Computer Applications in Materials Engineering

Lab Activity No.03

CS 325

Submitted By
Maroof Faheem (20MME-S1-313)
Muhammad Umar (20MME-S1-340)
Eisha Amin (20MME-S1-326)

Submitted To
Dr.-ing Waseem Amin
Assistant Professor

Submission Date:
June 5, 2023

Institute of Metallurgy and Materials Engineering

Faculty of Chemical and Materials Engineering
University of the Punjab,Lahore
Contents
1 Objective 2

2 Introduction 2
2.1 What is DREAM 3D? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.2 How it is helpful in Materials science and Engineering? . . . . . . . . . . . . . . . . . . . 2
2.3 What is Para view? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.4 What role does Paraview play? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

3 Literature Review 2
3.1 Overview of the User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
3.2 Data Structures: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
3.2.1 Geometry: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3.2.2 Features and Ensembles: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3.2.3 Filters,Plugins and Pipeline: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3.3 Creating and Building Pipeline: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3.4 StatsGenerator: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.4.1 Phase Properties: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.4.2 Size Distribution Tab: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.4.3 Omega3 Tab: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.4.4 Shape Distribution Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.4.5 ODF Tab: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.4.6 MDF Tab: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.5 Initialize Synthetic Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3.6 Establish Shape Types: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3.7 Pack Primary Phases: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3.8 Match Crystallography: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3.9 Generate IPF Colors: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3.10 Write DREAM.3D Data File: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

4 Procedure 7

5 Discussion 12

6 Conclusion 12

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To create a 3D micro structure using DREAM3D and view it in para
view software.

1. Objective
The objective the experiment is to aim:

• To create a 3D representation of the microstructure using DREAM3D software.

• To view this representative volume element in para view.

2. Introduction
2.1. What is DREAM 3D? • Designing and optimizing materials for spe-
cific performance.
DREAM 3D (Diffraction Reconstruction and Explo-
ration for Advanced Materials 3D) is an open-source
software tool that is specifically designed for the
analysis and simulation of microstructures in materi-
2.3. What is Para view?
ParaView is a multi-platform, open-source data anal-
als science and engineering. It plays a crucial role in
ysis and visualization program that is widely used
the field of materials science by providing a platform
in scientific and technical domains. It is useful for
for the reconstruction, visualization, and analysis of
visualizing and analyzing vast amounts of scientific
three-dimensional (3D) microstructural data.[1]
data, especially in the context of computational sim-
2.2. How it is helpful in Materials science ulations and simulation outcomes.[2]
and Engineering?
2.4. What role does Paraview play?
DREAM 3D is helpful in materials science by:
ParaView plays the following roles:
• Analysing and quantifying complex mi-
• Visualizing and analysing large-scale scien-
crostructures.
tific data.

• Enabling interactive exploration of complex

• Visualizing and exploring 3D representations
datasets.
of materials.
• Leveraging parallel and distributed computing
for efficient processing.
• Predicting material properties based on mi-
crostructure. • 4.Integrating with simulation codes for direct
analysis of simulation results.

3. Literature Review
3.1. Overview of the User Interface
DREAM.3D has 6 main sections of its user interface:
1. Pipeline View: The Pipeline View is a section
where you can see and organize the filters that
are currently being used. It shows the order
in which the filters are applied. You can add
filters by double-clicking on them or dragging

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 and dropping them from the Filter List or Filter
Library. You can also rearrange the filters by
dragging and dropping them in different posi-
tions. For more detailed instructions on creat-
ing pipelines, you can refer to the Creating a
Pipeline section.[4]
2. Filter Input View: The Filter Input View pro-
vides a clear overview of the filter’s param-
eters, required inputs, generated outputs, and
the resulting structure of the data after the fil-
ter has been executed.[4]
3. Data Structure: The Data Structure tool
shows you the current organization of your
data in the pipeline. It includes all the data
containers, attribute matrices, and data arrays
that are present in the pipeline’s data container
array.[4]
4. Filter List and Filter Library The Filter List
section organizes the Filters of DREAM.3D
alphabetically by name. Using the search bar,
the user can search for Filters based on the
display name, group name, subgroup name,
branding name, or compiled library name.The
Filter Library section organizes the Filters
of DREAM.3D according to their group and
subgroup. The user can expand a specific
group (and possibly a subgroup) to expose
the Filters. Filters are placed into groups and
subgroups based on their functionality. This
makes it easy to find Filters based on a desired
function. In general, the Filter group will cor-
respond to the Plugin that Filter resides in, but
this may not always be the case.[4]
5. Pipeline Output The Pipeline Output Log
displays any output messages associated with
GUI actions or Filters that are actively being
used in the Pipeline View.[4]
6. Pipeline Issues Table The Pipeline Error Ta-
ble displays any errors and/or warnings asso-
ciated with Filters that are actively being used
in the Pipeline View.[4]

