# Phynite Lab User Guide
This guide describes the implemented interface. Use it alongside solver documentation and convergence studies.
- [From structure to a paper figure](#workflow)
- [Tutorial: a first silicon calculation](#quickstart-silicon)
- [Tutorial: a first local MD simulation](#quickstart-md)
- [Projects, structures, and calculation records](#project)
- [Import and inspect a structure](#structure)
- [Edit atoms and cell geometry](#edit)
- [Periodic directions, vacuum, and dimensionality](#periodicity)
- [Procedure: prepare a two-dimensional slab](#slab-workflow)
- [Choose and connect calculations](#calculation)
- [Configure and validate Quantum ESPRESSO](#configure)
- [Procedure: design a convergence study](#convergence)
- [Execution, resources, and cancellation](#execution)
- [Open and interpret calculation results](#results)
- [Compose a figure](#figures)
- [Energy, k-path, DOS, and fair comparison](#alignment)
- [Workflows for material and parameter studies](#studies)
- [Templates, replacement, history, and archives](#reuse)
- [PDOS, unfolding, and insets](#advanced)
- [Export and preserve a reproducible figure](#export)
- [Procedure: prepare a publication figure](#publication)
- [Autosave, storage, and multiple devices](#saving)
- [Profile, usage, and subscriptions](#account)
- [Manage plans, billing, and resource usage](#billing)
- [Connect your computer with Phynite Compute](#local-compute)
- [Language, region, and accessibility](#language)
- [Keyboard and pointer shortcuts](#shortcuts)
- [Reference: calculation fields and units](#field-reference)
- [Troubleshooting and recovery](#troubleshooting)
- [Troubleshooting: locate a failed workflow stage](#diagnostics)
- [Availability and planned workflows](#roadmap)
- [Units, terms, and scientific references](#reference)
## From structure to a paper figure
A project is the container for a material study. It connects structures, calculation setups, execution records, numerical datasets, and reusable figures. Start with the physical question, then choose the calculations and comparisons that answer it.
### Your first complete workflow
1. Sign in. You arrive at Workspace, where recent projects and the DFT Lab and Figure Lab tools are available. Returning to the homepage while signed in opens Workspace again.
2. In Workspace, choose New project and enter a meaningful name such as Silicon convergence or MoS2 strain study. Open the project to continue in DFT Lab.
3. Add a structure by importing a file, building a cell, or using Materials Project. Check units, lattice vectors, species, and atom count before calculating.
4. Inspect the real-space structure. Choose periodic directions for the physical model; add vacuum explicitly where an isolated slab, wire, or molecule needs it.
5. Open Calculate and add a Total energy or Structural relaxation setup. Review the generated inputs, occupation policy, pseudopotentials, cutoffs, and k-point mesh.
6. Choose the compute destination. Shared compute uses available early-access capacity; Your computer requires the private worker described in this guide.
7. Run the setup and follow its execution log. A completed process is not automatically a converged or scientifically adequate result: inspect energy, convergence, forces, and messages.
8. Add band structure, DOS, phonon, or transport calculations as required. Use a completed compatible relaxation as a structure source when appropriate.
9. Choose Open in Figure Lab on a completed plottable run. Its existing figure reopens, or its numerical data creates a new figure automatically.
10. Compose comparisons, set scientific alignment, tune physical dimensions and typography, then export the figure and a Source package. Wait for Saved to cloud before relying on another device to reopen the latest edit.
### A useful division of work
| Place | What belongs here |
| --- | --- |
| Workspace | Choose a study, find recent projects, compare plans, open tools. |
| DFT Lab / Project | Organize projects and structures. |
| DFT Lab / Inspect | Prepare geometry and check the physical system. |
| DFT Lab / Calculate | Configure calculations, select dependencies, run, and inspect execution. |
| Figure Lab | Reuse numerical data, compare results, style and export publication figures. |
| Account | Profile, storage, compute accounting, plan, and personal worker connection. |
### Before calling a result final
- Record the source structure and computational cell used by every run.
- Converge the quantities you will report against relevant cutoffs, k/q meshes, vacuum, smearing, and solver thresholds.
- Check energy units and references before overlaying results.
- Keep the exact inputs and numerical source package alongside the exported figure.
- Describe the method, pseudopotential family, exchange-correlation functional, spin treatment, and normalization in the paper.
### Related topics
- [Projects, structures, and calculation records](/guide#project)
- [Tutorial: a first silicon calculation](/guide#quickstart-silicon)
- [Tutorial: a first local MD simulation](/guide#quickstart-md)
## Tutorial: a first silicon calculation
Complete a small ground-state calculation before attempting a large material study. This tutorial checks the structure-to-worker-to-result workflow; its numerical settings are starting values for an exercise, not a converged production method.
### Before you begin
- Sign in with the invited account that will own the project and results.
- Connect Your computer with Docker and keep Docker running while the computer is awake. You may close the terminal once the container is running in the background.
- Have a diamond-cubic silicon structure in CIF, POSCAR, or another supported format. Keep its source and lattice parameter with your notes.
- Use a primitive two-atom cell for this exercise. A conventional eight-atom cell is physically valid but has different total energy, reciprocal vectors, and computational cost.
### Create and inspect the project
1. In Workspace, choose New project. Enter Silicon ground state and an optional description, then choose Create project.
2. Open the new project from the confirmation or project list. Add your silicon structure.
3. Confirm Si is the only species and the intended primitive cell has two atoms. Inspect cell lengths, angles, units, and nearest neighbors.
4. Keep a, b, and c periodic for bulk silicon. The displayed repeated cells are a visualization, not extra atoms submitted to the solver.
5. Give the structure a source-specific name. Retain the original file before changing its lattice.
### Configure the exercise
| Choice | Starting point | Why to inspect it |
| --- | --- | --- |
| Workflow | Total energy / SCF | Produces the self-consistent ground state; it does not produce a band-path figure by itself. |
| Method | PBE with matching Si pseudopotential | Changing the functional or pseudopotential changes the physical model and energy zero. |
| Wavefunction cutoff | Use the resolved pseudopotential recommendation | A remembered cutoff from another potential is not transferable evidence of convergence. |
| Charge-density cutoff | Use the matching recommendation | The appropriate ratio depends on the pseudopotential type. |
| Integration mesh | 4 × 4 × 4 as an initial exercise | Repeat with denser meshes before interpreting small energy differences. |
| Occupations | Review the resolved insulating occupation policy | Do not infer metallic behavior from a numerical smearing choice. |
| Resources | A small allocation within the displayed account limits | Allocation controls available worker resources, not the accuracy of the method. |
### Run and inspect
1. Inspect the generated input and select the intended compute destination.
2. Run once. Open Log and follow Queued, Running, and the final state.
3. Look for a converged SCF result in the solver output. A finished process without self-consistency is not an acceptable ground state.
4. Record total energy, atom count, executed input, pseudopotential identity, and run ID.
5. If you need a dispersion plot, add Band structure and configure a reciprocal path for this cell. Complete it, then choose Open in Figure Lab from its result.
