From 49e4d7ea8347718070e51c91e699cdbcfe6dd301 Mon Sep 17 00:00:00 2001 From: Spencer Bryngelson Date: Tue, 17 Jun 2025 23:28:35 -0400 Subject: [PATCH 1/2] rp --- group-syllabus/research-process.md | 292 +++++++++++++++++++++++++++++ 1 file changed, 292 insertions(+) create mode 100644 group-syllabus/research-process.md diff --git a/group-syllabus/research-process.md b/group-syllabus/research-process.md new file mode 100644 index 0000000..7381811 --- /dev/null +++ b/group-syllabus/research-process.md @@ -0,0 +1,292 @@ +# Research Process in Computational Physics + +This document illustrates the typical research process in our computational physics group. +These visual guides will help you understand the workflow and methodologies we use. + +## Overall Research Workflow + +```mermaid +flowchart TD + Idea[Research Idea] --> Literature[Literature Review] + Literature --> Question[Research Question Formulation] + Question --> Methods[Method Selection] + Methods --> Implementation[Implementation] + Implementation --> Verification[Verification & Validation] + Verification --> Analysis[Analysis of Results] + Analysis --> Interpretation[Interpretation] + Interpretation --> Communication[Communication of Results] + Communication --> Publication[Publication] + Publication --> Impact[Impact & Next Steps] + + style Idea fill:#f9f9f9,stroke:#333,stroke-width:2px + style Question fill:#d5e5f9,stroke:#333,stroke-width:2px + style Implementation fill:#f9d5e5,stroke:#333,stroke-width:2px + style Analysis fill:#e5f9d5,stroke:#333,stroke-width:2px + style Publication fill:#f9e5d5,stroke:#333,stroke-width:2px +``` + +## Computational Method Development Cycle + +```mermaid +flowchart TD + Problem[Problem Definition] --> Theory[Theoretical Foundation] + Theory --> Algorithm[Algorithm Design] + Algorithm --> Implementation[Implementation] + Implementation --> Testing[Testing & Debugging] + Testing --> Verification[Verification] + Verification --> Validation[Validation] + Validation --> Performance[Performance Optimization] + Performance --> Documentation[Documentation] + Documentation --> Release[Release & Sharing] + + Testing -- Issues Found --> Algorithm + Verification -- Failed --> Algorithm + Validation -- Failed --> Theory + + style Problem fill:#f9f9f9,stroke:#333,stroke-width:2px + style Algorithm fill:#d5e5f9,stroke:#333,stroke-width:2px + style Implementation fill:#f9d5e5,stroke:#333,stroke-width:2px + style Verification fill:#e5f9d5,stroke:#333,stroke-width:2px + style Performance fill:#f9e5d5,stroke:#333,stroke-width:2px +``` + +## Publication Workflow + +```mermaid +flowchart TD + Research[Research Completion] --> Results[Significant Results] + Results --> Audience[Target Audience Identification] + Audience --> Venue[Journal/Conference Selection] + Venue --> Outline[Paper Outline] + Outline --> Draft[First Draft] + Draft --> Figures[Figure Preparation] + Figures --> Revision[Internal Revision] + Revision --> Feedback[Peer Feedback] + Feedback --> FinalDraft[Final Draft] + FinalDraft --> Submission[Submission] + Submission --> Review[Peer Review] + Review -- Accept --> Publication[Publication] + Review -- Revise --> Revisions[Major/Minor Revisions] + Revisions --> Resubmission[Resubmission] + Resubmission --> Review + Review -- Reject --> Rethink[Rethink & Resubmit Elsewhere] + Rethink --> Venue + + style Results fill:#d5e5f9,stroke:#333,stroke-width:2px + style Draft fill:#f9d5e5,stroke:#333,stroke-width:2px + style Submission fill:#e5f9d5,stroke:#333,stroke-width:2px + style Publication fill:#f9e5d5,stroke:#333,stroke-width:2px +``` + +## Verification and Validation Process + +```mermaid +flowchart TD + subgraph Verification["Verification (Are we solving the equations correctly?)"] + CodeReview[Code Review] --> UnitTests[Unit Tests] + UnitTests --> Convergence[Convergence Tests] + Convergence --> Benchmarks[Benchmark Problems] + Benchmarks --> MMS[Method of Manufactured Solutions] + end + + subgraph Validation["Validation (Are we solving the right equations?)"] + SimpleCases[Simple Test Cases] --> AnalyticalSolutions[Comparison with Analytical Solutions] + AnalyticalSolutions --> ExperimentalData[Comparison with