As shown in Figure 1,

Figure 1: (a)Overview of the User Interface

3.2. Data Structures: ogy and mesh structures. It’s a hierarchical structure
that helps represent complex information in a simple
According to the documentation [3], the data struc- and organized manner. Data Container Array: The
tures in DREAM.3D uses a special way to organize root node that holds all other objects. It can create
data that is based on ideas from combinatorial topol-

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and retrieve objects within its hierarchy. ious types:
Data Container: Contains Attribute Matrices for Element Attribute Matrices: Hold attribute data
data related to specific geometries. directly associated with the features of the Geome-
Attribute Matrix: Stores Attribute Arrays, which try, categorized by the unit Element type.
hold raw data. The type of Attribute Matrix deter- Feature Attribute Matrices: Group Elements into
mines the hierarchy level it corresponds to. features and associate data with them.
Attribute Array: Holds data in memory using a flat Ensemble Attribute Matrices: Group features into
storage approach, which improves computational ef- ensembles and associate data with them.
ficiency.
3.2.2. Features and Ensembles:
Features and Ensembles are composed of Elements
3.2.1. Geometry: of the same unit Element type. Each Feature or En-
The Geometry object defines the spatial organization semble has associated Ids, which are used to link
of the data and is associated with Data Containers. them to lower levels in the hierarchy.
Geometries are categorized based on the topology of
their unit Element, which can be a point, line, poly- 3.2.3. Filters,Plugins and Pipeline:
gon, or polyhedron. Filters are self-contained functions in DREAM.3D
Data attributes can be associated with different types that modify the data structure. They can be com-
of Elements as long as it makes sense for the topol- bined into Pipelines, where the data flows through
ogy. For example, a triangle mesh can have attributes multiple Filters. Filters are organized into Plugins,
associated with vertices, edges, and faces but not which are collections of Filters with similar func-
cells. tionality. The Plugin library determines the location
Attribute Matrices organize data and can be of var- of Filters within the interface.

Figure 2: (a)Element Object (b)Feature Object (c)Ensemble Object

3.3. Creating and Building Pipeline:
To create a Pipeline in DREAM.3D, you connect a
series of Filters to process your data. Filters modify
the data structure step by step. Remember that the
data is processed in place, so there’s only one copy
in memory, reducing memory usage. However, this
means the original data may be changed.[4]
When building the Pipeline, make sure each object
in the data structure has a unique name to avoid
conflicts. For example, you can’t have two objects
with the same name at the same level in the data
structure.[4]
Building a Pipeline involves selecting and connect-
ing Filters to perform specific tasks on your data.
Imagine the Pipeline as a sequence of tubes, where
each Filter represents a piece of the tube. The data
flows through the Filters, which can modify, com-

4
press, or add to it.[4]
To build an effective Pipeline, understand the
DREAM.3D data structure and its ontology. Con-
sider the type of data you have (e.g., images or sur-
face meshes) and where the data is located on the
elements of the data structure. This determines the
appropriate Attribute Matrix to use.[4]
Start by reading data from a file to create the ini-
tial data structure. Then, connect Filters to perform
analyses and manipulations on the data. Filters can
analyze the data, group elements into features, cal-
culate sizes and shapes, and more.[4]
Once you’ve completed the analysis, you may want
to export the modified data structure. DREAM.3D
supports various file formats for exporting, including
its native .dream3d format based on HDF5, which al-
lows easy data access.[4]
To streamline your workflow or share it with others,
save the Pipeline for future use. This helps main-
tain a consistent workflow and allows you to reuse
the Pipeline easily. Check the Saving and Opening
Pipelines section for more details on how to save and
open Pipelines in DREAM.3D.[4]

The Filters that we used in this experiment to create certain pipeline for 3D microstructure(REV) are
given below:

