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Merge pull request #208 from PhasicFlow/postProcessing 

readme.md file is added for postprocessing
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4
src/PostprocessData/postprocessData/postprocessData.cpp
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@ -100,6 +100,8 @@ pFlow::postprocessData::postprocessData
bool pFlow::postprocessData::execute() bool pFlow::postprocessData::execute()
{ {
if( inSimulation_ && !activeInSimulation_() ) return true;
const auto& ti = time_.TimeInfo(); const auto& ti = time_.TimeInfo();
for(auto& component:postprocesses_) for(auto& component:postprocesses_)
@ -118,6 +120,8 @@ bool pFlow::postprocessData::execute()
bool pFlow::postprocessData::write() const bool pFlow::postprocessData::write() const
{ {
if( inSimulation_ && !activeInSimulation_() ) return true;
for(auto& component:postprocesses_) for(auto& component:postprocesses_)
{ {
if(!component->executed()) if(!component->executed())

346
src/PostprocessData/readme.md Normal file
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@ -0,0 +1,346 @@
# PostprocessData Module in phasicFlow
The `PostprocessData` module in phasicFlow provides powerful tools for analyzing particle-based simulations both during runtime (in-simulation) and after simulation completion (post-simulation). This document explains how to configure and use the postprocessing features through the dictionary-based input system.
## Overview
Postprocessing in phasicFlow allows you to:
- Extract information about particles in specific regions of the domain
- Calculate statistical properties such as averages and sums of particle attributes
- Track specific particles throughout the simulation
- Apply different weighing methods when calculating statistics
- Perform postprocessing at specific time intervals
## Setting Up Postprocessing
Postprocessing is configured through a dictionary file named `postprocessDataDict` which should be placed in the `settings` directory. Below is a detailed explanation of the configuration options.
### Basic Configuration
The input dictionary, **settings/postprocessDataDict**, may look like this:
```cpp
// PostprocessData dictionary
// Enable/disable postprocessing during simulation
runTimeActive yes; // Options: yes, no
// Shape type - only needed when doing post-simulation processing
shapeType sphere; // Options depend on the simulation type: sphere, grain, etc.
// Default time control for postprocessing components
defaultTimeControl
{
timeControl timeStep; // Options: timeStep, simulationTime, settings
startTime 0; // Start time for postprocessing
endTime 1000; // End time for postprocessing
executionInterval 150; // How frequently to run postprocessing
}
// List of postprocessing components
components
(
// Component definitions here...
);
```
If you want to activate in-simulaiton postprocessing, you need to add these lines to the `settings/settingsDict` file:
```cpp
libs ("libPostprocessData.so");
auxFunctions postprocessData;
```
This will link the postprocessing library to your simulation, allowing you to use its features. Note that, anytime you want to deactivate the in-simulation postprocessing, you can simply change the `runTimeActive` option to `no` in `postprocessDataDict` file.
## Time Control Options
Each postprocessing component can either use the default time control settings or define its own. There are three main options for time control:
| Option | Description | Required Parameters |
|--------|-------------|---------------------|
| `timeStep` | Controls execution based on simulation time steps | `startTime`, `endTime`, `executionInterval` |
| `simulationTime` | Controls execution based on simulation time | `startTime`, `endTime`, `executionInterval` |
| `settings` | Uses parameters from settingsDict file | None (defined elsewhere) |
| `default` | Uses the default time control settings (uses `defaultTimeControl` settings)| None (uses default) |
If no time control is specified, the `default` option is used automatically.
## Processing Methods
The postprocessing module provides several methods for processing particle data. They are categorized into two main groups: bulk and individual methods.
- **Bulk Methods**: Operate on all particles that are located in a specified locations/regions (cells, spheres, etc.).
