ORNL · naughtont3 · Sep 23, 2024
diff --git a/examples/index.rst b/examples/index.rst
@@ -34,3 +34,4 @@ use cases are addressed by the architecture, including how the
    :caption: Architecture Examples Catalog
 
    aam/index
+   stem/index
diff --git a/examples/stem/index.rst b/examples/stem/index.rst
@@ -0,0 +1,46 @@
+.. _intersect:arch:examples:stem:
+
+Autonomous Microscopy
+=====================
+
+Over the last two decades, aberration corrected :term:`STEM` has become the
+mainstay of condensed matter physics, materials science, chemistry,
+catalysis, and nanotechnology. Yet both deriving fundamental physical
+insights from these multidimensional data sets and further using this
+knowledge towards making new and better materials for energy, quantum,
+and information technologies is stymied by the dearth of the methods and
+the data infrastructure necessary to handle the bespoke data sets.
+Similarly, human-driven operation of the microscopes is inherently
+limited at the age of fast data acquisition and multidimensional data.
+This project establishes the crucial link between the cutting-edge
+instrumental platforms at the :term:`CNMS` and the HPC capabilities at ORNL to
+enable the next generation of the HPC-driven scientific discovery
+(:numref:`intersect:arch:examples:stem:stem`). Specifically, the project
+targets three intertwined tasks, including (a) establishing a pipeline
+for direct data transfer from the :term:`STEM` to the :term:`MD`/:term:`DFT` environment, (b)
+high-fidelity structural reconstructions from 4D :term:`STEM` data, and (c)
+enabling the science-driven physical discovery via deep kernel learning.
+These targets, while closely linked scientifically, offer complementary
+challenges for the data infrastructure, prioritizing :term:`CPU` based
+calculations, :term:`GPGPU` and high-volume data transfer, and low-latency :term:`CPU`
+operations respectively.
+
+The :term:`Oak Ridge National Laboratory<ORNL>` project team consists of:
+
+- `Maxim Ziatdinov (Principal Investigator) <https://www.ornl.gov/staff-profile/maxim-ziatdinov>`_
+
+.. figure:: stem.png
+   :name: intersect:arch:examples:stem:stem
+   :align: center
+   :width: 800
+
+   An autonomous microscopy science use case
+
+.. toctree::
+   :name: intersect:arch:examples:stem:architecture
+   :maxdepth: 1
+   :caption: Architecture
+
+   pat
+   sos
+   ms
diff --git a/examples/stem/ms.rst b/examples/stem/ms.rst
@@ -0,0 +1,5 @@
+.. _intersect:arch:examples:stem:ms:
+
+Microservices Architecture
+--------------------------
+
diff --git a/examples/stem/pat.rst b/examples/stem/pat.rst
@@ -0,0 +1,75 @@
+.. _intersect:arch:examples:stem:pat:
+
+Science Use Case Design Patterns
+--------------------------------
+
+The autonomous microscopy science use
+case :cite:`doi:10.1021/acsnano.1c02104` implements the
+Experiment Steering strategic pattern
+(:numref:`intersect:arch:examples:stem:pat:strategic`), as an ongoing :term:`STEM`
+experiment is controlled by analyses of periodic experiment data. At the
+strategic pattern level of abstraction, the individual pattern
+components are as follows:
+
+-  The experiment plan contains a complete description of the
+   predetermined actions to be performed for running the experiment,
+   including any parameters for operating the :term:`STEM`, safety-related
+   responses and how to analyze and judge experiment progress and change
+   the plan accordingly. The experiment plan also contains the goal of
+   the :term:`STEM` experiment to steer it in the right direction and to stop
+   its closed loop control upon completion.
+
+-  The experiment controller executes an experiment using a
+   predetermined experiment plan and changes the plan’s parameters
+   during execution based on experiment progress. The plan’s execution
+   is autonomous, performed in a closed loop control and may involve
+   human interaction.
+
+-  The test performed in an experiment determines the properties of
+   microscopic structures.
+
+-  The experiment result is a combination of raw and analyzed :term:`STEM` data
+   and insights derived from this data.
+
+.. figure:: pat/strategic.png
+   :name: intersect:arch:examples:stem:pat:strategic
+   :align: center
+
+   Experiment Steering strategic pattern for the autonomous microscopy
+   science use case
+
+The autonomous microscopy science use case implements the Distributed
+Experiment Steering architectural pattern
+(:numref:`intersect:arch:examples:stem:pat:architectural`), as an ongoing :term:`STEM`
+experiment is controlled by remote analyses of periodic experiment data.
+At the architectural pattern level of abstraction, the individual
+pattern components are as follows:
+
+-  In addition to the properties identified by the Experiment Steering
+   strategic pattern, the experiment controller is either local or
+   remote and may feature a :term:`GUI` or some other :term:`HMI`.
+
+-  The actuator is part of the :term:`STEM` and moves the scanning electron
+   beam.
+
+-  The test is performed in the :term:`STEM` experiment determines the
+   properties of microscopic structures.
+
+-  The sensor is part of the :term:`STEM` and provides the raw microscope data.
+
+.. figure:: pat/architectural.png
+   :name: intersect:arch:examples:stem:pat:architectural
+   :align: center
+
+   Distributed Experiment Steering architectural pattern for the autonomous
+   microscopy science use case
+
+Note that the strategic and architectural patterns present design
+choices and not specifics about the implementation of the design. The
+patterns present the overall control, data and work flow, but not the
+detailed control messages, data transfers and orchestration. For
+example, the analysis system may be a small, dedicated computer, a
+larger, shared cluster computer, or an extreme-scale supercomputer. The
+controller may be a separate dedicated laptop or server, or co-located
+on the analysis system. Data transfers may be file-based or streaming.
+Network connections between these components may be dedicated or shared.
diff --git a/examples/stem/pat/architectural.drawio b/examples/stem/pat/architectural.drawio
@@ -0,0 +1,154 @@
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diff --git a/examples/stem/pat/architectural.pdf b/examples/stem/pat/architectural.pdf
diff --git a/examples/stem/pat/architectural.png b/examples/stem/pat/architectural.png
Original file line number	Diff line number	Diff line change
Expand Up		@@ -34,3 +34,4 @@ use cases are addressed by the architecture, including how the
		:caption: Architecture Examples Catalog

		aam/index
		stem/index