### Expected outcome
The project contains the original structure, an editable setup, and a historical execution record with output artifacts. A separate band or DOS run supplies plottable numerical data.
There is no universal target energy for this tutorial: the value depends on the potential, cell, cutoffs, and conventions. Verify internal convergence and consistent method identity instead of matching an unexplained number.
> If the job stays Queued, check the destination and worker connection before submitting duplicate runs. See Execution and the troubleshooting decision table.
### Failure and recovery
- If the worker is offline, reconnect it and wait for the queued job instead of submitting another.
- For Failed, inspect the saved input and first meaningful solver error in the log before changing a setting.
- For Cancelled, keep the partial log and submit a new run only after the prior job reaches a final state.
### Related topics
- [From structure to a paper figure](/guide#workflow)
- [Projects, structures, and calculation records](/guide#project)
- [Tutorial: a first local MD simulation](/guide#quickstart-md)
## Tutorial: a first local MD simulation
Use a small argon system to learn the structure-to-settings-to-execution-to-result path in MD Lab. This is a workflow exercise, not a validated physical study.
### Prepare your computer and structure
1. Sign in with the invited account and connect Your computer in Account. Keep its worker and Docker running.
2. Open MD Lab and create a project named Argon equilibration.
3. Import or build a small argon structure with a physically suitable periodic box. Check atom count, element identity, coordinates, box lengths, units, and atomic masses. An XYZ with Ar species or a LAMMPS data file with Masses works; a type-only dump has no mass for dynamics.
4. Retain the original structure file and record its source. A visual repeat does not add atoms to the simulation.
### Review the simulation
1. Open the configuration drawer and choose Guided mode. Select the built-in Lennard-Jones model for Ar; do not use Generic parameters without recording their source.
2. Choose a short equilibration recipe. Inspect temperature, timestep, boundary conditions, random seed, unit system, potential parameters, and output interval.
3. Run browser preflight and read the generated LAMMPS input. Confirm it uses the intended structure and potential.
### Execute once and inspect
1. Select Your computer and submit one run. Follow Queued and Running in the job record and check the worker connection.
2. If the worker is offline, reconnect it and wait for the queued job; do not submit a duplicate.
3. After completion, open the log, thermo data, trajectory, and retained input from the project. Check for LAMMPS errors and inspect whether temperature and energy behavior support the intended equilibration.
4. Completed means the process finished; it does not validate the force field, timestep, equilibration, or scientific conclusion.
### Failure and recovery
- For Failed, inspect the first meaningful LAMMPS error and saved input before changing settings.
- For Cancelled, review the partial log and submit a new run only after the previous job reaches a final state.
- For a missing trajectory, check output settings and retained artifacts. An empty viewer is not a physical result.
> There is no universal target energy or temperature trace. Record the actual input, potential identity, run ID, and output before comparing systems.
### Related topics
- [From structure to a paper figure](/guide#workflow)
- [Projects, structures, and calculation records](/guide#project)
- [Tutorial: a first silicon calculation](/guide#quickstart-silicon)
## Projects, structures, and calculation records
Use one project for a coherent study, then keep material variants as separate named structures within it. A calculation setup is editable; each execution is a historical record of a submitted input.
### Organize a study
1. In Workspace, choose New project, enter a name (up to 100 characters) and optional description (up to 500 characters), then choose Create project. The Project panel in DFT Lab provides another creation route.
2. Name it by question or dataset: strain response, alloy comparison, or convergence study.
3. Add structures and give variants explicit names, such as MoS2 strain -2 percent, 0 percent, and +2 percent.
4. Add the relevant calculation stack under each structure. Duplicate a setup when the same method should be reused.
5. Use project or structure menus for rename and duplicate. Read the confirmation before deleting anything.
### Understand the identities
A local structure, its uploaded cloud structure, and a submitted calculation are linked but distinct records. Editing the current structure does not rewrite a completed calculation.
A figure references immutable numerical datasets. Replacing data in a figure is an explicit action; changing a setup or source metadata does not silently alter existing published comparisons.
> The visual supercell repeat is a preview. Increasing the displayed repeats does not automatically submit a larger computational supercell.
### Find and reopen work
- Workspace searches project names, descriptions, and the primary chemical formula.
- Click Name, Activity, or Last edited to sort the project list; click again to reverse the direction. Open a row to resume its DFT Lab workspace.
- The URL preserves project and Figure Lab view. Browser Back/Forward returns to that view after the account workspace loads.
- An unavailable project link does not open an unrelated project figure. Select an existing project or restore the intended data.
### Related topics
- [From structure to a paper figure](/guide#workflow)
- [Tutorial: a first silicon calculation](/guide#quickstart-silicon)
- [Tutorial: a first local MD simulation](/guide#quickstart-md)
## Import and inspect a structure
DFT Lab shows direct, real space: lattice vectors and atoms. Reciprocal-space k-points and band paths belong to calculation configuration and result interpretation.
### Choose an input route
| Route | What to check |
| --- | --- |
| New structure | Set the cell lengths and angles, species, and atom positions explicitly. |
| CIF | Check occupancies, disorder, fractional coordinates, and whether the intended cell is primitive or conventional. |
| POSCAR / VASP | Verify the scale factor, element ordering, and Direct versus Cartesian positions. |
| XSF / XYZ / PDB | Confirm that the file contains a usable simulation cell; isolated coordinates alone do not define periodicity. |
| Quantum ESPRESSO input/output | Check the imported cell and whether the positions correspond to the intended ionic step. |
| Materials Project | Inspect source identity, composition, cell convention, and the suitability of the database structure for your question. |
### Import a file
1. Select the destination project.
2. Use Add structure / Import, or drop one supported structure file into the workspace.
3. Inspect the structure record, formula, number of atoms, and cell.
4. Rotate and repeat the cell visually to find misplaced atoms or unexpected neighbors.
5. Resolve parser warnings or partial occupancies before using the model for an ordered QE calculation.
### Fractional and Cartesian coordinates
Fractional coordinates locate an atom by a combination of the cell vectors: r = f1 a + f2 b + f3 c. Cartesian coordinates specify x, y, and z in a length unit. A value of 0.5 in a fractional field is half a lattice vector, not half an angstrom.
For tilted cells, cell length and perpendicular vacuum thickness are different. Check the full cell geometry instead of assuming the c vector points along the Cartesian z axis.
> Neighbor lines are distance-based coordination guides, not calculated chemical bond orders. Their cutoff and display cap can hide or include neighbors without changing the scientific structure.
### Related topics
- [Edit atoms and cell geometry](/guide#edit)
- [Periodic directions, vacuum, and dimensionality](/guide#periodicity)
- [Procedure: prepare a two-dimensional slab](/guide#slab-workflow)
## Edit atoms and cell geometry
Select, move, add, substitute, delete, and measure atoms in the viewport. Keep geometry changes deliberate and inspect the result before rerunning a calculation.
