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rheojax 0.6.1 documentation
rheojax 0.6.1 documentation

User Guide

  • User Guide: Graduate Student Learning Pathway
    • Section 1: Fundamentals (Weeks 1-2)
      • What is Rheology?
      • Material Classification
      • Test Modes in Rheology
      • Model Capabilities
      • Parameter Interpretation
    • Section 2: Model Usage (Weeks 3-6)
      • Getting Started with Model Fitting
      • Model Families Overview
      • Model Selection Guide
      • Fitting Strategies and Troubleshooting
    • Section 3: Advanced Topics (Weeks 7-12)
      • Bayesian Inference
      • Fractional Viscoelasticity: Mathematical Reference
      • Multi-Technique Fitting Guide
      • Time-Temperature Superposition (TTS)
      • Soft Glassy Rheology (SGR) Analysis
      • Sequence of Physical Processes (SPP)
      • ODE-Based Constitutive Models
      • Thixotropy and Yield Stress Analysis
      • Dense Suspensions and Glassy Materials
      • Transient Polymer Network Models (TNT + VLB)
      • Vitrimer and Nanocomposite Models
      • Complete Guide to Data Transforms
    • Section 4: Practical Guides (Weeks 13-16)
      • Pipeline API Tutorial
      • Modular API Tutorial
      • Model Inventory System
      • Data Format Reference
      • TA Instruments TRIOS Format
      • Data I/O Guide
      • Visualization Guide
      • Batch Processing
    • Section 5: Appendices
      • Experimental Design Guidelines
      • Material Property Database
      • Troubleshooting Guide
      • Glossary of Rheological Terms
    • GUI Reference Guide
      • Getting Started
      • Data Loading
      • Model Fitting
      • Bayesian Inference
      • Diagnostics
      • Transforms
      • Exporting
      • Menu Reference
      • Keyboard Shortcuts

API Reference

  • API Reference
    • Core Module (rheojax.core)
    • Models API
    • SPP Analysis API
    • Transforms API
    • Pipeline API
    • I/O Module (rheojax.io)
    • Utilities (rheojax.utils)
    • Logging (rheojax.logging)
    • Visualization (rheojax.visualization)