- **Individual Methods**: Operate on specific particles, allowing for targeted particle property extraction.
| Method | Property type | Description | Formula |
|--------|------------------|-------------|---------|
| `arithmetic` | bulk | Simple arithmetic mean/sum with equal weights | Each particle contributes equally |
| `uniformDistribution` | bulk | Each particle contributes inversely proportional to the total number of particles | $w_i = 1/n$ where $n$ is the number of particles |
| `GaussianDistribution` | bulk | Weight contribution based on distance from center with Gaussian falloff | $w_i = \exp(-\|x_i - c\|^2/(2\sigma^2))/\sqrt{2\pi\sigma^2}$ |
| `particleProbe` | individual | Extracts values from specific particles | Direct access to particle properties |
## Region Types
Regions define where in the domain the postprocessing operations are applied:
| Region Type | Description | Required Parameters | Compatible with |
|-------------|-------------|---------------------|-----------------|
| `sphere` | A spherical region | `radius`, `center` | bulk |
| `multipleSpheres` | Multiple spherical regions | `centers`, `radii` | bulk |
| `line` | Spheres along a line with specified radius | `p1`, `p2`, `nSpheres`, `radius` | bulk |
| `centerPoints` | Specific particles selected by ID | `ids` | individual |
## Processing Operations
Within each processing region of type `bulk`, you can define multiple operations to be performed:
### Available Functions
| Function | Property type | Description | Formula | Required Parameters |
|----------|---------------|-------------|---------|---------------------|
| `average` | bulk | Weighted average of particle field values | $\frac{\sum_{i \in \text{region}} w_i \cdot \phi_i \cdot \text{field}_i}{\sum_{i \in \text{region}} w_i \cdot \phi_i}$ | `field`, `phi` (optional), `threshold` (optional), `includeMask` (optional), `divideByVolume` (optional) |
| `sum` | bulk | Weighted sum of particle field values | $\sum_{i \in \text{region}} w_i \cdot \phi_i \cdot \text{field}_i$ | `field`, `phi` (optional),`threshold` (optional), `includeMask` (optional), `divideByVolume` (optional) |
### Derived Functions
In addition to the above basic functions, some derived functions are available for specific calculations:
| Function | Property type | Description | Formula | Required Parameters |
|----------|---------------|-------------|---------|---------------------|
|`avMassVelocity` | bulk | Average velocity weighted by mass | $\frac{\sum_{i \in \text{region}} m_i \cdot v_i}{\sum_{i \in \text{region}} m_i}$ | - |
### Available Fields
All the pointFields in the simulation database (for in-simulation processing), or the ones stored in the time folders (for post-simulation processing) can be referenced in the operations. In addition to them, some extra fields are available for use in the operations. The following fields are available for use in the operations:
1. Extra fileds to be used in post-processing operations:
| Field | Field Type | Description | Default Value |
|-------|------------|-------------|---------------|
| `position` | `realx3` | Particle positions | - |
| `one` | `real` | Value 1 for each particle | 1 |
| `mass` | `real` | Particle mass | - |
| `density` | `real` | Particle density | - |
| `volume` | `real` | Particle volume | - |
| `diameter` | `real` | Particle diameter | - |
| `I` | `real` | Moment of inertia | - |
2. Common fields which are available in the simulation database/time folders:
| Field | Field Type | Description |
|-------|------------|-------------|
| `velocity` | `realx3` | Particle velocity |
| `rVelocity` | `realx3` | Particle rotational velocity |
| `acceleration` | `realx3` | Particle acceleration |
| `rAcceleration` | `realx3` | Particle rotational acceleration |
| `contactForce` | `realx3` | Particle contact force |
| `contactTorque` | `realx3` | Particle contact torque |
| `id` | `integer` | Particle ID |
| `shapeIndex` | `integer` | Particle shape index |
The above fields may vary from one type of simulation to other. Pleas note that this is only a tentative list.
### Optional Parameters
| Parameter | Description | Default | Options |
|-----------|-------------|---------|---------|
| `divideByVolume` | Divide result by region volume | `no` | `yes`, `no` |
| `threshold` | Exclude regions with fewer particles | 1 | Integer value |
| `includeMask` | Filter particles based on a field value | `all` | `all`, `lessThan`, `greaterThan`, `between`, `lessThanOrEq`, `greaterThanEq`, `betweenEq` |
## Examples
### Example 1: Probing Individual Particles
```cpp
velocityProb
{
processMethod particleProbe;
processRegion centerPoints;
selector id;
field component(position,y);
ids (0 10 100);
timeControl default;
}
```
This example extracts the y-component of the position for particles with IDs 0, 10, and 100.
