💡 Explanations

Introduction

• Introduction
  • Purpose and Capabilities
  • Transferability and Compatibility
  • Your Guide to MDANSE
  • Collaboration and Feedback
• Getting Started
  • MDANSE Installation
  • Explore the Documentation
  • Sample Data
• Workflow
  • 1. Trajectory conversion
  • 2a. Analysis parameters
    • Frames
    • Atom selection
    • Resolution
    • Weighting
    • Output files
  • 2b. Analysis results
  • 3. Plotting

Trajectory

• Converters
  • Specific converters
  • General converters
• Editors
  • Center Of Masses Trajectory
  • Trajectory Editor

Analysis

• Dynamics
  • Density of States
  • Mean Square Displacement
  • Position Correlation Function
  • Position Power Spectrum
  • Reorientational Time Correlation Function
  • Root Mean Square Deviation
  • Root Mean Square Fluctuation
  • Van Hove Function
  • Velocity Correlation Function
• Scattering
  • Scattering Background
  • Current Correlation Function
  • Dynamic Coherent Structure Factor
  • Dynamic Incoherent Structure Factor
  • Elastic Incoherent Structure Factor
  • Gaussian Dynamic Incoherent Structure Factor
  • Neutron Dynamic Total Structure Factor
  • Scattering Length Density Profile
  • Static Structure Factor
  • Static Structure Factor 3D
  • Structure Factor From Scattering Function
  • X-ray Static Structure Factor
• Structure
  • Area Per Molecule
  • Coordination Number
  • Eccentricity
  • Molecular Trace
  • Pair Distribution Function
  • Radius of Gyration
  • Solvent Accessible Surface
  • Voronoi
• Infrared
  • Infrared
  • Dipole Autocorrelation Function
• Thermodynamics
  • Density
  • Temperature

Parameterisation

• Time Series
  • Correlation Functions
  • Fourier Spectrum
  • Resolution Functions
• Weighting Scheme
  • Partial properties
  • Rescaled Weights
    • Single Atom-Type Weights
    • Double Atom-Type Weights (DCSF and CCF)
    • Double Atom-Type Weights (Other)
  • Squared Weights
• Results Grouping
  • Atom Grouping
  • Molecule Grouping
  • Other Groupings Schemes
    • Root Mean Square Deviation
    • Root Mean Square Fluctuation
• Atom Selection
  • Atom Selection Mechanism
    • Reusable Selection
    • Selection Builder
    • Selection Criteria
  • Atom Selection Results
• q-Vector Generation
  • Reciprocal Lattice q-Vectors
  • Random sampling of reciprocal space

Miscellaneous

• File Formats
  • HDF5 Based File Formats
  • DAT File Format
  • CSV files
  • H5MD Files
• Symbols and Notation