List of scientific tools installed on Calvera
Chemical Spectroscopy
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| CP2K GUI | 0.3.0 | CP2K GUI | no | Link to Source | Link to Galaxy | |
| CP2K Output Parsing | 0.2.0 | Yongqiang Cheng | Extracts atomic coordinates and forces from the CP2K MD trajectory, and converts them into *.raw files needed by DeePMD. | no | Link to Source | Link to Galaxy |
| CP2K Simulation | 0.3.0 | Yongqiang Cheng | Runs DFT molecular dynamics (MD) with CP2K program. | no | Link to Source | Link to Galaxy |
| DeePMD Training | 0.2.0 | Yongqiang Cheng | Trains DeePMD model with inelastic neutron scattering data. | no | Link to Source | Link to Galaxy |
| INS Simulation with OCLIMAX | 0.2.0 | Yongqiang Cheng | Simulates inelastic neutron scattering spectra from LAMMPS MD trajectory. | no | Link to Source | Link to Galaxy |
| LAMMPS Simulation | 0.2.1 | Yongqiang Cheng | Simulates molecular dynamics trajectory using LAMMPS program. | no | Link to Source | Link to Galaxy |
| PClimax | 0.1.0 | Yongqiang Cheng | Prepares plot from OCLIMAX results. | no | Link to Source | Link to Galaxy |
Direct Geometry Spectroscopy
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| DCA Binning Tool (Cloud) | 0.4.0 | Thomas Maier | Runs DCA++ binning in ORC cloud infrastructure. | no | Link to Source | Link to Galaxy |
| DCA Binning Tool (HPC) | 0.5.0 | Thomas Maier | Runs DCA++ binning on HPC. | no | Link to Source | Link to Galaxy |
| DCA Bins for S of Q Omega (Cloud) | 0.2.0 | Thomas Maier | Extract Q values from DCA++ results, runs in ORC cloud infrastructure. | no | Link to Source | Link to Galaxy |
| DCA Bins for S of Q Omega (HPC) | 0.1.0 | Thomas Maier | Extract Q values from DCA++ results, runs on HPC. | no | Link to Source | Link to Galaxy |
| DCA Convergence (Cloud) | 0.4.0 | Thomas Maier | Runs DCA++ convergence in ORC cloud infrastructure. | no | Link to Source | Link to Galaxy |
| DCA Convergence (HPC) | 0.6.0 | Thomas Maier | Runs DCA++ convergence on HPC. | no | Link to Source | Link to Galaxy |
| DCA Convert to MaxEnt Input Format | 0.3.0 | Thomas Maier | Converts DCA++ analysis results to MaxEnt format. | no | Link to Source | Link to Galaxy |
| DCA MaxEnt | 0.2.1 | Thomas Maier | Processes DCA++ results using maximum entropy method. | no | Link to Source | Link to Galaxy |
| DCA Plot MaxEnt Results (Cloud) | 0.5.0 | Thomas Maier | Visualizes MaxEnt results, in ORC cloud infrastructure. | no | Link to Source | Link to Galaxy |
| DCA Plot MaxEnt Results (HPC) | 0.3.0 | Thomas Maier | Visualizes MaxEnt results, runs on HPC. | no | Link to Source | Link to Galaxy |
| DCA S of Q Omega Simulator | 0.4.0 | Thomas Maier | Runs S(Q,W) simulations. | no | Link to Source | Link to Galaxy |
| Get Instrument | 0.1.0 | Garrett Granroth | Creates a file with facility and instrument values for MCU workflow inputs. | no | Link to Source | Link to Galaxy |
| Incident Beamline Configurator | 0.2.0 | Garrett Granroth | Prepares input for incident beamline simulations using experimental data. | no | Link to Source | Link to Galaxy |
| Incident Beamline Simulator | 0.2.0 | Garrett Granroth | Runs incident beamline simulations. | yes | Link to Source | Link to Galaxy |
| MCPL Tool | 0.2.0 | Garrett Granroth | Extracts a header from a mcpl file. | no | Link to Source | Link to Galaxy |
| RPA Plot Chi(q,w) | 0.1.0 | Thomas Maier | Plots chi(q,w). | yes | Link to Source | Link to Galaxy |