### Example 2: Processing in a Spherical Region
```cpp
on_single_sphere
{
processMethod arithmetic;
processRegion sphere;
sphereInfo
{
radius 0.01;
center (-0.08 -0.08 0.015);
}
timeControl default;
operations
(
averageVel
{
function average;
field mag(velocity);
divideByVolume no;
threshold 3;
includeMask all;
}
par1Fraction
{
function average;
field one;
phi one;
divideByVolume no;
includeMask lessThan;
lessThanInfo
{
field diameter;
value 0.0031;
}
}
numberDensity
{
function sum;
field one;
phi one;
divideByVolume yes;
}
);
}
```
This example defines a sphere region and performs three operations:
1. Calculate the average of velocity magnitude of particles
2. Calculate the fraction of particles with diameter less than 0.0031
3. Calculate the number density by summing and dividing by volume
### Example 3: Processing Along a Line
In this example, a line region is defined. The `lineInfo` section specifies the start and end points of the line, the number of spheres to create along the line, and the radius of each point. Bulk properties are calculated in each sphere, based on the properties of particles contained in each sphere.
```cpp
along_a_line
{
processMethod arithmetic;
processRegion line;
timeControl simulationTime;
startTime 1.0;
endTime 3.0;
executionInterval 0.1;
lineInfo
{
p1 (0 0 0);
p2 (0 0.15 0.15);
nSpheres 10;
radius 0.01;
}
operations
(
bulkDensity
{
function sum;
field mass;
phi one;
divideByVolume yes;
}
volumeDensity
{
function sum;
field volume;
divideByVolume yes;
}
);
}
```
This example creates 10 spherical regions along a line from (0,0,0) to (0,0.15,0.15) and calculates the bulk density and volume density in each region.
## Advanced Features
### Special functions applied on fields
You can access specific components of vector fields (`realx3`) using the `component` function:
```cpp
field component(position,y); // Access the y-component of position
```
Here is a complete list of these special functions:
| Function Name | Valid field Type | Example |
|-----------------|------------|---------|
| `component` | `realx3` | `component(velocity,x)` |
| `abs` | `real` | `abs(s)` |
| `square` | `real` | `square(I)` |
| `cube` | `real` | `cube(diameter)` |
| `squre root` | `real` | `sqrt(mass)` |
| `magnitude` | `realx3` | `mag(contactForce)` |
| `magnitude square` | `realx3` | `magSquare(velocity)` |
| `magnitude cube` | `realx3` | `magCube(velocity)` |
| `magnitude square root` | `realx3` | `magSqrt(acceleration)` |
### Particle Filtering with includeMask
The `includeMask` parameter allows you to filter particles based on field values:
```cpp
includeMask lessThan;
lessThanInfo
{
field diameter;
value 0.0031;
}
```
Supported masks:
- `all`: Include all particles (default)
- `lessThan`: Include particles where field < value
- `greaterThan`: Include particles where field > value
- `between`: Include particles where value1 < field < value2
- `lessThanOrEq`: Include particles where field ≤ value
- `greaterThanOrEq`: Include particles where field ≥ value
- `betweenEq`: Include particles where value1 ≤ field ≤ value2
## Implementation Notes
- The postprocessing system can work both during simulation (`runTimeActive yes`) or after simulation completion.
- When using post-simulation mode, you must specify the correct `shapeType` to properly initialize the shape objects.
- Results are written to output files in the case directory with timestamps.
- The `threshold` parameter helps eliminate statistical noise in regions with few particles.
- Setting `divideByVolume` to `yes` normalizes results by the volume of the region, useful for calculating densities.
