uma-ase WebApp

## Input Details

Input file
Charge
Spin Multiplicity

### Summary

    No structure loaded.

Viewer loading...

Viewer file: No file selected
Loaded structure: None

## Input Details

Selected Input file No file selected
Charge
Spin Multiplicity
MLFF Checkpoint
MLFF Task
Run Type
Single Point GeoOpt Frequencies Transition State
Optimizer
Force (eV/Å)
Max GeoOpt Iter

Vib Analysis Settings

Temperature (K)
Pressure (Pa)

### Summary

    No structure loaded.

## Results

Select an input file and run a job to see results here.

## Input Details

Select a Folder
No folder selected
MLFF Checkpoint
MLFF Task
Run Type
Single Point GeoOpt Frequencies Transition State
Optimizer
Force (eV/Å)
Max Iter

Vib Analysis Settings

Temperature (K)
Pressure (Pa)

### Summary

    No folder selected.

## Results

## Analyze

### Input sources

Pick a folder of logs/XYZ files or add individual files for the analysis jobs.

Select a folder

No folder selected.

Select files

No files selected.

#### RMSD Report

Reads uma-ase .log files (Formula, RMSD, uma model, optimizer) and generates a bar plot and a table of RMSDs by formula.

#### XYZ Pair Analysis

Matches *.xyz files with their *geoopt-OPT* counterparts and detailed geometry analysis. Python script provided by A. Solé-Daura.

#### Simple Geometry Analysis

Calculate pairwise distance matrices for uploaded structures and visualize atom-pair distance distributions.

Structure
No structure selected.

##### Distance Matrix (Å)

##### Pair Distance Histogram

## Input Details

Selected Input file No file selected
Charge
Spin Multiplicity
MLFF Checkpoint
MLFF Task
Dynamics Engine
Steps
Timestep (fs)
Trajectory Interval (steps)
Log Interval (steps)
Target Temperature (K)
Friction (1/fs)
Thermostat Relaxation (fs)
Target Pressure (bar)
Compressibility (1/bar)
Barostat Relaxation (fs)

Nosé-Hoover Parameters

Thermostat Damping (fs)
Chain Length
Thermostat Sub-steps
Bussi Time Constant (fs)
Andersen Collision Probability

MTK Parameters

Thermostat Damping (fs)
Barostat Damping (fs)
Thermostat Chain Length
Barostat Chain Length
Thermostat Sub-steps
Barostat Sub-steps
BAOAB Thermostat Tau (fs)

BAOAB Barostat Options

Barostat Tau (fs)
Cell Mass (ASE units)
Mass Factor
Hydrostatic cell (preserve shape)

Melchionna Controls

Thermostat Time (fs)
Barostat Time (fs)
Bulk Modulus (GPa)
Mask (comma separated, e.g. 1,1,1)

Periodic Boundary Conditions

Apply periodic boundary conditions
Cell a (Å)
Cell b (Å)
Cell c (Å)
Alpha (°)
Beta (°)
Gamma (°)

### Summary

    No structure loaded.

## MD Output

Upload a structure and configure molecular dynamics options to begin.

### MD Simulations Live

Requires an active MD run.

### Trajectories

Load an ASE trajectory (.traj) or a multi-xyz (.xyz) file

No trajectory loaded.

### Vibrational Normal Modes

Modes archive (.zip)

No archive selected.

Reference log (.log)

No log selected.

Select the matching `-FREQS-modes.zip` bundle and its log file to enable normal-mode playback.

#### Normal Mode Controls

Select a mode to animate
Load an archive and log file to enable normal-mode controls.

### Playback Controls

Playback speed
30 fps

3D viewer idle. Load a trajectory to begin.

Frame: No frames loaded.

### Energy vs Time Step

## README documentation

Rendered directly from `README.md` via the backend.

The project documentation will appear here after it loads.