### Atom tools
| Tool | Use |
| --- | --- |
| Select (V) | Select an atom and inspect its properties. |
| Move (G) | Move a selection; choose an axis or plane, then apply or cancel the move. |
| Add atom (A) | Open the element selection flow and place the intended species. |
| Measure (M) | Select the atoms required by the distance or angle mode. |
| Focus (F) | Center the viewport on the selected atom. |
| Delete / Backspace | Delete the selected atom when the viewport has focus. |
### Constrained movement
In Move mode, X, Y, or Z constrains motion to that Cartesian axis. Shift+X, Shift+Y, or Shift+Z uses the perpendicular YZ, XZ, or XY plane. Enter applies the move; Escape cancels it.
Use coordinate fields when you need an exact displacement. Numeric editors allow an intermediate draft such as a minus sign or exponent; commit with Enter or by leaving the field. Escape restores the previous value.
### Cell edits and visual appearance
- Cell metric edits change the actual lattice. Inspect whether the resulting geometry represents the strain or model you intend.
- The vacuum action increases separation normal to the a-b plane and preserves Cartesian atomic distances; it is not a general arbitrary-axis slab builder.
- Atom size, bond size, labels, neighbor cutoff, and displayed repeat count affect visualization.
- Undo/redo applies to supported editor actions in the current editing session. Keep explicit structure copies for scientific variants you want to retain permanently.
### Related topics
- [Import and inspect a structure](/guide#structure)
- [Periodic directions, vacuum, and dimensionality](/guide#periodicity)
- [Procedure: prepare a two-dimensional slab](/guide#slab-workflow)
## Periodic directions, vacuum, and dimensionality
The a, b, and c checkboxes describe intended periodic directions in the real-space display. Quantum ESPRESSO still solves a periodically repeated three-dimensional simulation cell.
### What unchecking a direction does
Unchecking c stops the visual repetition and periodic-neighbor connection in that direction; its display repeat returns to one. It does not shrink the cell, remove the c vector, insert vacuum, or activate an electrostatic correction.
This separation is intentional: a checkbox cannot infer your slab thickness, the amount of converged vacuum, or the electrostatic boundary treatment. Silently resizing a cell could change atomic separations or the physical density.
> For a slab, keep a finite simulation-cell height, add and converge vacuum explicitly, use a single k-point in the nonperiodic direction, and choose a suitable electrostatic treatment in the actual QE input.
### Common systems
| System | Display periodicity | Computational checks |
| --- | --- | --- |
| Bulk crystal | a, b, c | Converge a three-dimensional k mesh; use the intended primitive or conventional cell. |
| Slab / 2D sheet in a-b plane | a, b | Converge perpendicular vacuum and in-plane k mesh; usually one k-point along c. Review dipole or 2D isolation treatment when appropriate. |
| Wire along c | c | Converge vacuum in both transverse directions and sampling along the wire. The built-in c-vacuum action alone does not prepare this geometry. |
| Molecule / cluster | None | Use a sufficiently large 3D box; typically Gamma-only sampling. Check charged-system and dipole treatment as needed. |
### A reproducible slab check
1. Orient the slab so its surface lies in the a-b plane.
2. Uncheck c to make the intended display boundary clear.
3. Add vacuum and inspect the actual cell and positions.
4. Set the k mesh to N by M by 1; choose N and M through convergence.
5. Inspect generated or expert input for the appropriate electrostatic setup.
6. Repeat with larger vacuum and denser in-plane sampling until the target quantity is stable.
> A rendering choice is not proof that a model is physically isolated. Verify the executed input and convergence results.
### Related topics
- [Import and inspect a structure](/guide#structure)
- [Edit atoms and cell geometry](/guide#edit)
- [Procedure: prepare a two-dimensional slab](/guide#slab-workflow)
## Procedure: prepare a two-dimensional slab
Use this procedure for a sheet or slab whose surface spans the a-b plane. The renderer can display reduced periodicity, while QE still requires a finite three-dimensional cell.
### Geometry prerequisites
- Start from a physically meaningful termination, composition, and surface orientation.
- Inspect fractional and Cartesian coordinates. A tilted cell needs vacuum measured normal to the surface, not merely the length of c.
- Check that the slab has the intended thickness and no unintended cross-boundary bonds.
- Duplicate the structure before changing the cell so the original bulk or slab remains available.
### Prepare the model
1. Orient the surface in the a-b plane. Verify the lattice-vector geometry instead of relying only on camera orientation.
2. Uncheck c under Periodic directions. This turns off display repetition along c; it does not delete the lattice vector.
3. Use the explicit vacuum action for the a-b surface. Inspect the updated cell and confirm interatomic Cartesian distances remain appropriate.
4. Choose an in-plane mesh N × M × 1, with N and M established by convergence.
5. Review the electrostatic treatment in the generated or expert QE input. Asymmetric, polar, and charged slabs need specific consideration.
6. Converge slab thickness, vacuum, and in-plane sampling against the quantity of interest.
### Understand a strained slab
Biaxial in-plane strain modifies the in-plane metric. Record the strain tensor, reference lattice, and whether atoms are relaxed at fixed in-plane cell.
Changing vacuum height changes the three-dimensional cell volume without changing the physical sheet thickness. A reported stress or conductivity normalized by this arbitrary volume may require a clearly defined two-dimensional conversion.
The c-vacuum helper does not construct every wire, arbitrary Miller-index slab, or isolated cluster. Import or prepare the appropriate geometry when the required operation is outside the builder tools.
### Validate before submission
| Check | Evidence to retain |
| --- | --- |
| Surface and orientation | Cell vectors, coordinates, termination, and original source. |
| Vacuum | Normal separation and at least two tested separations around the selected value. |
| Sampling | Executed k mesh and in-plane convergence results. |
| Electrostatics | Exact QE settings and their physical justification. |
| Relaxation | Fixed and free degrees of freedom, force threshold, and final geometry. |
### Related topics
- [Import and inspect a structure](/guide#structure)
- [Edit atoms and cell geometry](/guide#edit)
- [Periodic directions, vacuum, and dimensionality](/guide#periodicity)
## Choose and connect calculations
The Calculate panel separates DFT setups, the execution log, and reusable configurations. Select the scientific task first; the generated workflow then creates the required solver stages.
### Available workflows
| Calculation | Purpose | Main tools |
| --- | --- | --- |
| Total energy | SCF electronic ground state and energy. | pw.x |
| Structural relaxation | Optimize ions; optionally optimize permitted cell degrees of freedom. | pw.x relax / vc-relax |
| Band structure | Sample eigenvalues along a specified reciprocal-space path. | pw.x + bands.x |
| Density of states | Sample a uniform mesh for a DOS and optional projections. | pw.x + dos.x / projection inputs |
| Phonon dispersion | DFPT and real-space force constants, then a phonon path. | ph.x + q2r.x + matdyn.x |
| Thermoelectric properties | Interpolated electronic bands and semiclassical transport. | QE + BoltzTraP2 |
### Build a calculation stack
1. Select a structure and open Calculate / DFT.
2. Choose Add calculation and select the task.
3. Configure the setup and inspect its input files.
4. For a calculation that should use a relaxed structure, select the appropriate structure source.
5. Run one calculation, Run selected, or Run all. Required predecessors can be submitted first and reused when compatible.