3.4. StatsGenerator: ing the Alpha and Beta parameters. The associated
plot provides a visual representation of object shapes
According to the documentation of [5] , this Filter
based on the superellipsoid class, showing the nor-
creates the arrays necessary to generate synthetic mi-
malized affine invariant as a function of the shape
crostructures. The StatsGenerator Filter was created
parameter.
to allow users to quickly generate a set of statistics
that can be used to create a synthetic microstructure.
Using this Filter, the user can generate the neces- 3.4.4. Shape Distribution Tab
sary statistics that describe a microstructure, with the
aid of visual plots of the statistics, and immediately The Shape Distribution Tab allows users to specify
use them in the Pipeline to generate a synthetic mi- the aspect ratios of the features using the alpha and
crostructure. The statistics data can also be saved to beta parameters of a beta distribution. These param-
a DREAM.3D file for later use. As shown in Figure eters control the distribution of aspect ratios and ul-
3. timately determine the shape characteristics of the
generated features.As shown in Figure 4.
3.4.1. Phase Properties:
The StatsGenerator GUI provides buttons to man- 3.4.5. ODF Tab:
age phases in the microstructure, allowing the user
to add, remove, or edit phase properties through the The ODF Tab enables users to control the crystal-
Phase Properties Manager. Parameters such as crys- lographic texture of the synthetic structure by enter-
tal structure, volume fraction, phase type, fraction ing specific orientations and weights or loading an-
of precipitate on boundary, and phase name can be gle data from a file. The calculated ODF and gen-
specified to accurately generate statistics for each erated pole figures provide visual representations of
phase. the texture for further analysis and inspection. De-
scribes the statistical distribution of crystallographic
3.4.2. Size Distribution Tab: orientations within a material. It provides informa-
tion about the preferred crystallographic orientations
The Size Distribution tab provides controls to define or texture present in the sample.
the size distribution of Features, including average
value, standard deviation, truncation, binning, and
initial defaults for correlated statistics. The Create 3.4.6. MDF Tab:
Data button is crucial to finalize the input and popu-
The MDF GUI allows users to manipulate and en-
late other tabs with default values.
hance specific misorientations in the generated mis-
orientation distribution function. By adding weights
3.4.3. Omega3 Tab: to desired angles and axes, users can customize the
The Omega3 tab allows users to control the mor- distribution to align with specific characteristics or
phological shape of the generated features by adjust- experimental observations.

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3.5. Initialize Synthetic Volume
According to the documentation of [10], the ”Initial-
ize Synthetic Volume” filter sets up the empty vol-
ume, Image Geometry, and necessary data structures
required for generating a synthetic microstructure.
Users can define the volume size, origin, and reso-
lution, and estimate the number of features based on
specified statistics for further processing. As shown
in Figure 5.
3.6. Establish Shape Types:
According to the documentation of [6],the ”Establish
Shape Types” filter allows users to assign specific
shape types to ensembles in a synthetic structure. It
should be used before packing filters and after ini-
tializing the synthetic volume. The available shape
types include Ellipsoid, Super Ellipsoid, Cube Octa-
hedron, Cylinder, and Unknown Shape Type. Ellip-
soid represents a rounded and symmetric shape, Su-
per Ellipsoid allows for shape customization, Cube
Octahedron combines a cube and an octahedron, and
Cylinder represents a cylindrical shape. The Un-
known Shape Type is used for error detection and
should not be used for normal synthetic structures.
This filter gives users control over the morphology
of the generated synthetic structure. As shown in
Figure 6.
3.7. Pack Primary Phases:
According to the documentation of [7],the ”Pack Pri-
mary Phases” filter is part of the ”Synthetic Build-
ing” group and is used for packing precipitate fea-
tures in a synthetic microstructure. It places precip-
itate features based on their sizes, shapes, physical
orientations, and locations according to the speci-
fied goal statistics. The packing process ensures that
the features do not overlap. The filter allows for
matching parameters such as fraction of precipitates
on a grain boundary, size distribution, volume frac-
tion, orientation distribution, and radial distribution
function. Users can choose periodic boundary condi-
6
tions, write out the goal attributes of the packed pre-
cipitates, and even read in a list of pre-defined pre-
cipitates. The filter creates various shape description
arrays for each packed feature, including axis Euler
angles, axis lengths, centroids, equivalent diameters,
neighborhoods, omega3 values, and volumes. These
arrays provide detailed information about the packed
features and enable further analysis and evaluation.
As shown in Figure 7.
3.8. Match Crystallography:
According to the documentation of [8],the ”Match
Crystallography” filter, found within the ”Synthetic
Building” group, aims to match a specified orienta-
tion distribution function (ODF) to a set of features
in a synthetic microstructure. The filter employs an
iterative algorithm that involves two processes: ran-
domly swapping the orientation of a feature with a
new orientation sampled from the desired ODF, and
randomly switching the orientations of two features.
These operations are accepted if they reduce the er-
ror between the current ODF and misorientation dis-
tribution function (MDF) and the target ODF. The
process continues for a user-defined number of it-
erations or until the texture functions are matched
within a specified precision. The filter helps align
the crystallographic properties of the synthetic mi-
crostructure with the desired distribution. As shown
in Figure 9.
3.9. Generate IPF Colors:
According to the documentation of [9], IPF stands
for Inverse Pole Figure. This filter generates IPF col-
ors, which are visual representations of crystal orien-
tations or orientations of individual elements within
the data structure.As shown in Figure 10.
3.10. Write DREAM.3D Data File:
This step involves writing the modified or processed
data structure to a DREAM.3D data file format. It
saves the changes made during the pipeline pro-
cess.As shown in Figure 11.
 4. Procedure
• Opened the Stats Generator module and adjusted the parameters to create the desired size distribution
as shown in figure below:

Figure 3: Showing Stats Generator Window

• Clicked the ”Create data” button to generate initial distributions, including the omega3 distribution,
B/A and C/A axis ratios and Neighbor distribution. As shown in figure below:

Figure 4: (a) Showing Omega3 window (b) Showing B/A (c) Showing C/A (d) Showing Feature Neighbor

• Initialized the synthetic volume by setting up the necessary configurations. As shown in figure below

7
 Figure 5: Showing Initialize synthetic Volume Window

• Created ellipsoid shapes using established shape types. As shown in figure below:

Figure 6: Showing Establishing shape types Window

• Configured the parameters for packing primary phases in the synthetic volume. As shown in figure
below:

8
 Figure 7: Showing Packing Primary Phases Window

• Set the parameters for finding feature neighbors in the synthetic microstructure. As shown in figure
below:

Figure 8: Showing Feature Neighbors Window

• Configured the parameters for matching crystallography in the synthetic microstructure. As shown in
figure below:

9
 Figure 9: Showing Matching Crystallography

• Set parameters for generating IPF colors to visualize orientation relationships. As shown in figure
below:

Figure 10: Showing Generating IPF colors

• Selected the file name and location to write the DREAM3D data file. Used the ”Write DREAM3D
Data File” function to save the synthetic microstructure. As shown in the figure below:

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 Figure 11: Showing Write Dream.3d file Window

• The file name “synthetic. Dream3d” was exported to Paraview. Then visualization was observed as
shown in the figure below:

Figure 12: Visualizing 3D microstructure in Para View

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 5. Discussion
DREAM3D software enables researchers in ma- the microstructure. Filters, organized into plugins,
terials science and engineering to analyze and simu- allow for the application of specific tasks on the data,
late complex microstructures. By creating a pipeline such as generating statistical metrics and manipulat-
of filters within DREAM3D, users can process and ing the microstructure. The resulting data can then
modify microstructural data to extract valuable in- be visualized and explored in ParaView, a power-
sights. The software’s hierarchical data structure ful open-source data analysis and visualization tool,
organizes data containers, attribute matrices, and at- further enhancing the understanding of material be-
tribute arrays, providing a comprehensive view of havior at a microscale.

6. Conclusion
The experiment aims to utilize DREAM3D software and ParaView to analyze, visualize, and modify mi-
crostructural data. The pipeline of filters in DREAM3D allows for efficient processing and analysis of the
data, while ParaView enables interactive exploration and visualization of the results. This combination of
tools and techniques is valuable in materials science and engineering for understanding the properties and
behavior of materials at a microscale.

References
[1] Introduction, Documentation and issues tracking. [Online]. Available at: https://github.com/
BlueQuartzSoftware/DREAM3D (Accessed: June 3, 2023).
[2] Introduction to Para view. [Online]. Available at: https://docs.paraview.org/en/latest/
UsersGuide/introduction.html (Accessed: June 3, 2023).
[3] DREAM.3D Data Structure. [Online]. Available at: http://dream3d.bluequartz.net/Help/1_
UsingDREAM3D/%5BA%5D_DataStructure/ (Accessed: June 3, 2023).
[4] Overview of the User interface(Dreamm3d). [Online]. Available at: http://dream3d.bluequartz.
net/Help/1_UsingDREAM3D/%5BB%5D_UserInterface/ (Accessed: June 3, 2023).
[5] StatsGenerator. [Online]. Available at: http://dream3d.bluequartz.net/Help/Filters/
SyntheticBuildingFilters/StatsGeneratorFilter/ (Accessed: June 3, 2023).
[6] Establish Shape Types. [Online]. Available at: http://dream3d.bluequartz.net/Help/Filters/
SyntheticBuildingFilters/StatsGeneratorFilter/ (Accessed: June 3, 2023).
[7] Pack Primary Phases. [Online]. Available at: http://dream3d.bluequartz.net/Help/Filters/
SyntheticBuildingFilters/PackPrimaryPhases/ (Accessed: June 3, 2023).
[8] Match Crystallography. [Online]. Available at: http://dream3d.bluequartz.net/Help/
Filters/SyntheticBuildingFilters/MatchCrystallography/ (Accessed: June 3, 2023).
[9] Generate IPF Colors. [Online]. Available at: http://dream3d.bluequartz.net/Help/Filters/
OrientationAnalysisFilters/GenerateIPFColors/#generate-ipf-colors (Accessed: June
3, 2023).
[10] Initialize Synthetic Volume. [Online]. Available at: http://dream3d.bluequartz.net/Help/
Filters/SyntheticBuildingFilters/InitializeSyntheticVolume/ (Accessed: June 3,
2023).

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