## Mathematical Formulations
For weighted `bulk` properties calculation:
$$ \text{average} = \frac{\sum_{i \in \text{region \& includeMask}} w_i \cdot \phi_i \cdot \text{field}_i}{\sum_{i \in \text{region}} w_i \cdot \phi_i} $$
For weighted summing:
$$ \text{sum} = \sum_{i \in \text{region \& includeMask}} w_i \cdot \phi_i \cdot \text{field}_i $$
If `divideByVolume` is set to `yes`, the result is divided by the volume of the region:
$$ \text{volumetric result} = \frac{\text{result}}{V_{\text{region}}} $$

24
src/PostprocessData/region/regionPoints/lineRegionPoints/lineRegionPoints.cpp
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@ -14,7 +14,7 @@ pFlow::lineRegionPoints::lineRegionPoints
selectedPoints_("selectedPoints") selectedPoints_("selectedPoints")
{ {
const auto& lDict = dict.subDict("lineInfo"); const auto& lDict = dict.subDict("lineInfo");
uint32 nPoints = lDict.getValMax<uint32>("numPoints",2); uint32 nSpheres = lDict.getValMax<uint32>("nSpheres",2);
realList raddi; realList raddi;
if( lDict.containsDataEntry("radii")) if( lDict.containsDataEntry("radii"))
@ -24,24 +24,24 @@ pFlow::lineRegionPoints::lineRegionPoints
else else
{ {
auto r = lDict.getVal<real>("radius"); auto r = lDict.getVal<real>("radius");
raddi = realList(nPoints, r); raddi = realList(nSpheres, r);
} }
if(raddi.size() != nPoints) if(raddi.size() != nSpheres)
{ {
fatalErrorInFunction fatalErrorInFunction
<< "The number elements in of radii list should be equal to the " << "The number of elements in the radii list should be equal to the "
<< "number of points"<<endl; << "nSpheres"<<endl;
fatalExit; fatalExit;
} }
sphereRegions_.resize(nPoints, sphere(realx3(0,0,0),1)); sphereRegions_.resize(nSpheres, sphere(realx3(0,0,0),1));
centerPoints_.resize(nPoints); centerPoints_.resize(nSpheres);
volumes_.resize(nPoints); volumes_.resize(nSpheres);
diameters_.resize(nPoints); diameters_.resize(nSpheres);
selectedPoints_.resize(nPoints); selectedPoints_.resize(nSpheres);
real dt = 1.0/(nPoints-1); real dt = 1.0/(nSpheres-1);
for(uint32 i = 0; i < nPoints; ++i) for(uint32 i = 0; i < nSpheres; ++i)
{ {
centerPoints_[i] = line_.point(i*dt); centerPoints_[i] = line_.point(i*dt);
sphereRegions_[i] = pFlow::sphere(centerPoints_[i], raddi[i]); sphereRegions_[i] = pFlow::sphere(centerPoints_[i], raddi[i]);

106
src/PostprocessData/sampleDictionary/postprocessDataDict
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@ -7,18 +7,30 @@ objectType dictionary;;
fileFormat ASCII; fileFormat ASCII;
/*---------------------------------------------------------------------------*/ /*---------------------------------------------------------------------------*/
// Yes: postprocessing is active during the simulation
// No: postprocessing is not active during the simulation
// and it can be done after simulation
runTimeActive yes; runTimeActive yes;
// shapeType: defines the type of the shape that is used in the simulation
// (for example: sphere, grain, etc).
// shapeType is only used when postprocessing is done after simulation
// to initialize the shape object for post processing operatoins
shapeType sphere;
// default time control to be used in the postprocessing components
defaultTimeControl defaultTimeControl
{ {
timeControl timeStep; timeControl timeStep; // timeStep, simulationTime are the options here
startTime 0; startTime 0;
endTime 1000; endTime 1000;
executionInterval 150; executionInterval 150;
} }
// list of postprocessing components
components components
( (
// probing particles for their state variables, like velocity, position, etc
velocityProb velocityProb
{ {
processMethod particleProbe; processMethod particleProbe;
@ -26,23 +38,31 @@ components
selector id; selector id;
field component(position,y); field component(position,y);
ids (0 10 100); ids (0 10 100);
timeControl default; // other options are settings, timeStep, simulationTime
// settings: uses parameters from settingsDict file
// timeStep: uses the time step of the simulation controlling the execution of postprocessing
// simulationTime: uses the simulation time of the simulation controlling the execution of postprocessing
// default: uses the default time control (defined in defaultTimeControl).
// default behavior: if you do not specify it, parameters in defaultTimeControl is used.