Handbooks

  • Models Handbook
    • Models Summary & Selection Guide
    • Classical Viscoelastic Models
      • Maxwell (Classical)
      • Zener (Standard Linear Solid)
      • SpringPot (Scott-Blair Element)
    • Fractional Viscoelastic Models
      • Fractional Maxwell Gel (Fractional)
      • Fractional Maxwell Liquid (Fractional)
      • Generalized Fractional Maxwell (Two-Order)
      • Fractional Kelvin-Voigt (Fractional)
      • Fractional Kelvin-Voigt-Zener (Fractional)
      • Fractional Zener Solid-Solid (Fractional)
      • Fractional Zener Solid-Liquid (Fractional)
      • Fractional Zener Liquid-Liquid (Fractional)
      • Fractional Jeffreys Model (Fractional)
      • Fractional Burgers Model (Fractional)
      • Fractional Poynting-Thomson (Fractional)
    • Generalized Maxwell Model (Multi-Mode)
    • Giesekus Nonlinear Viscoelastic Models
      • Giesekus Model — Handbook
    • Flow Curve Models
      • Power-Law (Ostwald–de Waele)
      • Bingham Plastic
      • Carreau Model
      • Carreau–Yasuda Model
      • Cross Model
      • Herschel-Bulkley Model
    • Isotropic-Kinematic Hardening (IKH) Models
      • Maxwell-Isotropic-Kinematic Hardening (MIKH)
      • Multi-Lambda Isotropic-Kinematic Hardening (ML-IKH)
    • Fractional IKH (FIKH) Models
      • Fractional Isotropic-Kinematic Hardening (FIKH)
      • Fractional Multi-Lambda IKH (FMLIKH)
    • DMT Thixotropic Models
      • DMT Thixotropic Models
    • Fluidity Models
      • Fluidity Local (Homogeneous Fluidity Model) — Handbook
      • Fluidity Nonlocal (Coussot-Ovarlez Cooperative Model) — Handbook
      • Fluidity-Saramito EVP Model
    • Hébraud-Lequeux (HL) Models
      • Hébraud–Lequeux (HL) Model — Handbook
    • Shear Transformation Zone (STZ) Models
      • Shear Transformation Zone (STZ)
    • Elasto-Plastic Models (EPM)
      • Elasto-Plastic Models (EPM)
      • JAX Implementation Utilities
      • Advanced Physics
      • Tensorial Elasto-Plastic Model (EPM)
      • Bayesian Inference for Tensorial EPM
      • Advanced Normal Stress Physics
      • Anisotropic Yielding: Hill Criterion Details
      • Enhanced Experimental Protocols
    • Soft Glassy Rheology (SGR) Models
      • SGR Conventional (Soft Glassy Rheology) — Handbook
      • SGR GENERIC (Thermodynamically Consistent)
    • ITT-MCT Models
      • ITT-MCT Schematic (F_1_2)
      • ITT-MCT Isotropic (ISM)
      • ITT-MCT Protocol Equations
    • Transient Network Theory (TNT)
      • TNT Protocol Equations — Shared Reference
      • TNT Knowledge Extraction Guide
      • TNT Tanaka-Edwards (Basic Transient Network) — Handbook
      • TNT Bell (Force-Dependent Breakage) — Handbook
      • TNT FENE-P (Finite Extensibility) — Handbook
      • TNT Non-Affine (Gordon-Schowalter) — Handbook
      • TNT Stretch-Creation (Enhanced Reformation) — Handbook
      • TNT Loop-Bridge (Two-Species Kinetics) — Handbook
      • TNT Sticky Rouse (Multi-Mode Sticker Dynamics) — Handbook
      • TNT Cates (Living Polymers / Wormlike Micelles) — Handbook
      • TNT Multi-Species (Multiple Bond Types) — Handbook
    • VLB Transient Network Models
      • VLB Transient Network Models
      • VLBVariant — Bell, FENE-P & Temperature
      • VLBNonlocal — Shear Banding PDE
      • VLB Protocol Equations & Derivations
      • VLB — What You Can Learn
      • VLB Advanced Theory & Numerical Methods
    • HVM (Hybrid Vitrimer Model)
      • HVM Model Reference
      • HVM Protocol Equations & Derivations
      • HVM Advanced Theory & Numerical Methods
      • HVM Knowledge Extraction Guide
    • HVNM (Hybrid Vitrimer Nanocomposite Model)
      • HVNMLocal — Full Model Reference
      • HVNM Protocol Equations & Derivations
      • HVNM Advanced Theory & Numerical Methods
      • HVNM Knowledge Extraction Guide
    • DMTA / DMA Analysis
      • DMTA Theory & Conversion
      • DMTA Model Selection & Applicability
      • Numerical Implementation
      • DMTA Workflows
      • DMTA Measurement Protocols
      • Knowledge Extraction from DMTA Data
      • Future Extensions
    • Sequence of Physical Processes (SPP) Models
      • SPP Decomposer (Sequence of Physical Processes)
      • SPP Yield Stress Model
  • Transforms
    • Transforms Summary & Workflow Guide
    • FFTAnalysis
    • Mastercurve (Time-Temperature Superposition)
    • MutationNumber
    • OWChirp
    • SmoothDerivative
    • Sequence of Physical Processes (SPP) Transform
    • Strain-Rate Frequency Superposition (SRFS)
    • PronyConversion
    • SpectrumInversion
    • LVEEnvelope
    • CoxMerz

Tutorial Notebooks

  • Tutorial Notebooks

Model Verification

  • Model Verification Reports

Developer Documentation

  • Architecture Overview
  • Contributing to RheoJAX

Additional Resources

  • Installation
  • Quickstart Guide
  • Development Status & Performance
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Menu Reference¶

Complete inventory of the RheoJAX menu bar, listing every QAction with its label, keyboard shortcut, status-bar tooltip, handler method, and notes on special behaviour (disabled, checkable, etc.).

