diff --git a/src/content/collab_proj_course.rst b/src/content/collab_proj_course.rst index 17f92a6115e90edca08b87a92814615fa3b51237..8e02b6c5f276ae5c36b4427aa4885cc0b86c74a4 100644 --- a/src/content/collab_proj_course.rst +++ b/src/content/collab_proj_course.rst @@ -9,7 +9,7 @@ Collaborative Software Engineering Project in Computational Physics =================================================================== -**Register by email to: rickard.armiento [at] liu.se** +**Register by email to: rickard.armiento [at] liu.se** (limited space available). Info ---- @@ -40,7 +40,7 @@ The course takes place in the autumn term starting end of august/begninning of s Dates ----- -**August 30 - October 15** *Introductionary part:* During this time there will be 10 lectures and 4 practical hands-on exercises. During this period the project groups organize, plan, and prepare their projects. +**August 30 - October 15** *Introductionary part:* During this time there will be 10 lectures (2h with 15 break) and 4 practical hands-on exercises (each 4h). During this period the project groups organize, plan, and prepare their projects. **November 1 - December 17** *Project execution part:* During this time the project groups conduct the project work. The work is coordinated over the Internet using the tools for collaborative software engineering covered in the course. @@ -49,7 +49,7 @@ The project execution part ends with an oral presentation and a written final re Content details --------------- -The course is aimed at those who want to elevate their skills beyond "programming" and learn modern practices in collaborative software development and software engineering. The course covers methods, tools, and workflows that enables joint software projects. These topics are covered in a series of lectures, hands-on exercises, and a group project in computational physics. The exercises and the project work will primarily use Python. +The course is aimed at those who want to elevate their skills beyond "programming" and get experience with modern practices in collaborative software development and software engineering. The course covers methods, tools, and workflows that enables working together on large software projects. These topics are covered in a series of lectures, hands-on exercises, and a group project in computational physics. The exercises and the project work primarily uses Python. The lectures span over both theoretical and practical aspects of software engineering as well as computational physics. They introduce agile project models, version control of software, documentation, software testing (automated unit and integration tests, CI/CD), parallel and concurrent execution, databases, exploratory data analysis with visualization, molecular dynamics, and computer simulation of materials. @@ -68,73 +68,76 @@ After completing the course the participants will be able to: Preliminary lecture outline --------------------------- -**Lecture 1:** Course Introduction and Project Models. +**Lecture 1:** *Course Introduction and Project Models* - Overview, background, course plan, CDIO, waterfall vs. agile project models, LIPs, Scrum. -**Lecture 2:** Software Versioning and Collaborative Development. +**Lecture 2:** *Software Versioning and Collaborative Development* - Version control systems (git, svn), commits/branching/mergning, collaborative workflows with pull requests and reviews (GitHub). -**Hands-on exercise 1:** Git and GitHub. +**Hands-on exercise 1:** *Git and GitHub* - Working with a local repository: commits, branches, merging. - Collaborative software development with pull-requests, reviews, and approvals. - Creating the shared online repository for your project. -**Lecture 3:** Exploratory Data Analysis by Visualization and Computer simulations. +**Lecture 3:** *Exploratory Data Analysis by Visualization and Introduction to Computer simulations* - Single and multi-property exploration, identifying outliers, descriptors, heatmaps, PCA. -- Introduction to computer simulations in computational physics. +- Introduction to materials simulations in computational physics. +- Implementation considerations: representations of periodic structures, boundary conditions. -**Lecture 4:** Software Documentation and Licensing. +**Lecture 4:** *Software Documentation and Licensing* -- Documentation: UML, Comments, Embedded documentation, Sphinx. +- Documentation: UML, Source code comments, Embedded documentation, Sphinx. - Software licensing: Open and closed source licenses (GPL, MIT, BSD, CC, etc.), CLAs. -**Lecture 5:** Software Engineering in Industry *(intended to be a guest lecture).* +**Lecture 5:** *Software Engineering in Industry (intended to be a guest lecture)* -**Hands-on exercise 2:** Exploratory Data Analysis and Documentation. +**Hands-on exercise 2:** *Exploratory Data Analysis and Documentation* - Visualization and data exploration in Python (matplotlib, and more.) - Extracting inline software documentation with Sphinx. -**Lecture 6:** Computational physics. +**Lecture 6:** *Introduction to Computational Physics and Molecular Dynamics* -- Basics of solid state physics. -- Representing materials in computer programs, crystal structures, implementation considerations. +- Theoretical modeling of solid state properties. +- The anatomy of a molecular dynamics program: interaction potentials, integration of equations of motion. -**Lecture 7:** Software Testing, Debugging, and Profiling. +**Lecture 7:** *Software Testing, Debugging, and Profiling* - Unit/integration/system/acceptance tests, black/white box, (non-)functional, test-driven development, coverage, CI/CD. -- Debuggers, profiling tools. +- Debuggers, profiling tools, algorithmic complexity. -**Lecture 8:** Molecular dynamics. +**Lecture 8:** *Molecular Dynamics (cont.)* -- Molecular dynamics simulations; integrators, potentials. -- Anatomy of a molecular dynamics simulation program. +- Calculating instantaneous properties, timesteps, thermalization. +- More advanced interaction potentials. +- Time and ensemble averages; pressure, heat capacity, MSD, Lindemann criterion, self-diffusion cofficient. +- Finding equlibrium. -**Hands-on exercise 3:** Molecular dynamics and software testing. +**Hands-on exercise 3:** *Molecular dynamics and software testing* - Molecular dynamics with ASE and ASAP. - Unit tests and continous integration with GitHub actions. -**Lecture 9:** Concurrency and Parallelism. +**Lecture 9:** *Concurrency and Parallelism* -- Concurrency with coroutines, threads (OpenMP), processes (MPI) +- Concurrency with coroutines; parallel threads (OpenMP), processes (MPI) - Supercomputers. -**Hands-on excerise 4:** Supercomputing. +**Hands-on excerise 4:** *Supercomputing* - Supercomputer usage, queue scripts, high-throughput computations, etc. - Running ASAP-simulations on supercomputers. -**Lecture 10:** Databases, Wrap-up. +**Lecture 10:** *Databases and wrap-up* -- Relational databases, Normalization, Transactions/ACID, SQL; noSQL, mongoDB. -- Access to data via open APIs. -- Computer security aspects in software development. +- Relational databases, normalization, transactions/ACID, SQL; noSQL, mongoDB. +- Making data available via open APIs. - Final remarks about the project execution and final phases. +There is also some "extra credit" material distributed on: advanced programming concepts: programming paradigms, multi-paradigm programming, programming patterns; and computer security aspects in software development.