} }
onSingleSphere on_single_sphere
{ {
// method of performing the sum (arithmetic, uniformDistribution, GaussianDistribution) // method of performing the sum (arithmetic, uniformDistribution, GaussianDistribution)
processMethod arithmetic; processMethod arithmetic;
processRegion sphere; // type of region on which processing is performed
// Postprocessing is done on particles whose centers are inside this spehre
processRegion sphere;
sphereInfo sphereInfo
{ {
radius 0.01; radius 0.01; // radius of sphere
center (-0.08 -0.08 0.015); center (-0.08 -0.08 0.015); // center of sphere
} }
timeControl default; // settings, timeStep, simulationTime timeControl default;
/// all the post process operations to be done /// all the postprocess operations to be done on sphere region
operations operations
( (
// computes the arithmetic mean of particle velocity // computes the arithmetic mean of particle velocity
@ -50,16 +70,23 @@ components
{ {
function average; function average;
field velocity; field velocity;
divideByVolume no; //default divideByVolume no; // default is no
threshold 3; //default is 1; threshold 3; // default is 1
includeMask all; includeMask all; // default is all
} }
// - function: average, sum, and other derived ones from sum and average
// - field: names of the fields in the simulation. Some special fields
// are: mass, density, volume, position, one, I.
// - divideByVolume: whether the result is divided by the volume of the region
// - threshold: exclude regions that contains particles less than threshold
// - includeMask: all, lessThan, greaterThan, between, lessThanOrEq, greaterThanEq, betweenEq
// computes the fraction of par1 in the region // computes the fraction of par1 in the region
par1Fraction par1Fraction
{ {
function average; function average;
field one; field one; // default
phi one; // default phi one; // default
divideByVolume no; divideByVolume no;
includeMask lessThan; includeMask lessThan;
@ -69,7 +96,6 @@ components
lessThanInfo lessThanInfo
{ {
field diameter; field diameter;
value 0.0031; value 0.0031;
} }
} }
@ -78,16 +104,17 @@ components
{ {
function sum; function sum;
field one; field one;
phi one; // default phi one;
divideByVolume yes; divideByVolume yes;
} }
); );
} }
alongALine along_a_line
{ {
processMethod arithmetic; processMethod arithmetic;
processRegion line; processRegion line;
// the time interval for executing the post-processing // the time interval for executing the post-processing
@ -103,7 +130,7 @@ components
{ {
p1 (0 0 0); p1 (0 0 0);
p2 (0 0.15 0.15); p2 (0 0.15 0.15);
numPoints 10; nSpheres 10;
radius 0.01; radius 0.01;
} }
@ -120,10 +147,57 @@ components
volumeDensity volumeDensity
{ {
function sum; function sum;
field cube(diameter); // d^3, although it differs by pi/6 field volume; //
divideByVolume yes; //default is no divideByVolume yes; //default is no
} }
); );
} }
); );
/*
About processMethod
This defines the type of the processing method to be done.
The processing is done either on a collection of selected particles (the first three ones)
or individual particles (particleProbe).
Options are:
- arithmetic
- uniformDistribution
- GaussianDistribution
- particleProbe (only used with centerPoints)
When you use the first three optoins, then you can either perform two types of processing is possible
- sum
\f[
\text{result} = \sum_{i \in \text{processRegion and includeMask}} w_i \cdot \phi_i \cdot \text{field}_i
\f]
- average
\f[
\text{result} = \frac{1}{V_{\text{region}}} \frac{\sum_{j \in \text{includeMask}} w_j \cdot \phi_j \cdot \text{field}_j}
{\sum_{i \in \text{processRegion}} w_i \cdot \phi_i}
\f]
*/
/*
About processRegion
processRegion, defines processing regions on which postprocess operation are performed. Particles
whose centers are inside the regions are selected for post processing operation. Note that
you are allowed to use a correct combination of processRegion and processMethod.
For example centerPoints only works with particleProbe.
Options are:
- sphere
- multipleSpheres
- line
- centerPoints (only works with particleProbe)
- rectMesh: Not implemented yet
- generalMesh: not implemented yet
*/