The menu bar is implemented by rheojax.gui.app.menu_bar.MenuBar and wired to handlers in rheojax.gui.app.main_window.RheoJAXMainWindow.

Menu Groups

  • File Menu

  • Edit Menu

  • View Menu

  • Data Menu

  • Models Menu

    • Classical

    • Flow (Non-Newtonian)

    • Fractional > Maxwell Family

    • Fractional > Zener Family

    • Fractional > Advanced

    • Multi-Mode

    • Soft Glassy Rheology (SGR)

    • SPP (LAOS)

    • STZ (Shear Transformation Zone)

    • EPM (Elasto-Plastic)

    • Fluidity

    • Saramito (EVP)

    • IKH (Isotropic Kinematic Hardening)

    • FIKH (Fractional IKH)

    • Hébraud-Lequeux

    • ITT-MCT

    • DMT (Thixotropic)

    • Giesekus

    • TNT (Transient Network)

    • VLB (Viscoelastic Liquid-Bridge)

    • HVM (Hybrid Vitrimer)

    • HVNM (Vitrimer Nanocomposite)

  • Transforms Menu

  • Analysis Menu

  • Pipeline Menu

  • Tools Menu

  • Help Menu

  • Summary

File Menu¶

Attribute

Label

Shortcut

Status Tip

Handler

new_file_action

&New

Ctrl+N

Create a new project

_on_new_file

open_file_action

&Open…

Ctrl+O

Open an existing project

_on_open_file

save_file_action

&Save

Ctrl+S

Save the current project

_on_save_file

save_as_action

Save &As…

Ctrl+Shift+S

Save the current project with a new name

_on_save_as

import_action

&Import Data…

Ctrl+I

Import rheological data

_on_import

export_action

&Export Results…

Ctrl+E

Export analysis results

_on_export

exit_action

E&xit

Ctrl+Q

Exit the application

close

The File menu also contains a Recent Files submenu (initially empty).

Edit Menu¶

Attribute

Label

Shortcut

Status Tip

Handler

undo_action

&Undo

Ctrl+Z

Undo last action

_on_undo

redo_action

&Redo

Ctrl+Shift+Z

Redo last undone action

_on_redo

cut_action

Cu&t

Ctrl+X

Cut selection to clipboard

_on_cut

copy_action

&Copy

Ctrl+C

Copy selection to clipboard

_on_copy

paste_action

&Paste

Ctrl+V

Paste from clipboard

_on_paste

preferences_action

&Preferences…

Ctrl+,

Open preferences dialog

_on_preferences

Note

undo_action and redo_action are created disabled and are enabled dynamically when undo/redo history is available.

View Menu¶

Attribute

Label

Shortcut

Status Tip

Handler

zoom_in_action

Zoom &In

Ctrl+=

Zoom in on plot

_on_zoom_in

zoom_out_action

Zoom &Out

Ctrl+-

Zoom out on plot

_on_zoom_out

reset_zoom_action

&Reset Zoom

Ctrl+0

Reset plot zoom to default

_on_reset_zoom

view_data_dock_action

&Data Panel

—

Toggle data panel visibility

toggle sidebar visibility

view_log_dock_action

&Log Panel

—

Toggle log panel visibility

toggle log dock visibility

Theme submenu (View > Theme):

Attribute

Label

Shortcut

Status Tip

Handler

theme_light_action

&Light

—

—

_on_theme_changed("light")

theme_dark_action

&Dark

—

—

_on_theme_changed("dark")

theme_auto_action

&Auto (System)

—

—

_on_theme_changed("auto")

Note

view_data_dock_action, view_log_dock_action, and all three theme actions are checkable toggles. theme_auto_action is checked by default.