6. Inspect each individual run in Log; a dependency may keep a downstream job queued.
### Dependencies and reruns
A downstream job waits until its declared prerequisites have completed. Reuse is based on compatible execution records, not merely a similar display name.
Changing a structure, functional, charge, spin state, or cutoff may invalidate scientific reuse. If in doubt, create a new run and retain the old one as a comparison.
Save selected stores the calculation configurations for reuse. It does not execute a solver. Figure Lab has its own automatic save flow and does not require a Save revision button.
### Related topics
- [Configure and validate Quantum ESPRESSO](/guide#configure)
- [Execution, resources, and cancellation](/guide#execution)
- [Procedure: design a convergence study](/guide#convergence)
## Configure and validate Quantum ESPRESSO
Smart defaults provide a starting point. They do not replace a convergence study or knowledge of the material. Generated inputs and expert raw input have different responsibilities.
### Core choices
| Setting | Meaning | Check before running |
| --- | --- | --- |
| Functional | Exchange-correlation approximation. | Use pseudopotentials and a solver workflow compatible with it; UI selection alone does not establish method support for every advanced case. |
| ecutwfc / ecutrho | Plane-wave wavefunction and charge-density cutoffs. | Converge the reported energy, forces, stress, or response; respect pseudopotential recommendations. |
| k-point mesh | Sampling for Brillouin-zone integration. | Use a uniform mesh for SCF/DOS; do not substitute a high-symmetry band path. |
| Occupations / smearing | How electronic states are filled and integrated. | Match metallic, insulating, spin, and temperature assumptions. |
| nbnd | Number of computed bands. | Include enough unoccupied states for the target energy window or transport analysis. |
| SCF thresholds / mixing | Self-consistency stopping and iteration behavior. | Inspect convergence; raising the iteration limit does not fix every physical or numerical instability. |
| Charge / magnetization / spin | Electronic state assumptions. | Use compatible pseudopotentials and a justified reference state. |
### Adaptive and expert modes
Adaptive mode resolves editable occupation and cutoff defaults from the workflow and material context. User overrides remain explicit.
Expert raw input is authoritative for the submitted text. Adaptive occupation and cutoff resolution does not silently rewrite it. You take responsibility for compatible cards, paths, species, units, and solver options.
Review the executed input from the result artifacts, not only an earlier editor preview. The worker may resolve required runtime data such as pseudopotential provenance.
### Convergence example
1. Fix one structure and method; create a baseline Total energy calculation.
2. Vary ecutwfc and the compatible ecutrho while keeping the k mesh fixed.
3. Track energy per atom and, when relevant, forces or stress instead of only total cell energy.
4. Choose a sufficient cutoff, then vary the k mesh.
5. For low-dimensional systems, repeat the vacuum check independently.
6. Record the tolerance used to call the reported quantity converged.
> Preset names such as Fast, Balanced, and High accuracy are setup conveniences. They are not certificates of publication accuracy.
### Related topics
- [Choose and connect calculations](/guide#calculation)
- [Execution, resources, and cancellation](/guide#execution)
- [Procedure: design a convergence study](/guide#convergence)
## Procedure: design a convergence study
A convergence study establishes how numerical choices affect a reported physical quantity. Define the quantity and tolerance first, then vary a controlled parameter while preserving all other inputs.
### Define a comparison that answers the paper
For a phase-energy comparison, converge the energy difference using comparable cells and normalization. For relaxation, inspect force and stress stability. For a band edge, transport coefficient, or phonon mode, converge that observable directly.
A stable total energy does not imply every response property has converged. Keep the target tolerance in your project description or method notes.
### Run a controlled series
1. Duplicate a reference setup and give each variant a name containing the varied parameter and unit.
2. Vary ecutwfc with a compatible ecutrho. Keep geometry, pseudopotentials, k mesh, spin, occupations, and SCF threshold fixed.
3. At a sufficiently high cutoff, vary the uniform k mesh. Inspect smearing sensitivity independently for metals.
4. For low-dimensional systems, vary actual vacuum separation without changing the slab geometry or in-plane cell.
5. Run the necessary combinations near the chosen settings to check that separately converged choices remain sufficient together.
6. Retain every run and calculate the difference from the most resolved reference. Export the observations as a numerical table for plotting.
### Record a minimal results table
Replace placeholders with observed values; the table is a recording template, not simulated data. For the same composition and cell, delta per atom = (E - E_reference) / atom_count. Convert Ry to the unit reported in the paper consistently.
Do not subtract raw total energies of unrelated compositions as if they were a formation energy. Such comparisons require defined reference chemical potentials and stoichiometry.
```text
cutoff_Ry,k_mesh,energy_Ry,atoms,delta_meV_per_atom,run_id
40,4x4x4,,2,,
50,4x4x4,,2,,
60,4x4x4,,2,,
```
### Choose a stopping rule
| Observable | Inspect | Frequent mistake |
| --- | --- | --- |
| Energy difference | Change between successively more resolved calculations | Choosing a universal threshold without regard to the effect being studied. |
| Forces and stress | Largest relevant component and equilibrium geometry | Relaxing at low cutoff, then assuming a high-cutoff single point fixes the geometry. |
| Band extrema | k sampling and the actual location of extrema | Assuming the band gap always lies on the plotted high-symmetry path. |
| Phonons | SCF/DFPT thresholds, k/q meshes, acoustic behavior | Removing negative modes cosmetically before understanding them. |
| Transport | Dense electronic sampling, interpolation, chemical potential and temperature | Treating an interpolated smooth curve as evidence of convergence. |
### Related topics
- [Choose and connect calculations](/guide#calculation)
- [Configure and validate Quantum ESPRESSO](/guide#configure)
- [Execution, resources, and cancellation](/guide#execution)
## Execution, resources, and cancellation
A run moves through preparation, queueing, worker execution, upload, and completion. The execution log tells you which stage needs attention.
### Read the run state
| State | Meaning | Next action |
| --- | --- | --- |
| Draft / Ready | Configuration exists; no active solver is implied. | Review input and run when ready. |
| Queued | Waiting for a worker or a dependency. | Check the selected destination, its connection, and prerequisite jobs. |
| Running | The worker has claimed the job. | Inspect stage, log tail, and resource details; allow time for expensive stages. |
| Completed | The result was uploaded and accepted. | Inspect convergence and scientific validity, then open results. |
| Failed | Preparation, execution, or upload failed. | Read the reason and solver log before retrying. |
| Cancellation requested | A running job is being asked to stop. | Wait for the worker heartbeat and terminal status. |
| Cancelled | The run was stopped or removed from the queue. | Retain useful logs; start a new run if needed. |
### What cores and RAM mean
Recorded cores are the allocated vCPUs or worker processes, and RAM is the configured memory limit. These are different from actual CPU utilization or installed physical memory.
