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Cleanup tools

We need to clean up the tool definitions and layout in the tool panel before we go live. Here is the suggested grouping and ordering of tools. Some tools are also missing help information and there is inconsistency in names. I've tried to clean that up here. Please go through each tool and update the relevant information. I may have missed some tools so please list them here and we can work out where they should go.

Get Data

  • Register Neutron Data <--- what is the difference between this and "Register Data Folder"?
  • Upload File
  • Initiate data ingress <--- inconsistent capitalization. what is this? I think "Automated Data Upload" with a proper description would be better
  • Register Data Folder

Powder Diffraction

  • PDF DiffPy-CMI Refinement: A tool to run a PDF Rietveld refinement using DiffPy-CMI.
  • GSAS2 BBO Refinement: A tool to run a black box optimized (BBO) GSAS2 Rietveld refinement.
  • GSAS2 Refinement: A tool to run a GSAS2 Rietveld refinement.
  • Pattern Matching: A tool to pattern match a group of patterns using clustering algorithms.
  • Single Peak Fitting: A tool to fit a single peak in a pattern.

Single Crystal Diffraction

  • IMAGINE-X image converter: Converts input files into .pngs for use with peak finding tool.
  • IMAGINE-X image generator: Image generation for IMAGINE-X beamline data reduction.
  • Occupancy Fitting: Fit occupancies to neutron data.
  • PDB to PQR Converter: Convert .pdb files to .pqr, fully adding all protons to all sites.
  • Peak Finding: A tool to find peaks in single crystal diffraction.
  • Topaz Combine: TOPAZ data combine tool
  • Topaz Reduce: TOPAZ data reduction tool
  • Topaz Data Reduction: Interactive user interface for TOPAZ Data Reduction
  • Jana2020 Visualizer: Runs the Jana2020 Crystallographic Computing System for Standard and Modulated Structures Software

Imaging

  • Amira Visualizer: Runs the Amira-Avizo 3D Software
  • Computed Tomography Reconstruction: This Computed Tomography Reconstruction interactive tool runs a full CT reconstruction in Jupyter Notebook.

Reflectometry

  • Refl1D Visualizer: Runs the Refl1D tool for analyzing 1D reflectometry measurements made with X-ray and neutron beamlines

SANS

  • GPSANS Reduction: GPSANS data reduction tool
  • USANS Reduction: USANS data reduction tool
  • SANS Data Reduction: Interactive user interface for SANS Data Reduction
  • Desmear_Iq: Desmear data and remove the instrument-resolution effect.
  • LAMMPS simulation - LJ+Yukawa: A tool to run a LAMMPS simulation of a colloidal suspension and then calculate the scattering spectra using FFTW
  • Plot_Iq: Generate LogLog plot of the input ascii file
  • Rebin_Iq: Rebin x-data of input file following the x-data of the reference input file.
  • SASView Visualizer: Runs the Small Angle Scattering Analysis Software

Direct-Geometry Spectroscopy

  • Incident Beamline Configurator: A tool to prepare input for incident beamline simulations from experimental data
  • Incident Beamline Simulator: A tool to run MCViNE incident beamline simulations
  • MCPL Tool: A tool to extract a header from an mcpl file.
  • Sample Simulator: A tool to run McVine simulations of a Sample
  • DCA Convert to MaxEnt input format: A tool to convert analysis results to MaxEnt format
  • DCA Binning Tool: A tool to run DCA binning.
  • DCA Bins for S of Q Omega: A tool to extract Q values from DCA++ results
  • DCA Convergence: A tool to run DCA convergence.
  • DCA MaxEnt: A tool to run Maxent.py
  • DCA Plot MaxEnt results: A tool to visualize MaxEnt results
  • DCA S of Q Omega Simulator: A tool to run s of q omega simulations
  • RPA simulation: A tool to run simulations of neutron scattering and superconductivity in correlated electron systems using the MRPA++ code
  • RPA plot chi(q,w): A tool to plot chi(q,w)

Chemical Spectroscopy

  • QClimax: Runs the QClimax code.
  • QClimax Ini File Creator: Create Ini file for QClimax
  • CP2K simulation: Runs DFT molecular dynamics (MD) with CP2K. Returns atomic coordinates and forces along the MD trajectory saved in xyz format.
  • CP2K output parsing: Extracts atomic coordinates and forces from the CP2K MD trajectory, and converts them into *.raw files needed by DeePMD.
  • LAMMPS simulation:
  • INS simulation with OCLIMAX: Simulation of INS spectra from LAMMPS MD trajectory
  • PClimax: Runs PClimax Tool
  • DeePMD training: Trains DeePMD model with INS data

Miscellaneous

  • Interactive Jupyter Notebook: Runs a Jupyter interactive notebook
  • Thinlinc: Runs an interactive Thinlinc session