Data Menu¶

Attribute

Label

Shortcut

Status Tip

Handler

new_dataset_action

&New Dataset…

Ctrl+Shift+N

Create a new dataset

_on_new_dataset

delete_dataset_action

&Delete Dataset

Delete

Delete selected dataset

_on_delete_dataset

Set Test Mode submenu (Data > Set Test Mode):

Attribute

Label

Shortcut

Status Tip

Handler

test_mode_oscillation

&Oscillation

—

—

_on_set_test_mode("oscillation")

test_mode_relaxation

&Relaxation

—

—

_on_set_test_mode("relaxation")

test_mode_creep

&Creep

—

—

_on_set_test_mode("creep")

test_mode_rotation

R&otation

—

—

_on_set_test_mode("rotation")

test_mode_flow_curve

&Flow Curve

—

—

_on_set_test_mode("flow_curve")

test_mode_startup

&Startup

—

—

_on_set_test_mode("startup")

test_mode_laos

&LAOS

—

—

_on_set_test_mode("laos")

Attribute

Label

Shortcut

Status Tip

Handler

auto_detect_mode_action

&Auto-detect Test Mode

Ctrl+Shift+D

Automatically detect test mode from data

_on_auto_detect_mode

Models Menu¶

All model actions dispatch SET_ACTIVE_MODEL to the state store and navigate to the Fit page. Handler: _on_select_model(model_id).

Classical¶

Attribute

Label

Model ID

model_maxwell

Maxwell

maxwell

model_zener

Zener (SLS)

zener

model_springpot

SpringPot

springpot

Flow (Non-Newtonian)¶

Attribute

Label

Model ID

model_power_law

Power Law

power_law

model_carreau

Carreau

carreau

model_carreau_yasuda

Carreau-Yasuda

carreau_yasuda

model_cross

Cross

cross

model_herschel_bulkley

Herschel-Bulkley

herschel_bulkley

model_bingham

Bingham

bingham

Fractional > Maxwell Family¶

Attribute

Label

Model ID

model_fmaxwell_gel

Maxwell Gel

fractional_maxwell_gel

model_fmaxwell_liquid

Maxwell Liquid

fractional_maxwell_liquid

model_fmaxwell_model

Maxwell Model

fractional_maxwell_model

model_fkelvin_voigt

Kelvin-Voigt

fractional_kelvin_voigt

Fractional > Zener Family¶

Attribute

Label

Model ID

model_fzener_sl

Solid-Liquid (FZSL)

fractional_zener_sl

model_fzener_ss

Solid-Solid (FZSS)

fractional_zener_ss

model_fzener_ll

Liquid-Liquid (FZLL)

fractional_zener_ll

model_fkv_zener

KV-Zener (FKVZ)

fractional_kv_zener

Fractional > Advanced¶

Attribute

Label

Model ID

model_fburgers

Burgers (FBM)

fractional_burgers

model_fpoynting

Poynting-Thomson (FPT)

fractional_poynting_thomson

model_fjeffreys

Jeffreys (FJM)

fractional_jeffreys

Multi-Mode¶

Attribute

Label

Model ID

model_gmaxwell

Generalized Maxwell

generalized_maxwell

Soft Glassy Rheology (SGR)¶

Attribute

Label

Model ID

model_sgr_conventional

SGR Conventional

sgr_conventional

model_sgr_generic

SGR GENERIC

sgr_generic

SPP (LAOS)¶

Attribute

Label

Model ID

model_spp_yield_stress

SPP Yield Stress

spp_yield_stress

STZ (Shear Transformation Zone)¶

Attribute

Label

Model ID

model_stz_conventional

STZ Conventional

stz_conventional

EPM (Elasto-Plastic)¶

Attribute

Label

Model ID

model_lattice_epm

Lattice EPM

lattice_epm

model_tensorial_epm

Tensorial EPM

tensorial_epm

Fluidity¶

Attribute

Label

Model ID

model_fluidity_local

Fluidity Local

fluidity_local

model_fluidity_nonlocal

Fluidity Nonlocal

fluidity_nonlocal

Saramito (EVP)¶

Attribute

Label

Model ID

model_saramito_local

Saramito Local

fluidity_saramito_local

model_saramito_nonlocal

Saramito Nonlocal

fluidity_saramito_nonlocal

IKH (Isotropic Kinematic Hardening)¶

Attribute

Label

Model ID

model_mikh

MIKH

mikh

model_mlikh

MLIKH

ml_ikh

FIKH (Fractional IKH)¶

Attribute

Label

Model ID

model_fikh

FIKH

fikh

model_fmlikh

FMLIKH

fmlikh

Hébraud-Lequeux¶

Attribute

Label

Model ID

model_hebraud_lequeux

Hébraud-Lequeux

hebraud_lequeux

ITT-MCT¶

Attribute

Label

Model ID

model_itt_mct_schematic

Schematic (F₁₂)

