	  "pFlow::twoPartContactSearchKernels::broadSearchPP",
-	  deviceRPolicyStatic(0, nMirror),
-	  LAMBDA_HD(const uint32 mrrI, uint32& getFullUpdate) {
-		  realx3  p_m = mirrorPoints(mrrI) + transferVec;
-
-		  int32x3 ind_m;
-		  if (!searchCells.pointIndexInDomain(p_m, ind_m))
-			  return;
-
-		  real d_m = sizeRatio * mirrorDiams[mrrI];
-
-		  for (int ii = -1; ii < 2; ii++)
-		  {
-			  for (int jj = -1; jj < 2; jj++)
-			  {
-				  for (int kk = -1; kk < 2; kk++)
-				  {
-					  auto ind = ind_m + int32x3{ ii, jj, kk };
-
-					  if (!searchCells.inCellRange(ind))
-						  continue;
-
-					  uint32 thisI = head(ind.x(), ind.y(), ind.z());
-					  while (thisI !=  static_cast<uint32>(-1))
-					  {
-						  auto d_n = sizeRatio * diams[thisI];
-
-						  // first item is for this boundary and second itme,
-						  // for mirror
-						  if(sphereSphereCheckB(p_m, points[thisI], d_m, d_n)&&
-                       ppPairs.insert(thisI,mrrI) == static_cast<uint32>(-1))
-						  {
-							  getFullUpdate++;
-						  }
-
-						  thisI = next(thisI);
-					  }
-				  }
-			  }
-		  }
-	  },
-	  getFull
-	);
-
-	return getFull;
-}
-
-pFlow::uint32
-pFlow::twoPartContactSearchKernels::broadSearchPP(
-  csPairContainerType&                      ppPairs,
-  const deviceScatteredFieldAccess<realx3>& points1,
-  const deviceScatteredFieldAccess<real>&   diams1,
-  const realx3Vector_D&                     points2,
-  const realVector_D&                       diams2,
-  const deviceViewType3D<uint32>&           head,
-  const deviceViewType1D<uint32>&           next,
-  const cells&                              searchCells,
-  real                                      sizeRatio
-)
-{
-	if (points1.empty())
-		return 0;
-	if (points2.empty())
-		return 0;
-
-	auto   nP2         = points2.size();
-	auto   points2View = points2.deviceView();
-	auto   diams2View  = diams2.deviceView();
-
-	uint32 getFull = 0;
-
-	Kokkos::parallel_reduce(
-	  "pFlow::twoPartContactSearchKernels::broadSearchPP",
-	  deviceRPolicyStatic(0, nP2),
-	  LAMBDA_HD(const uint32 i2, uint32& getFullUpdate) {
-		  realx3  p_m = points2View(i2);
-
-		  int32x3 ind_m;
-		  if (!searchCells.pointIndexInDomain(p_m, ind_m))
-			  return;
-
-		  real d_m = sizeRatio * diams2View[i2];
-
-		  for (int ii = -1; ii < 2; ii++)
-		  {
-			  for (int jj = -1; jj < 2; jj++)
-			  {
-				  for (int kk = -1; kk < 2; kk++)
-				  {
-					  auto ind = ind_m + int32x3{ ii, jj, kk };
-
-					  if (!searchCells.inCellRange(ind))
-					  {
-						  continue;
-					  }
-
-					  uint32 i1 = head(ind.x(), ind.y(), ind.z());
-					  while (i1 != static_cast<uint32>(-1))
-					  {
-						  auto d_n = sizeRatio * diams1[i1];
-
-						  // first item is for this boundary and second itme,
-						  // for mirror
-						  if(sphereSphereCheckB(p_m, points1[i1], d_m, d_n)&&
-                       ppPairs.insert(i1,i2) == static_cast<uint32>(-1))
-						  {
-							  getFullUpdate++;
-						  }
-
-						  i1 = next(i1);
-					  }
-				  }
-			  }
-		  }
-	  },
-	  getFull
-	);
-
-	return getFull;
-}

src/Interaction/contactSearch/boundaries/twoPartContactSearch/twoPartContactSearchKernels.hpp

@@ -1,49 +0,0 @@
-#ifndef __twoPartContactSearchKernels_hpp__
-#define __twoPartContactSearchKernels_hpp__
-
-#include "contactSearchGlobals.hpp"
-#include "cells.hpp"
-#include "contactSearchFunctions.hpp"
-#include "scatteredFieldAccess.hpp"
-#include "VectorSingles.hpp"
-
-namespace pFlow::twoPartContactSearchKernels
-{
-
-void buildNextHead(
-    const deviceScatteredFieldAccess<realx3> &points,
-    const cells              &searchCells,
-    deviceViewType3D<uint32> &head, 
-    deviceViewType1D<uint32> &next );
-
-
-uint32 broadSearchPP
-(
-	csPairContainerType 						&ppPairs,
-	const deviceScatteredFieldAccess<realx3> 	&points, 
-	const deviceScatteredFieldAccess<real> 		&diams, 
-	const deviceScatteredFieldAccess<realx3>	&mirrorPoints, 
-	const deviceScatteredFieldAccess<real> 		&mirrorDiams, 
-	const realx3 								&transferVec,
-    const deviceViewType3D<uint32>				&head,
-    const deviceViewType1D<uint32>				&next,
-    const cells									&searchCells,
-	real sizeRatio
-);
-
-uint32
-broadSearchPP(
-	csPairContainerType&                      ppPairs,
-	const deviceScatteredFieldAccess<realx3>& points1,
-	const deviceScatteredFieldAccess<real>&   diams1,
-	const realx3Vector_D&                     points2,
-	const realVector_D&                       diams2,
-	const deviceViewType3D<uint32>&           head,
-	const deviceViewType1D<uint32>&           next,
-	const cells&                              searchCells,
-	real                                      sizeRatio
-);
-}
-
-
-#endif //__twoPartContactSearchKernels_hpp__