Expand resource details in the execution log to inspect reported backend allocation, elapsed time, MPI processes, and QE memory or timing estimates when available. Missing historical data is shown as not reported.
A local worker is still constrained by service-side job limits. The current deployment limits appear in Account and the compute destination panel. Jobs requesting more than the server permits are rejected instead of silently resized.
### Cancel intentionally
- A queued local job can be removed from the queue.
- A running cancellation reaches the worker through its heartbeat, so completion is not instantaneous.
- Closing the browser does not cancel a submitted calculation.
- Disconnecting a personal credential revokes access and may interrupt upload; use the calculation cancellation action before replacing a credential during an active run.
### Related topics
- [Choose and connect calculations](/guide#calculation)
- [Configure and validate Quantum ESPRESSO](/guide#configure)
- [Procedure: design a convergence study](/guide#convergence)
## Open and interpret calculation results
Use the log for execution evidence and downloads. Use Figure Lab for plot editing, comparisons, layout, and publication export.
### Open a result directly
1. Find the completed run in Log.
2. Inspect its convergence message and recorded numerical summary.
3. Choose Open in Figure Lab when the result contains plottable data.
4. The most recently edited active figure using that run reopens. If none exists, Figure Lab imports the numerical source and prepares a figure.
5. If a retained source cannot be loaded, use Retry, check source availability, or import your original numerical file.
### Distinguish numerical data from a preview
A PNG preview is a rendered image. Numerical datasets preserve samples and metadata that allow future restyling, alignment, and export.
New supported calculation outputs retain a compact research dataset separately from temporary raw-artifact access. Older runs without retained data may require original CSV/text files or a new run.
The ordinary artifact access window is typically three days. Storage lifecycle cleanup is configured separately. An expired download link is not evidence that a retained research dataset is lost.
### Read physical claims carefully
- A band gap estimate requires meaningful occupations or an energy reference. Unknown reference data must not be treated as zero Fermi energy.
- DOS normalization must refer to the actual computational cell, atoms, formula units, or volume.
- Phonon imaginary frequencies can reflect an instability or incomplete convergence; inspect the model and method.
- Transport results depend on interpolation, sampling, temperature, chemical-potential conventions, and the relaxation-time model. Conductivity divided by relaxation time is not an absolute conductivity unless a justified time is supplied.
### Related topics
- [Compose a figure](/guide#figures)
- [Energy, k-path, DOS, and fair comparison](/guide#alignment)
- [Workflows for material and parameter studies](/guide#studies)
## Compose a figure
Figure Lab uses a results library on the left, the publication page in the center, and an inspector on the right. On smaller screens, Results and Inspector become drawers.
### Choose a layout
| Layout | Best use | Check |
| --- | --- | --- |
| Single plot | One result, one message. | Quantity, axes, units, and title. |
| Overlay | Several curves sharing a comparable physical coordinate. | Path compatibility, alignment, normalization, and readable legends. |
| One panel per result | Different materials or results needing independent panels. | Consistent dimensions and a fair common range where justified. |
| Band + DOS pairs | Dispersion beside corresponding density of states. | Matching geometry/electronic identity and energy convention. |
| Parameter series | Ordered strain, pressure, temperature, or other variants. | Matching parameter name and unit plus numerical values. |
### Build the page
1. Select completed results from the active project and import their numerical datasets.
2. Search the library and select the datasets you want to compare.
3. Choose a layout. A dataset can appear in multiple figures without changing its original samples.
4. Set figure width and height in millimeters. Choose a one-column or two-column size appropriate to the target journal.
5. Select a panel in the canvas or inspector. Adjust ranges, panel span, order, legend, and linked axes.
6. Use Data controls to name layers, choose channels, replace sources, and set colors and line styles.
7. Review scientific context notes, let the cloud save finish, then export.
### Canvas interaction
Use + and - to enlarge or reduce the page view; 0 or Fit returns it to the available canvas area. The zoom range is 25 to 400 percent relative to the fitted view.
Space+drag, Alt+drag, or middle-button drag pans an enlarged canvas. Ctrl/Cmd+wheel zooms. Clicking a plotted panel selects it for inspection.
Canvas zoom does not change the exported dimensions, axis limits, or numerical values. To change the plotted range, use panel minimum and maximum fields.
> Curve strokes and markers are clipped to the axis rectangle. A Γ label denotes the Brillouin-zone center; original source metadata is retained.
### Related topics
- [Open and interpret calculation results](/guide#results)
- [Energy, k-path, DOS, and fair comparison](/guide#alignment)
- [Workflows for material and parameter studies](/guide#studies)
## Energy, k-path, DOS, and fair comparison
A comparison can look tidy while mixing incompatible physical references. Establish the meaning of each axis before adjusting its appearance.
### Energy alignment
| Mode | Meaning | Appropriate interpretation |
| --- | --- | --- |
| Source energy | Keep the numerical reference as imported. | Use only when source conventions are understood. |
| Each Fermi = 0 | Shift every dataset by its own recorded Fermi level. | Compare dispersion shapes relative to each electronic chemical potential; not absolute band offsets. |
| Each VBM = 0 | Shift by a recorded valence-band maximum. | Compare band-edge-relative features when the VBM is meaningful. |
| Vacuum alignment | Use a recorded vacuum reference. | A common-reference comparison when vacuum levels are physically justified. |
| Manual shift | Apply a stated explicit energy offset. | Use a documented alignment procedure and retain the chosen offset. |
### Band + DOS
A verified pair requires matching recorded geometry and electronic source identity, along with compatible Fermi-relative data. A matching filename or material formula alone is insufficient.
The paired layout gives band and DOS panels a shared physical vertical energy axis, typically in a 2:1 width ratio. Adjusting a linked energy bound updates both panels.
Replacing one source with an unrelated calculation invalidates the verified-pair claim. Use ordinary comparison panels when sources are intentionally different.
### K-path compatibility
The labels Γ, X, or K are not enough to establish the same reciprocal coordinate. Cell basis, path endpoints, and segment coordinates matter.
Physical path comparisons require compatible source geometry and coordinates. Segment normalization can align corresponding endpoints when the required metadata exists, but changes the displayed horizontal scale.
Disconnected branches must remain separated by gaps. Do not connect their endpoints into a fictitious continuous band.
### DOS normalization and spin
- Per-cell DOS is the default meaning of many QE outputs. Do not silently label it per atom.
- Per-atom normalization needs a verified atom count; per-formula-unit normalization needs the formula-unit count; per-volume normalization needs a valid cell volume.
- Spin-down mirroring reflects a channel visually to distinguish it. It does not make physical DOS negative.
- Inspect whether a channel is total DOS, an orbital/atom projection, or an arbitrary imported column. Channel names should state the actual meaning.
