Research workspaces
| Icon / label | Purpose | Keep in mind |
|---|---|---|
| Flask — DFT Lab | Prepare structures and Quantum ESPRESSO calculation workflows. | A setup is editable; an execution record preserves the submitted attempt. |
| Three waves — MD Lab | Inspect trajectories, configure LAMMPS stages, and analyze frames. | Frame display and actual physical time are different quantities. |
| Axes and line — Figure Lab | Compose numerical datasets into scientific figures and export sources. | Figure styling never changes the executed scientific input. |
| Stepped spark — AI | Open the project AI workspace and review proposed actions. | The Phynite AI entry icon is distinct from provider logos in Settings. |
Canvas and execution controls
| Control | What it does |
|---|---|
| Plus — Add module | Opens the module catalogue. Add a source, scientific task, analysis, or Figure module and connect compatible ports. |
| Curved arrows — Undo / Redo | Moves through supported editing history; it does not undo an already executed solver job. |
| Play — Run / Run selected / Run all | Prepares Review run, includes prerequisites once, and reuses compatible retained results. Start run confirms the reviewed plan. |
| Clock — Run history | Shows workflow attempts, per-module status, errors, and available cancellation actions. |
| Activity line — Research context | Opens the project run ledger, timeline, recent comparison, and read-only AI context. |
Geometry and trajectory tools
| Tool / key | Use | Scope |
|---|---|---|
| Select / V | Select atoms or particles for inspection. | Active viewport. |
| Move / G | Move selected atoms; inspect the resulting coordinates before applying. | Structure editor. |
| Measure / M | Measure selected geometry using the current distance/angle mode. | Structure or trajectory viewport. |
| Slice cross-section / S | Inspect a cross-section of the displayed trajectory. | MD Lab |
| Fit structure / F | Frame the structure in the camera; it does not resize the cell. | MD Lab |
| View angle | Choose an orientation or supported multiple-view layout. | Viewport camera. |
| Display overlays | Change display aids without rewriting the scientific source. | MD Lab |
| Capture snapshot | Save a viewport image for illustration. | An image does not replace numerical export or provenance. |
Read status and evidence icons
| Label | Meaning |
|---|---|
| Ready / Configuration ready | The relevant checks passed at that stage. Still inspect execution prerequisites and scientific choices. |
| Queued / Running | The job is waiting or executing. Wait for the final state and avoid duplicate submissions. |
| Completed | The app retained the result. Inspect convergence, warnings, units, and physical assumptions. |
| Failed / Cancelled | Open the recorded reason and logs. Preserve partial evidence before a retry. |
| Integrity / Elements / Runtime | MD potential indicators identify separate checks. They do not validate a force field for your study. |
| Not recorded / unavailable | The source did not provide that measurement. Do not interpret it as zero. |