| RPA Simulation | 0.2.0 | Thomas Maier | Runs simulations of neutron scattering and superconductivity in correlated electron systems using the MRPA++ code. | yes | Link to Source | Link to Galaxy |
| Sample Simulator | 0.1.1 | Garrett Granroth | Runs McVine simulations of a sample. | no | Link to Source | Link to Galaxy |
Get Data
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| Live Neutron Data Monitor | 0.4.0 | NDIP Team | This tool enables users to automatically ingress their experiment data in realtime. | no | Link to Source | Link to Galaxy |
| Load Neutron Data | 0.3.0 | NDIP Team | Loads file or folder on SNS/HFIR storage to Galaxy. | no | Link to Source | Link to Galaxy |
| Register File | 0.2.0 | NDIP Team | Registers file in Galaxy (internal tool, not exposed to users). | no | Link to Source | Link to Galaxy |
Imaging
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| Amira Visualizer | 0.1.0 | Jean Belheux | Runs the Amira-Avizo 3D Software. | no | Link to Source | Link to Galaxy |
| Computed Tomography Reconstruction | 2.0.0 | Jean Belheux | Runs a computed tomography reconstruction interactive tool in Jupyter Notebook. | no | Link to Source | Link to Galaxy |
| SAMMY R-Matrix Code | 0.8.0 | SAMMY is an R-matrix Bayesian fitting program used in the analysis of nuclear cross section data. | yes | Link to Source | Link to Galaxy |
Misc
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| Get Experiment Location | 0.1.0 | NDIP Team | Creates a file with facility and instrument values for workflow inputs. | no | Link to Source | Link to Galaxy |
| Interactive Jupyter Notebook | 0.2.1 | NDIP Team | Runs a generic Jupyter Notebook in interactive or non-interactive mode. | no | Link to Source | Link to Galaxy |
| Paraview Server | 0.1.0 | NDIP Team | Starts a remote Paraview Server. | no | Link to Source | Link to Galaxy |
| Thinlinc | 0.1.0 | NDIP Team | Runs an interactive Thinlinc session. | no | Link to Source | Link to Galaxy |
Powder Diffraction
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| GSAS2 BBO Refinement | 0.2.0 | Marshall McDonnell | Runs a black box optimized (BBO) GSAS2 Rietveld refinement. | no | Link to Source | Link to Galaxy |
| GSAS2 Refinement | 0.4.0 | Marshall McDonnell | Runs GSAS2 Rietveld refinement. | no | Link to Source | Link to Galaxy |
| PDF DiffPy-CMI Refinement | 0.3.0 | Marshall McDonnell | Runs a PDF Rietveld refinement using DiffPy-CMI. | no | Link to Source | Link to Galaxy |
| Pattern Matching | 0.3.0 | Marshall McDonnell | Matches a group of patterns using clustering algorithms. | yes | Link to Source | Link to Galaxy |
| Single Peak Fitting | 0.3.0 | Marshall McDonnell | Fits a single peak in a pattern. | yes | Link to Source | Link to Galaxy |
Reflectometry
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| Refl1D | 0.1.1 | Mathieu Doucet | Starts Refl1D interactive tool. | no | Link to Source | Link to Galaxy |
Sans
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| BIOSANS | 0.2.0 | Alan Hicks | Runs BIOSANS data reduction. | no | Link to Source | Link to Galaxy |
| Bio-SANS Data Reduction | 0.10.3 | Alan Hicks | Bio-SANS data reduction Trame application. | no | Link to Source | Link to Galaxy |
| Desmear_Iq | 0.1.1 | Changwoo Do | Desmears data and removes the instrument-resolution effect. | no | Link to Source | Link to Galaxy |