### Related topics
- [Open and interpret calculation results](/guide#results)
- [Compose a figure](/guide#figures)
- [Workflows for material and parameter studies](/guide#studies)
## Workflows for material and parameter studies
Choose a layout according to the scientific comparison, then reuse a stable style. Avoid forcing every result into one dense overlay.
### Several materials in one paper
1. Place the structures in one study project, with clear source names.
2. Use a method whose differences and approximations are documented consistently.
3. Run the appropriate band or DOS calculations for each material.
4. Use a grid for incompatible k-paths or very different energy scales. Use an overlay only when coordinates and references support it.
5. Name layers by material, use a small deliberate color set, and label energy references explicitly.
6. Save the layout as a template for subsequent materials.
### One material at several strains
1. Duplicate the baseline structure before applying each strain.
2. Record whether the strain is uniaxial, biaxial, volumetric, or another tensor deformation; a single percent label does not encode the full tensor.
3. Use consistent relaxation constraints and electronic settings across variants.
4. For each imported dataset, record the same condition parameter name and unit plus its numerical value.
5. Choose Parameter series to order panels numerically, including negative strain values.
6. Compare the relevant quantities using a justified energy reference and explain any path normalization.
### Band structure next to DOS
1. Use compatible geometry and electronic assumptions for the two calculations.
2. Load both numerical datasets in Figure Lab.
3. Choose Band + DOS pairs and inspect the compatibility notes.
4. Set a common vertical energy interval and verify the zero reference.
5. Tune line density and DOS horizontal range without distorting the shared energy scale.
6. Export a vector figure and retain its Source package.
### Convergence or temperature series
Use a generic numerical dataset for derived quantities such as energy per atom versus cutoff, or a quantity-specific transport dataset when available.
Record the parameter and unit explicitly. Keep error estimates and method assumptions in the caption or source metadata rather than implying precision from extra decimal places.
A figure template helps keep sizes and typography stable across the paper, while each dataset retains its own provenance.
### Related topics
- [Open and interpret calculation results](/guide#results)
- [Compose a figure](/guide#figures)
- [Energy, k-path, DOS, and fair comparison](/guide#alignment)
## Templates, replacement, history, and archives
Reuse a visual method without losing the identity of the numerical sources. Templates describe a layout; figures bind that layout to concrete datasets.
### Reuse a template
1. Finish the layout, typography, panel arrangement, and layer style of an example figure.
2. Save it as a template. Source bindings become reusable slots.
3. Select replacement datasets in slot order and apply the template.
4. Inspect the rebound titles, quantities, and channel choices.
5. Edit custom captions explicitly; a template cannot know the new scientific conclusion.
### Replace a dataset without starting over
Use Replace source on the selected layer. Color, line style, and compatible channel settings are preserved. Automatically generated titles follow the replacement; custom text remains editable.
Editing source metadata creates a new dataset identity. Existing figures retain their original source until you explicitly replace it.
An inset can reuse the same source slot with independent bounds. It does not require copying or resampling the raw data.
### Undo, checkpoints, and cloud conflicts
- Undo/redo covers up to 50 editing steps in the current Figure Lab session.
- Routine edits save automatically; an optional Ctrl/Cmd+S keeps a deliberate checkpoint in History.
- Automatic edits replace a working copy instead of creating endless permanent revisions.
- History lets you inspect and restore saved versions. Restoration creates an editable current figure.
- If another tab or device changes the cloud revision, automatic overwrite stops. Review the local and cloud versions in History before choosing the intended one.
### Archives and other projects
Archive hides a saved figure from the active list and allows Restore. Archiving is not deletion and does not free its retained history allowance.
Include other projects exposes your own datasets from other studies. It does not grant access to another account.
Importing a Source package copies the figure and its sources into the selected project, with source hashes checked where available.
### Related topics
- [Open and interpret calculation results](/guide#results)
- [Compose a figure](/guide#figures)
- [Energy, k-path, DOS, and fair comparison](/guide#alignment)
## PDOS, unfolding, and insets
Advanced imports expose the information actually present in the file. They do not infer a missing orbital identity, calculate unfolding from ordinary eigenvalues, or establish a physical reference automatically.
### Projected DOS columns
Import a text or CSV file using Projected DOS columns. The first numerical column is energy and subsequent columns are projections. Name the channels by their true atom/orbital/spin identity.
Choose visible channels and style them in Data. Record the energy unit and reference, and use normalization only when the computational-cell basis is known.
```text
# energy_eV site_1_s site_1_p
-1.0 0.20 0.05
0.0 0.00 0.00
1.0 0.10 0.30
```
> These values illustrate the file shape; they are not scientific results.
### Precomputed unfolded weights
Use an unfolded-data import for k coordinate, energy, and nonnegative spectral weight. The plot represents the supplied weights as weighted samples.
Ordinary band energies do not contain enough information to derive unfolding weights. Compute the spectral weights with an appropriate external method first.
```text
# k energy_eV weight
0.0 -1.0 0.10
0.0 1.0 0.95
1.0 0.5 0.40
```
### Insets
1. Select a panel and enable an inset.
2. Choose the intended source and bounds for the magnified region.
3. Set its position and size so it does not cover important data or axis labels.
4. Check readability at final publication size, not only while zoomed in.
5. Keep the inset reference and units consistent with the main panel or explain the difference.
### Related topics
- [Open and interpret calculation results](/guide#results)
- [Compose a figure](/guide#figures)
- [Energy, k-path, DOS, and fair comparison](/guide#alignment)
## Export and preserve a reproducible figure
Set the intended physical size before exporting. A source package preserves numerical and visual provenance; a rendered image alone does not.
### Choose an output
| Format | Use | Properties |
| --- | --- | --- |
| SVG | Vector editing and web publication. | Vector paths; preserve the supplied font information. |
| PDF | Paper submission and document layout. | Vector output with selectable text and embedded publication fonts. |
| PNG | Raster workflows, slides, previews. | Pixel dimensions derive from physical millimeters and DPI; up to 40 megapixels. |
| Source package | Archive, handoff, and later re-editing. | Figure JSON, used datasets, SVG, font license, source identity, and checksums. |
### Practical export checklist
1. Use the journal column width as the starting size; 85 mm and 180 mm are common examples, not universal requirements.
2. Set type in points and check axes, legends, and panel letters at final size.
3. Verify min/max bounds, clipping, units, Γ labels, and energy reference.
4. Choose SVG or PDF for line art when the target supports vector output.
5. For PNG, choose an appropriate DPI and inspect the resulting dimensions.
6. Download the Source package and retain it with executed inputs and method notes.
### Fidelity and limitations
The renderer preserves all line vertices. Alignment, normalization, color, and mirrored spin display are transformations on the view, while original numerical samples remain in the dataset.
Publication fonts must be available from the frontend or browser cache. Export reports a failure when a required resource cannot be loaded; retry online.