itt_mct_schematic

model_itt_mct_isotropic

Isotropic (ISM)

itt_mct_isotropic

DMT (Thixotropic)¶

Attribute

Label

Model ID

model_dmt_local

DMT Local

dmt_local

model_dmt_nonlocal

DMT Nonlocal

dmt_nonlocal

Giesekus¶

Attribute

Label

Model ID

model_giesekus_single

Single Mode

giesekus_single

model_giesekus_multi

Multi Mode

giesekus_multi

TNT (Transient Network)¶

Attribute

Label

Model ID

model_tnt_single_mode

Single Mode

tnt_single_mode

model_tnt_cates

Cates

tnt_cates

model_tnt_loop_bridge

Loop-Bridge

tnt_loop_bridge

model_tnt_multi_species

Multi-Species

tnt_multi_species

model_tnt_sticky_rouse

Sticky Rouse

tnt_sticky_rouse

VLB (Viscoelastic Liquid-Bridge)¶

Attribute

Label

Model ID

model_vlb_local

Local

vlb_local

model_vlb_multi_network

Multi-Network

vlb_multi_network

model_vlb_variant

Variant (Bell/FENE)

vlb_variant

model_vlb_nonlocal

Nonlocal

vlb_nonlocal

HVM (Hybrid Vitrimer)¶

Attribute

Label

Model ID

model_hvm_local

HVM Local

hvm_local

HVNM (Vitrimer Nanocomposite)¶

Attribute

Label

Model ID

model_hvnm_local

HVNM Local

hvnm_local

Transforms Menu¶

All transform actions dispatch APPLY_TRANSFORM and run the transform via TransformService, either asynchronously through WorkerPool or synchronously as a fallback. Handler: _on_apply_transform(transform_id).

Attribute

Label

Status Tip

Transform ID

transform_fft

&FFT (Fourier Transform)

Apply Fast Fourier Transform

fft

transform_mastercurve

&Mastercurve (TTS)

Time-Temperature Superposition

mastercurve

transform_srfs

&SRFS (Strain-Rate Frequency Superposition)

Strain-Rate Frequency Superposition

srfs

transform_mutation

Mutation &Number

Calculate mutation number

mutation_number

transform_owchirp

&OWChirp

Optimally Windowed Chirp transform

owchirp

transform_derivatives

&Derivatives

Calculate numerical derivatives

derivative

transform_spp

S&PP (LAOS Analysis)

Sequence of Physical Processes yield stress extraction

spp

transform_cox_merz

Cox-&Merz Rule

Validate Cox-Merz rule (|η*| vs η)

cox_merz

transform_lve_envelope

LVE &Envelope

Linear viscoelastic startup stress envelope

lve_envelope

transform_prony

&Prony Conversion

Time ↔ frequency domain via Prony series decomposition

prony_conversion

transform_spectrum

&Spectrum Inversion

Recover relaxation spectrum H(τ) from G(t) or G*(ω)

spectrum_inversion

Note

mastercurve, srfs, and cox_merz are multi-dataset transforms that require ≥ 2 loaded datasets. If fewer are available the handler shows a status-bar warning and returns without executing.