Experimental Data] + ExperimentalData --> OtherCodes[Comparison with Other Codes] + OtherCodes --> UQ[Uncertainty Quantification] + end + + Implementation[Code Implementation] --> Verification + Verification --> Validation + Validation --> Confidence[Confidence in Results] + + style Implementation fill:#f9f9f9,stroke:#333,stroke-width:2px + style Verification fill:#d5e5f9,stroke:#333,stroke-width:2px + style Validation fill:#f9d5e5,stroke:#333,stroke-width:2px + style Confidence fill:#e5f9d5,stroke:#333,stroke-width:2px +``` + +## Data Analysis Pipeline + +```mermaid +flowchart LR + subgraph Simulation["Simulation"] + Config[Configuration] --> Run[Simulation Run] + Run --> RawData[Raw Data] + end + + subgraph Processing["Data Processing"] + RawData --> Filtering[Filtering & Cleaning] + Filtering --> Transform[Transformations] + Transform --> Feature[Feature Extraction] + end + + subgraph Analysis["Analysis"] + Feature --> Visualization[Visualization] + Visualization --> Statistics[Statistical Analysis] + Statistics --> ML[Machine Learning/Pattern Recognition] + end + + subgraph Interpretation["Interpretation"] + ML --> Compare[Comparison with Theory] + Compare --> Insights[Physical Insights] + Insights --> Conclusions[Conclusions] + end + + style Simulation fill:#d5e5f9,stroke:#333,stroke-width:2px + style Processing fill:#f9d5e5,stroke:#333,stroke-width:2px + style Analysis fill:#e5f9d5,stroke:#333,stroke-width:2px + style Interpretation fill:#f9e5d5,stroke:#333,stroke-width:2px +``` + +## Collaborative Research Model + +```mermaid +flowchart TD + subgraph Team["Research Team"] + PI[Principal Investigator] --- PostDocs[Postdoctoral Researchers] + PI --- PhDs[PhD Students] + PI --- Masters[Masters Students] + PI --- Undergrads[Undergraduate Researchers] + PostDocs --- PhDs + PhDs --- Masters + PhDs --- Undergrads + end + + subgraph Collaborators["External Collaborators"] + Academic[Academic Partners] --- Industry[Industry Partners] + Academic --- Labs[National Labs] + Academic --- International[International Collaborators] + end + + Team --- Collaborators + + subgraph Infrastructure["Research Infrastructure"] + Computing[Computing Resources] --- Software[Software Tools] + Computing --- Data[Data Resources] + Software --- Methods[Methods & Algorithms] + end + + Team --- Infrastructure + Collaborators --- Infrastructure + + style Team fill:#d5e5f9,stroke:#333,stroke-width:2px + style Collaborators fill:#f9d5e5,stroke:#333,stroke-width:2px + style Infrastructure fill:#e5f9d5,stroke:#333,stroke-width:2px +``` + +## Problem-Solving Approach + +```mermaid +flowchart TD + Problem[Problem Identification] --> Simplify[Simplify & Abstract] + Simplify --> Literature[Literature Search] + Literature --> Approach[Approach Selection] + + Approach --> Analytical[Analytical Approach] + Approach --> Numerical[Numerical Approach] + Approach --> Hybrid[Hybrid Approach] + + Analytical --> Model[Mathematical Model] + Numerical --> Discretization[Discretization] + Hybrid --> Combined[Combined Methods] + + Model --> Solution[Analytical Solution] + Discretization --> Implementation[Numerical Implementation] + Combined --> Integration[Integrated Solution] + + Solution --> Validation[Validation] + Implementation --> Validation + Integration --> Validation + + Validation --> Refinement[Refinement] + Refinement -- If needed --> Approach + Validation --> Results[Results & Interpretation] + + style Problem fill:#f9f9f9,stroke:#333,stroke-width:2px + style Approach fill:#d5e5f9,stroke:#333,stroke-width:2px + style Model fill:#f9d5e5,stroke:#333,stroke-width:2px + style Discretization fill:#f9d5e5,stroke:#333,stroke-width:2px + style Combined fill:#f9d5e5,stroke:#333,stroke-width:2px + style Validation fill:#e5f9d5,stroke:#333,stroke-width:2px + style Results fill:#f9e5d5,stroke:#333,stroke-width:2px +``` + +## Computational Physics Research Areas + +```mermaid +mindmap + root((Computational
