diff --git a/src/content/collab_proj_course.rst b/src/content/collab_proj_course.rst index 3e24756bc250b24d1b943cc9270fc6c3e69f7b26..f38e744f4b6df290fcf355f0483134865250aca5 100644 --- a/src/content/collab_proj_course.rst +++ b/src/content/collab_proj_course.rst @@ -22,7 +22,7 @@ Interested participants from academia and industry are most welcome to apply for * Next course start: **August 30, 2021.** * Course outline: 10 lectures, 4 hands-on exercises, and group work on a collaborative software project in computational physics. -* Sucessfully completeing the course corresponds to 9 ECTS points. +* Successfully completing the course corresponds to 9 ECTS points. * Teacher: `Rickard Armiento <https://liu.se/en/employee/ricar47>`__, associate professor in Physical Modelling and head of the Materials Design and Informatics unit at Linköping University. * Course homepage: https://mdi.gitlab-pages.liu.se/collab_proj_course.html * For any questions or concerns: contact `Rickard Armiento <https://liu.se/en/employee/ricar47>`__, rickard.armiento [at] liu.se @@ -42,15 +42,15 @@ Interested participants from academia and industry are most welcome to apply for - Molecular dynamics in Python with ASE and ASAP and automated testing (CI). - High-throughput computations on supercomputers. -The course takes place in the autumn term starting end of august/begninning of september. **For the fall 2021 round (during corona) participation will be possible fully by distance / video link.** (The degree to which this will be offered in the future is not yet determied.) +The course takes place in the autumn term starting end of August/beginning of September. **For the fall 2021 round (during Corona), participation will be possible fully by distance / video link.** (The degree to which this will be offered in the future is not yet determined.) **Dates** -* **August 30 - October 15** *Introductionary part* with 10 lectures (2h with 15 min break) and 4 practical hands-on exercises (each 4h). During this part the project groups organize, plan, and prepare their projects. +* **August 30 - October 15** *Introductionary part* with 10 lectures (2h with 15 min break) and 4 practical hands-on exercises (each 4h). During this part, the project groups organize, plan, and prepare their projects. * **November 1 - December 17** *Project execution part* in which the project groups do the primary part of the project work. The work is coordinated over the Internet using the tools for collaborative software engineering covered in the course. -* The project execution part ends with an oral presentation and a written final report. These are meant to be completed before the holidays, but in case the final report needs further revision there is an absolute final deadline in mid-January. +* The project execution part ends with an oral presentation and a written final report. These are meant to be completed before the holidays, but in case the final report needs further revision, there is an absolute final deadline in mid-January. **Prerequisites** @@ -63,17 +63,17 @@ The course takes place in the autumn term starting end of august/begninning of s Course Content Details ---------------------- -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 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 use 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. The hands-on computer exercises provide practical training in version control in collaborative software projects, automated testing (CI), visualization, and computer simulations based on computational physics. -The participants then apply the aquired skills in practice in a collaborative project to develop a software package for molecular dynamics simulations according to an agile project model. The software will be implemented, tested, documented, and run in high-throughput to generate big data which is explored, visualzed, and inserted in a database that is made externally accessible via an open API. The primary part of the project work is ongoing November-December and ends with a final examination in form of an oral presentation by the group and a final report. +The participants then apply the acquired skills in practice in a collaborative project to develop a software package for molecular dynamics simulations according to an agile project model. The software will be implemented, tested, documented, and run in high-throughput to generate big data, which is explored, visualized, and inserted in a database that is made externally accessible via an open API. The primary part of the project work is ongoing November-December. It ends with a final examination in the form of an oral presentation by the group and a final report. The course provides sufficient training on essential computational physics and molecular dynamics to allow students with less experience in these topics to participate. Nevertheless, the project also allows engaging more deeply in the computational physics aspects for those with more experience in the topic. -After completing the course the participants will be able to: +After completing the course, the participants will be able to: * identify and apply central concepts of collaborative software development and engineering, and be familiar with the basic functions of standard tools. * design, model, implement, test, document, and deliver a software system using modern practices and methodologies in software engineering, using an agile project model. @@ -88,7 +88,7 @@ Preliminary Outline of Lectures and Exercises **Lecture 2:** *Software Versioning and Collaborative Development* -- Version control systems (git, svn), commits/branching/mergning, collaborative workflows with pull requests and reviews (GitHub). +- Version control systems (git, svn), commits/branching/merging, collaborative workflows with pull requests and reviews (GitHub). **Hands-on exercise 1:** *Git and GitHub* @@ -116,7 +116,7 @@ Preliminary Outline of Lectures and Exercises **Lecture 6:** *Introduction to Computational Physics and Molecular Dynamics* -- Theoretical modeling of solid state properties. +- 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* @@ -128,20 +128,20 @@ Preliminary Outline of Lectures and Exercises - Calculating instantaneous properties, timesteps, thermalization. - More advanced interaction potentials. -- Time and ensemble averages; pressure, heat capacity, MSD, Lindemann criterion, self-diffusion cofficient. -- Finding the equlibrium structure. +- Time and ensemble averages; pressure, heat capacity, MSD, Lindemann criterion, self-diffusion coefficient. +- Finding the equilibrium structure. **Hands-on exercise 3:** *Molecular dynamics and software testing* - Molecular dynamics with ASE and ASAP. -- Unit tests and continous integration with GitHub actions. +- Unit tests and continuous integration with GitHub actions. **Lecture 9:** *Concurrency and Parallelism* - Concurrency with coroutines; parallel threads (OpenMP), processes (MPI) - Supercomputers. -**Hands-on excerise 4:** *Supercomputing* +**Hands-on exercise 4:** *Supercomputing* - Supercomputer usage, queue scripts, high-throughput computations, etc. - Running ASAP-simulations on supercomputers. @@ -154,4 +154,4 @@ Preliminary Outline of Lectures and Exercises -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. +There will also be some "extra credit" material distributed on: advanced programming concepts: programming paradigms, multi-paradigm programming, programming patterns; and computer security aspects in software development.