| GP-SANS Data Reduction | 0.10.0 | Yingrui Shang | GP-SANS data reduction Trame application. | no | Link to Source | Link to Galaxy |
| GPSANS | 0.3.0 | Yingrui Shang | Runs GPSANS data reduction. | no | Link to Source | Link to Galaxy |
| Interactive drtsans Notebook | 0.1.0 | NDIP Team | Runs a Jupyter Notebook with drtsans in interactive mode. | no | Link to Source | Link to Galaxy |
| LAMMPS Simulation - LJ+2Yukawa | 0.1 | Changwoo Do | Runs a LAMMPS simulation of a colloidal suspension and calculates the scattering spectra, using double Yukawa potential. | no | Link to Source | Link to Galaxy |
| LAMMPS Simulation - LJ+Yukawa | 0.1 | Changwoo Do | Runs a LAMMPS simulation of a colloidal suspension and calculates the scattering spectra, using Yukawa potential. | no | Link to Source | Link to Galaxy |
| Plot_Iq | 0.1.1 | Changwoo Do | Generates LogLog plot of the input ASCII file. | no | Link to Source | Link to Galaxy |
| Rebin_Iq | 0.1 | Changwoo Do | Rebins x-data of input file following the x-data of the reference input file. | no | Link to Source | Link to Galaxy |
| SASView | 0.1.0 | NDIP Team | Starts SASView interactive application. | no | Link to Source | Link to Galaxy |
| USANS | 0.1.0 | Yingrui Shang | Runs USANS data reduction. | no | Link to Source | Link to Galaxy |
Send Data
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| Export Datasets | 0.3.1 | NDIP Team | Exports data to SNS/HFIR storage. | no | Link to Source | Link to Galaxy |
Single Crystal Diffraction
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| Garnet | 0.2.0 | Zachary Morgan | Starts interactive single crystal grapical advanced reduction neutron event toolkit (GARNET). | no | Link to Source | Link to Galaxy |
| IMAGINE-X Image Converter | 0.1.0 | Marshall McDonnell | Converts input files into .pngs for use with peak finding tool. | no | Link to Source | Link to Galaxy |
| IMAGINE-X Image Generator | 0.1.0 | Marshall McDonnell | Generates images for IMAGINE-X beamline data reduction. | no | Link to Source | Link to Galaxy |
| Jana2020 Visualizer | 0.14 | Xiaoping Wang | Starts the interactive Jana2020 Crystallographic Computing System for Standard and Modulated Structures Software. | no | Link to Source | Link to Galaxy |
| Occupancy Fitting | 0.1.1 | Marshall McDonnell | Fits occupancies to neutron data. | no | Link to Source | Link to Galaxy |
| PDB to PQR Converter | 1.1.0 | Marshall McDonnell | Converts .pdb files to .pqr, fully adding all protons to all sites. | no | Link to Source | Link to Galaxy |
| Peak Finding | 0.1.0 | Marshall McDonnell | Finds peaks in single crystal diffraction. | yes | Link to Source | Link to Galaxy |
| Topaz Combine | 0.4.0 | Xiaoping Wang | Runs TOPAZ data reduction - combine part. | no | Link to Source | Link to Galaxy |
| Topaz Data Reduction | 0.15.0 | Xiaoping Wang | Starts interactive user interface for TOPAZ Data Reduction. | no | Link to Source | Link to Galaxy |
| Topaz Reduce | 0.4.0 | Xiaoping Wang | Runs TOPAZ data reduction - reduce part. | no | Link to Source | Link to Galaxy |
Triple Axis Spectroscopy
| Name | Version | Contact | Description | Tests | Source | Galaxy Link |
|---|---|---|---|---|---|---|
| Sunny - Interactive Jupyter Notebook ORNL | 0.3.0 | GRAVITAS Team | Runs a generic Jupyter Notebook in interactive or non-interactive mode. | no | Link to Source | Link to Galaxy |
Total: 65 tools
autogenerated (at 2025-05-28 14:21:45) from the main branch of the tools repository