Physics)) + Fluid Dynamics + ::icon(fa fa-water) + Multiphase Flows + Turbulence Modeling + Compressible Flows + Microfluidics + Materials Science + ::icon(fa fa-cube) + Molecular Dynamics + Quantum Chemistry + Material Properties + Phase Transitions + High Performance Computing + ::icon(fa fa-microchip) + Parallel Algorithms + GPU Computing + Exascale Computing + Performance Optimization + Machine Learning + ::icon(fa fa-brain) + Physics-Informed Neural Networks + Surrogate Modeling + Data-Driven Discovery + Uncertainty Quantification + Numerical Methods + ::icon(fa fa-calculator) + Finite Element Methods + Spectral Methods + Meshless Methods + Adaptive Mesh Refinement +``` + +## Typical Project Timeline + +```mermaid +gantt + title Research Project Timeline + dateFormat YYYY-MM + axisFormat %b %Y + + section Planning + Literature Review :a1, 2023-01, 2m + Problem Formulation :a2, after a1, 1m + Method Selection :a3, after a2, 1m + + section Implementation + Initial Implementation :b1, after a3, 2m + Testing & Debugging :b2, after b1, 1m + Verification & Validation :b3, after b2, 2m + + section Analysis + Data Collection :c1, after b3, 3m + Data Analysis :c2, after c1, 2m + Result Interpretation :c3, after c2, 1m + + section Dissemination + Paper Writing :d1, after c3, 2m + Internal Review :d2, after d1, 1m + Submission & Revision :d3, after d2, 3m + Conference Presentation :milestone, m1, 2024-01, 1d + Publication :milestone, m2, 2024-04, 1d +``` + +## Using These Diagrams + +These diagrams provide visual guides to our research processes. They are meant to: + +1. **Clarify expectations**: Understand the steps involved in research projects +2. **Provide structure**: Follow established workflows for efficiency +3. **Enable planning**: Anticipate upcoming phases of your research +4. **Facilitate communication**: Use common terminology and process understanding + +Remember that real research is often non-linear and iterative. These diagrams represent idealized processes that will need to be adapted to specific research challenges. \ No newline at end of file From cd20007ca59cbd1da4325de5c241c2dfdcc2717b Mon Sep 17 00:00:00 2001 From: Spencer Bryngelson Date: Tue, 17 Jun 2025 23:32:51 -0400 Subject: [PATCH 2/2] asdf --- group-syllabus/research-process.md | 292 ----------------------------- readme.md | 2 - 2 files changed, 294 deletions(-) delete mode 100644 group-syllabus/research-process.md diff --git a/group-syllabus/research-process.md b/group-syllabus/research-process.md deleted file mode 100644 index 7381811..0000000 --- a/group-syllabus/research-process.md +++ /dev/null @@ -1,292 +0,0 @@ -# Research Process in Computational Physics - -This document illustrates the typical research process in our computational physics group. -These visual guides will help you understand the workflow and methodologies we use. - -## Overall Research Workflow - -```mermaid -flowchart TD - Idea[Research Idea] --> Literature[Literature Review] - Literature --> Question[Research Question Formulation] - Question --> Methods[Method Selection] - Methods --> Implementation[Implementation] - Implementation --> Verification[Verification & Validation] - Verification --> Analysis[Analysis of Results] - Analysis --> Interpretation[Interpretation] - Interpretation --> Communication[Communication of Results] - Communication --> Publication[Publication] - Publication --> Impact[Impact & Next Steps] - - style Idea fill:#f9f9f9,stroke:#333,stroke-width:2px - style Question fill:#d5e5f9,stroke:#333,stroke-width:2px - style Implementation fill:#f9d5e5,stroke:#333,stroke-width:2px - style Analysis fill:#e5f9d5,stroke:#333,stroke-width:2px - style Publication fill:#f9e5d5,stroke:#333,stroke-width:2px -``` - -## Computational Method Development Cycle - -```mermaid -flowchart TD - Problem[Problem Definition] --> Theory[Theoretical Foundation] - Theory --> Algorithm[Algorithm Design] - Algorithm --> Implementation[Implementation] - Implementation --> Testing[Testing & Debugging] - Testing --> Verification[Verification] - Verification --> Validation[Validation] - Validation --> Performance[Performance Optimization] - Performance --> Documentation[Documentation] - Documentation --> Release[Release & Sharing] - - Testing -- Issues Found --> Algorithm - Verification -- Failed --> Algorithm - Validation -- Failed --> Theory - - style Problem fill:#f9f9f9,stroke:#333,stroke-width:2px - style Algorithm fill:#d5e5f9,stroke:#333,stroke-width:2px - style Implementation fill:#f9d5e5,stroke:#333,stroke-width:2px - style Verification fill:#e5f9d5,stroke:#333,stroke-width:2px - style Performance fill:#f9e5d5,stroke:#333,stroke-width:2px -``` - -## Publication Workflow - -```mermaid -flowchart TD - Research[Research Completion] --> Results[Significant Results] - Results --> Audience[Target Audience Identification] - Audience --> Venue[Journal/Conference Selection] - Venue --> Outline[Paper Outline] - Outline --> Draft[First Draft] - Draft --> Figures[Figure Preparation] - Figures --> Revision[Internal Revision] - Revision --> Feedback[Peer Feedback] - Feedback --> FinalDraft[Final Draft] - FinalDraft --> Submission[Submission] - Submission --> Review[Peer Review] - Review -- Accept --> Publication[Publication] - Review -- Revise --> Revisions[Major/Minor Revisions] - Revisions --> Resubmission[Resubmission] - Resubmission --> Review - Review -- Reject --> Rethink[Rethink & Resubmit Elsewhere] - Rethink --> Venue - - style Results fill:#d5e5f9,stroke:#333,stroke-width:2px - style Draft fill:#f9d5e5,stroke:#333,stroke-width:2px - style Submission fill:#e5f9d5,stroke:#333,stroke-width:2px - style Publication fill:#f9e5d5,stroke:#333,stroke-width:2px -``` - -## Verification and Validation Process - -```mermaid -flowchart TD - subgraph Verification["Verification (Are we solving the equations correctly?)"] - CodeReview[Code Review] --> UnitTests[Unit Tests] - UnitTests --> Convergence[Convergence Tests] - Convergence --> Benchmarks[Benchmark Problems] - Benchmarks --> MMS[Method of Manufactured Solutions] - end - - subgraph Validation["Validation (Are we solving the right equations?)"] - SimpleCases[Simple Test Cases] --> AnalyticalSolutions[Comparison with Analytical Solutions] - AnalyticalSolutions --> ExperimentalData[Comparison with Experimental Data] - ExperimentalData --> OtherCodes[Comparison with Other Codes] - OtherCodes --> UQ[Uncertainty Quantification] - end - - Implementation[Code Implementation] --> Verification - Verification --> Validation - Validation --> Confidence[Confidence in Results] - - style Implementation fill:#f9f9f9,stroke:#333,stroke-width:2px - style Verification fill:#d5e5f9,stroke:#333,stroke-width:2px - style Validation fill:#f9d5e5,stroke:#333,stroke-width:2px - style Confidence fill:#e5f9d5,stroke:#333,stroke-width:2px -``` - -## Data Analysis Pipeline - -```mermaid -flowchart LR - subgraph Simulation["Simulation"] - Config[Configuration] --> Run[Simulation Run] - Run --> RawData[Raw Data] - end - - subgraph Processing["Data Processing"] - RawData --> Filtering[Filtering & Cleaning] - Filtering --> Transform[Transformations] - Transform --> Feature[Feature Extraction] - end - - subgraph Analysis["Analysis"] - Feature --> Visualization[Visualization] - Visualization --> Statistics[Statistical Analysis] - Statistics --> ML[Machine Learning/Pattern Recognition] - end - - subgraph Interpretation["Interpretation"] - ML --> Compare[Comparison with Theory] - Compare --> Insights[Physical Insights] - Insights --> Conclusions[Conclusions] - end - - style Simulation fill:#d5e5f9,stroke:#333,stroke-width:2px - style Processing fill:#f9d5e5,stroke:#333,stroke-width:2px - style Analysis fill:#e5f9d5,stroke:#333,stroke-width:2px - style Interpretation fill:#f9e5d5,stroke:#333,stroke-width:2px -``` - -## Collaborative Research Model - -```mermaid -flowchart TD - subgraph Team["Research Team"] - PI[Principal Investigator] --- PostDocs[Postdoctoral Researchers] - PI --- PhDs[PhD Students] - PI --- Masters[Masters Students] - PI --- Undergrads[Undergraduate Researchers] - PostDocs --- PhDs - PhDs --- Masters - PhDs --- Undergrads - end - - subgraph Collaborators["External Collaborators"] - Academic[Academic Partners] --- Industry[Industry Partners] - Academic --- Labs[National Labs] - Academic --- International[International Collaborators] - end - - Team --- Collaborators - - subgraph Infrastructure["Research Infrastructure"] - Computing[Computing Resources] --- Software[Software Tools] - Computing --- Data[Data Resources] - Software --- Methods[Methods & Algorithms] - end - - Team --- Infrastructure - Collaborators --- Infrastructure - - style Team fill:#d5e5f9,stroke:#333,stroke-width:2px - style Collaborators fill:#f9d5e5,stroke:#333,stroke-width:2px - style Infrastructure fill:#e5f9d5,stroke:#333,stroke-width:2px -``` - -## Problem-Solving Approach - -```mermaid -flowchart TD - Problem[Problem Identification] --> Simplify[Simplify & Abstract] - Simplify --> Literature[Literature Search] - Literature --> Approach[Approach Selection] - - Approach --> Analytical[Analytical Approach] - Approach --> Numerical[Numerical Approach] - Approach --> Hybrid[Hybrid Approach] - - Analytical --> Model[Mathematical Model] - Numerical --> Discretization[Discretization] - Hybrid --> Combined[Combined Methods] - - Model --> Solution[Analytical Solution] - Discretization --> Implementation[Numerical Implementation] - Combined --> Integration[Integrated Solution] - - Solution --> Validation[Validation] - Implementation --> Validation - Integration --> Validation - - Validation --> Refinement[Refinement] - Refinement -- If needed --> Approach - Validation --> Results[Results & Interpretation] - - style Problem fill:#f9f9f9,stroke:#333,stroke-width:2px - style Approach fill:#d5e5f9,stroke:#333,stroke-width:2px - style Model fill:#f9d5e5,stroke:#333,stroke-width:2px - style Discretization fill:#f9d5e5,stroke:#333,stroke-width:2px - style Combined fill:#f9d5e5,stroke:#333,stroke-width:2px - style Validation fill:#e5f9d5,stroke:#333,stroke-width:2px - style Results fill:#f9e5d5,stroke:#333,stroke-width:2px -``` - -## Computational Physics Research Areas - -```mermaid -mindmap - root((Computational
Physics)) - Fluid Dynamics - ::icon(fa fa-water) - Multiphase Flows - Turbulence Modeling - Compressible Flows - Microfluidics - Materials Science - ::icon(fa fa-cube) - Molecular Dynamics - Quantum Chemistry - Material Properties - Phase Transitions - High Performance Computing - ::icon(fa fa-microchip) - Parallel Algorithms - GPU Computing - Exascale Computing - Performance Optimization - Machine Learning - ::icon(fa fa-brain) - Physics-Informed Neural Networks - Surrogate Modeling - Data-Driven Discovery - Uncertainty Quantification - Numerical Methods - ::icon(fa fa-calculator) - Finite Element Methods - Spectral Methods - Meshless Methods - Adaptive Mesh Refinement -``` - -## Typical Project Timeline - -```mermaid -gantt - title Research Project Timeline - dateFormat YYYY-MM - axisFormat %b %Y - - section Planning - Literature Review :a1, 2023-01, 2m - Problem Formulation :a2, after a1, 1m - Method Selection :a3, after a2, 1m - - section Implementation - Initial Implementation :b1, after a3, 2m - Testing & Debugging :b2, after b1, 1m - Verification & Validation :b3, after b2, 2m - - section Analysis - Data Collection :c1, after b3, 3m - Data Analysis :c2, after c1, 2m - Result Interpretation :c3, after c2, 1m - - section Dissemination - Paper Writing :d1, after c3, 2m - Internal Review :d2, after d1, 1m - Submission & Revision :d3, after d2, 3m - Conference Presentation :milestone, m1, 2024-01, 1d - Publication :milestone, m2, 2024-04, 1d -``` - -## Using These Diagrams - -These diagrams provide visual guides to our research processes. They are meant to: - -1. **Clarify expectations**: Understand the steps involved in research projects -2. **Provide structure**: Follow established workflows for efficiency -3. **Enable planning**: Anticipate upcoming phases of your research -4. **Facilitate communication**: Use common terminology and process understanding - -Remember that real research is often non-linear and iterative. These diagrams represent idealized processes that will need to be adapted to specific research challenges. \ No newline at end of file diff --git a/readme.md b/readme.md index 2b0caae..4ab6c09 100644 --- a/readme.md +++ b/readme.md @@ -10,8 +10,6 @@ Welcome to the Computational Physics @ GT Group Documentation! This repository c - [Welcome to the group!](group-syllabus/intro-to-group.md) - [FAQ - Frequently Asked Questions](group-syllabus/faq.md) -- [Research Process Diagrams](group-syllabus/research-process.md) -- [PhD Timeline & Milestones](group-syllabus/phd-timeline.md) ## 🎓 Syllabus