A Source package can reproduce the figure. Rerunning a simulation also requires the computational environment, compatible pseudopotentials, complete inputs, and any required intermediate data.
### Related topics
- [Open and interpret calculation results](/guide#results)
- [Compose a figure](/guide#figures)
- [Energy, k-path, DOS, and fair comparison](/guide#alignment)
## Procedure: prepare a publication figure
Prepare the scientific comparison first, then the page geometry, typography, and export. Keep the editable source with every figure you deliver.
### Check source compatibility
1. Open a completed result in Figure Lab or select retained datasets from the results library.
2. Read quantity, units, geometry identity, energy reference, and k-path metadata for each source.
3. Choose a grid for distinct k paths; use overlay only when coordinates and references are scientifically comparable.
4. For Band + DOS, confirm the pair describes compatible geometry and electronic assumptions. Review the linked energy range.
5. State the alignment convention. Each Fermi = 0 compares relative electronic structure and does not establish absolute band offsets.
### Set the page
| Control | Practical choice | Verification |
| --- | --- | --- |
| Width / height | Use the target journal dimensions | A column-width PDF viewed at 100% remains readable. |
| Typography | One publication font, restrained hierarchy | Axis labels, tick values, legends, and panel letters have distinct roles. |
| Line style | Use color plus dash or markers when needed | Curves remain distinguishable in grayscale and for common color-vision differences. |
| Bounds | Use explicit comparable bounds where justified | No data is hidden by an unexplained crop; curve strokes stay clipped inside the axes. |
| Legend | Material or condition names with units | Avoid run IDs as the sole scientific description. |
| Inset | A clearly located detail with explicit bounds | The reader can identify which source and region it represents. |
### Export and verify
1. Wait for the Figure Lab cloud status to confirm the current edit.
2. Choose PDF or SVG for vector line art, or set physical size and DPI before exporting PNG.
3. Open the exported file in the application used for the manuscript. Inspect the final physical scale, Greek symbols, font rendering, panel labels, and clipped boundaries.
4. Export the Source package separately. Store it next to the figure and executed simulation inputs.
5. If you change a dataset or method, replace the source explicitly, review every legend and reference, and produce a new export.
### Caption recording template
This is a checklist for the author, not an automatically generated scientific claim. Include only information supported by the executed calculation and retained numerical sources.
```text
Quantity and material:
Structure source and cell:
Method, functional, pseudopotentials:
k/q sampling and numerical convergence:
Energy reference and normalization:
Parameter values and units:
Meaning of colors, lines, and panels:
Source package and run identifiers:
```
### Related topics
- [Open and interpret calculation results](/guide#results)
- [Compose a figure](/guide#figures)
- [Energy, k-path, DOS, and fair comparison](/guide#alignment)
## Autosave, storage, and multiple devices
DFT Lab and Figure Lab show save status for the active editing context. The Workspace dashboard does not show Saved to cloud; project synchronization continues in the background. A local copy and a confirmed cloud copy have different recovery paths.
### Save states
| Label | Meaning | What to do |
| --- | --- | --- |
| Saving... | A local draft or cloud synchronization is in progress. | Keep working; allow a short pause before relying on another device. |
| Saved to cloud | The current figure and its required datasets, or workspace snapshot, are confirmed remotely. | You can reopen the saved work with the same account. |
| Saved on device / Offline | A browser copy exists; cloud upload has not completed. | Keep browser data intact and reconnect. |
| Sync pending | The local copy is retained while upload retries. | Check network access and storage limits. |
| Sync conflict | The remote revision differs from the one being edited. | Review the versions in History; avoid blindly overwriting another device. |
### Figure Lab autosave behavior
Figure Lab saves a local draft after approximately 350 ms without a new edit and starts cloud synchronization after approximately 1.2 seconds. Active uploads are serialized; an edit during upload is saved next.
Leaving Figure Lab flushes pending draft edits. Online and focus events help retry pending cloud saves. A failed save remains visible instead of being labeled successful.
There is no required Save revision button. Ctrl/Cmd+S is an optional explicit history checkpoint.
### Limits and retained history
| Resource | Current limit |
| --- | --- |
| Workspace snapshot | 4.5 MB per saved workspace snapshot. |
| Research document | 4 MB per dataset, figure, or template document. |
| Dataset samples | 250,000 points per dataset. |
| Figure composition | 64 panels; 32 layers per panel. |
| Figure checkpoints | 100 explicit revisions plus the current automatic working copy. |
| Figure Lab allowance | 200 MB of retained research-document revisions per account. |
| Data-file import | 20 MB input-file limit; resulting documents must still meet their own limits. |
| Source package | 200 MB package/selected expanded JSON limit, plus individual document limits. |
### Keep a portable copy
- Export a Source package for important figures.
- Retain original structure files and executed calculation inputs.
- Browser storage has its own device quota and can be removed by clearing site data.
- An archive still occupies storage; it is intended for organization, not deletion.
- Account storage shows current cloud objects separately from the research-document allowance. It is not a bill or a measure of all historical storage versions.
### Related topics
- [Profile, usage, and subscriptions](/guide#account)
- [Connect your computer with Phynite Compute](/guide#local-compute)
- [Manage plans, billing, and resource usage](/guide#billing)
## Profile, usage, and subscriptions
Account brings your research identity, measured usage, plan, and personal computer connection into one place. Usage is based on recorded data; unmeasured values are not invented.
### Edit your profile
1. Open the avatar menu and choose Research profile.
2. Set display name, institution, role, and research area.
3. Choose a JPG, PNG, or WebP photo up to 8 MB. The browser crops the center to a 256-pixel square and compresses it before upload.
4. Review the preview and choose Save profile. Remove clears the selected photo after you save.
5. Open Preferences from the avatar menu to choose the default appearance. Save appearance synchronizes it; the header theme control changes this device immediately.
### Account navigation
The avatar opens Research profile, Usage & storage, Billing & plans, Your computer, Preferences, and Account guide. Each destination opens a separate page. Account pages do not have article previous/next controls.
Use the sidebar button beside its section title to collapse the desktop sidebar to icons. Your choice is remembered on this browser. On mobile the button opens a navigation drawer; Escape, the close button, or the backdrop closes it. The account menu also supports arrow keys, Home, End, and Escape.
### Set a sign-in username
1. Create an account with email and confirm that email first.
2. Open Research profile from the avatar menu. Your display name can include spaces and does not need to be unique.
3. In Username, enter 3–30 characters, starting with a letter or number. Letters, digits, periods, hyphens, and underscores are supported; reserved names cannot be claimed.
4. Choose Save profile. The service checks uniqueness without case sensitivity. If someone else claimed the name, choose another.
5. On your next sign-in, enter either this username or your email with the same password. Changing a username immediately retires the old name; it may become available to another account. Password recovery always uses your verified email.
> A username does not create another account, share your projects, or change your email. Existing users keep email sign-in and choose a username whenever they need one.
