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.

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.

README documentation

Rendered directly from README.md via the backend.

The project documentation will appear here after it loads.

uma-ase v0.8.5

Input Details

Summary

Input Details

Summary

Results

Input Details

Summary

Results

Analyze

Input sources

RMSD Report

XYZ Pair Analysis

Simple Geometry Analysis

Distance Matrix (Å)

Pair Distance Histogram

Input Details

Summary

MD Output

MD Simulations Live

Trajectories

Vibrational Normal Modes

Normal Mode Controls

Playback Controls

Energy vs Time Step

About uma-ase

README documentation