Analysis Menu¶

Attribute

Label

Shortcut

Status Tip

Handler

analysis_fit_nlsq

&Fit (NLSQ)

Ctrl+F

Fit model using non-linear least squares

_on_fit

analysis_fit_bayesian

Fit &Bayesian (NUTS)

Ctrl+B

Fit model using Bayesian inference with NUTS

_on_bayesian

analysis_batch_fit

&Batch Fit…

—

Fit multiple datasets in parallel

_on_batch_fit

analysis_compare

&Compare Models…

—

Compare multiple model fits

_on_compare_models

analysis_compatibility

Check &Compatibility

—

Check model-data compatibility

_on_check_compatibility

Pipeline Menu¶

Attribute

Label

Shortcut

Status Tip

Handler

pipeline_new_action

&New Pipeline

Ctrl+Alt+N

Create a new empty pipeline

_on_new_pipeline

pipeline_open_action

&Open Pipeline…

—

Open a pipeline from a YAML file

_on_open_pipeline

pipeline_save_action

&Save Pipeline…

Ctrl+Shift+S

Save current pipeline to a YAML file

_on_save_pipeline

From Template submenu (Pipeline > From Template):

The template actions are stored in self.pipeline_template_actions (dict[str, QAction]) and each maps to _on_load_pipeline_template(key).

Dict Key

Label

Description

nlsq_fitting

NLSQ Fitting

Load → Fit (NLSQ) → Export workflow

bayesian_inference

Bayesian Inference

Load → Fit (NLSQ) → Bayesian (NUTS) → Export workflow

transform_fit

Transform + Fit

Load → Transform → Fit → Export workflow

Note

pipeline_save_action shares Ctrl+Shift+S with save_as_action (File menu). Qt resolves the ambiguity based on which menu is active. The Ctrl+Alt+N shortcut for New Pipeline was chosen to avoid colliding with Ctrl+Shift+N (New Dataset in Data menu).

Tools Menu¶

Attribute

Label

Shortcut

Status Tip

Handler

tools_console

&Python Console

Ctrl+Shift+P

Python console (coming soon)

_on_python_console

tools_jax_profiler

&JAX Profiler

—

JAX profiler (coming soon)

_on_jax_profiler

tools_memory_monitor

&Memory Monitor

—

Memory monitor (coming soon)

_on_memory_monitor

tools_preferences

&Preferences…

Ctrl+,

Open preferences dialog

_on_preferences

Note

tools_console, tools_jax_profiler, and tools_memory_monitor are created disabled — these features are planned but not yet implemented.

Help Menu¶

Attribute

Label

Shortcut

Status Tip

Handler

help_docs

&Documentation

F1

Open online documentation

_on_open_docs

help_tutorials

&Tutorials

—

View tutorials

_on_open_tutorials

help_shortcuts

&Keyboard Shortcuts

—

View keyboard shortcuts

_on_show_shortcuts

help_about

&About RheoJAX

—

About RheoJAX

_on_about

Summary¶

Menu

Actions

Notes

File

7

  • Recent Files submenu

Edit

6

Undo/Redo start disabled

View

8

5 checkable toggles

Data

10

7 test-mode submenu items

Models

53

20 family submenus

Transforms

11

3 multi-dataset transforms

Analysis

5

Pipeline

6

3 template actions in dict

Tools

4

3 disabled (future)

Help

4

Total

114

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On this page
  • Menu Reference
    • File Menu
    • Edit Menu
    • View Menu
    • Data Menu
    • Models Menu
      • Classical
      • Flow (Non-Newtonian)
      • Fractional > Maxwell Family
      • Fractional > Zener Family
      • Fractional > Advanced
      • Multi-Mode
      • Soft Glassy Rheology (SGR)
      • SPP (LAOS)
      • STZ (Shear Transformation Zone)
      • EPM (Elasto-Plastic)
      • Fluidity
      • Saramito (EVP)
      • IKH (Isotropic Kinematic Hardening)
      • FIKH (Fractional IKH)
      • Hébraud-Lequeux
      • ITT-MCT
      • DMT (Thixotropic)
      • Giesekus
      • TNT (Transient Network)
      • VLB (Viscoelastic Liquid-Bridge)
      • HVM (Hybrid Vitrimer)
      • HVNM (Vitrimer Nanocomposite)
    • Transforms Menu
    • Analysis Menu
    • Pipeline Menu
    • Tools Menu
    • Help Menu
    • Summary