### Browse calculation history
Open Usage & storage and scroll to Recent calculations. Six records appear on each page, ordered by creation time, newest first. Each row includes its creation date and local time, calculation type, destination, allocated cores and RAM, and recorded status.
Next and Previous change the calculation table page. The resource totals describe your entire account, not just the visible rows. Refresh updates the measurement and current table page. A missing timestamp is shown as unavailable rather than estimated.
### Read usage correctly
| Metric | How it is calculated |
| --- | --- |
| Current cloud files | Current S3 object sizes under your account prefix; excludes old object versions, database metadata, and your local disk. |
| Recorded run time | Sum of completed timing intervals from worker start to completion, including setup and upload overhead. Failed/cancelled runs count when both timestamps exist. |
| Allocated CPU-hours | Recorded run seconds multiplied by allocated cores, divided by 3600. This is allocation, not actual CPU activity. |
| On your computer | Recorded time for runs explicitly targeted to your personal worker. |
| Last 30 days | Recorded duration for runs completed during the preceding 30 days. |
| Unmeasured runs | Historical terminal runs with missing or invalid timing; excluded from duration totals. |
### Plan choices and billing
Free provides structure preparation, private projects, Figure Lab, and DFT and MD simulations on your own connected computer. Cloud compute requires separate activation.
Cloud beta is a separate invitation-only pilot for DFT and LAMMPS simulations. It appears only with an unexpired grant, an active Cloud session and available capacity: one job at a time, at most 2 vCPU, 6 GiB and 15 minutes per job. Beta grants keep the Free plan and do not deduct Quanta.
Your computer is the default destination for new Free accounts. Connect a worker before running. Changing the destination never migrates an existing run.
Cloud accepts interest registration on your account. Pricing, managed capacity, and activation are not yet a connected checkout. Institution opens a consultation path. No payment, active paid entitlement, or card charge is implied by clicking Register interest.
> Local compute consumes your own hardware, electricity, and local disk. It still needs internet access for job coordination, pseudopotential downloads when needed, and result synchronization. Existing storage and transfer limits apply.
### Related topics
- [Autosave, storage, and multiple devices](/guide#saving)
- [Connect your computer with Phynite Compute](/guide#local-compute)
- [Manage plans, billing, and resource usage](/guide#billing)
## Manage plans, billing, and resource usage
Billing & usage collects the current plan, compute destination, recorded usage, and available plan actions. A resource measurement and a monetary invoice are different records.
### Review your account
1. Open Billing in the header or Billing & usage in the studio navigation.
2. Read the active plan, subscription status, and per-run allocation. These values come from your account.
3. Open Recorded usage and choose Refresh after a calculation finishes or cloud files change.
4. Review the Figure Lab storage allowance separately from all current cloud files.
5. Choose Export usage to download a dated JSON record. The export contains resource measurements, not a payment receipt.
### Plan actions
| Plan | Action | Effect |
| --- | --- | --- |
| Free | Use Free | Includes local DFT and MD runs. Your computer is the default for new Free accounts; connect a worker before running. |
| Research | Register interest | Stores the requested plan. It does not activate paid entitlement or charge a card. |
| Enterprise | Discuss requirements | Opens the contact route for institutional capacity and terms. |
### Interpret time and storage
Recorded run time sums valid worker-start-to-completion intervals. It can include setup and result upload, as well as failed or cancelled runs that have valid timing.
Allocated CPU-hours multiply recorded duration by allocated cores. They do not measure CPU utilization, electricity consumption, or a tariff.
Current cloud storage counts current object versions. Older versions, metadata records, and your local disk are outside that number. A plus sign means the inventory reached its object limit and the displayed size is a lower bound.
The Figure Lab allowance counts retained datasets, figure documents, templates, and revisions. Archiving a figure does not remove those records or free that allowance.
### Payments and invoices
Paid checkout and invoice issuing are not connected in this release. The page does not collect card numbers, show invented invoices, or promise automatic paid activation.
Cloud and Institution capacity require agreed terms before activation. Local compute is free, but your hardware, internet, storage, and electricity remain your responsibility.
> Usage exports can contain calculation names and identifiers. Share them only with the intended collaborator or support contact.
### Related topics
- [Autosave, storage, and multiple devices](/guide#saving)
- [Profile, usage, and subscriptions](/guide#account)
- [Connect your computer with Phynite Compute](/guide#local-compute)
## Connect your computer with Phynite Compute
Run DFT and molecular-dynamics calculations on your own computer through one Phynite connection. Download the helper for your operating system, open it, and approve the connection in your account. Phynite Compute prepares the verified Quantum ESPRESSO, LAMMPS, and OVITO runtimes for you.
### Before you start
Phynite Compute reserves up to 4 CPUs and 8 GiB for a job. A computer with 16 GB of installed RAM is a useful starting point. Required capacity still depends on the atoms, cutoffs, k-points, bands, and calculation type.
Keep several GB of disk space free for the verified runtime and scientific libraries, plus working space for results. Internet is needed to connect the account, receive calculations, and upload results.
| Computer | Download | Open |
| --- | --- | --- |
| macOS | Phynite Compute for macOS | Open Phynite Compute.command |
| Windows 10 / 11 | Phynite Compute for Windows | Open Phynite Compute.cmd |
| Linux | Phynite Compute for Linux | ./phynite-compute |
- [Download Phynite Compute](/account/computer)
### 1. Download and open
1. Open Your computer from the avatar menu. The website recommends the correct download for your operating system; links for other supported systems remain available.
2. Extract the ZIP and open its launcher. The helper checks the local engine and opens its official installer page only when that prerequisite is missing.
3. The first setup downloads a pinned, architecture-compatible scientific runtime. Later launches reuse it and preserve the private Phynite Compute volume.
- [Open Your computer](/account/computer)
### 2. Approve this computer
1. The launcher returns to Your computer with the 12-digit Connection code already filled in. Review the page and choose Connect computer.
2. Each code works once and expires after 10 minutes. Only approve a computer you control.
3. If another computer is linked, finish or cancel its active calculations before confirming replacement.
4. After approval, Phynite Compute downloads and verifies the scientific libraries. Wait until the web status changes to Connected. That single connection enables both DFT Lab and MD Lab.
> The short-lived code authorizes one computer without exposing its private credential.
### 3. Run your first calculation
1. Open DFT Lab and begin with a small silicon Total energy calculation. Select Your computer as the compute destination.
2. Watch the execution log. A queued job waits for your connected computer and earlier dependencies. One calculation runs at a time on this computer.
3. For a successful SCF result, check convergence, JOB DONE, and the final Completed state. Completion also requires result upload.
4. Open Figure Lab from the completed result. Its data remains linked to the project, source calculation, and numerical settings.
5. Open MD Lab and run a small Lennard-Jones equilibration. It uses the same connected computer and does not require a second pairing.
- [Silicon tutorial](/guide#quickstart-silicon)
- [Read execution logs](/guide#execution)
### Everyday use
The private Phynite Compute volume remembers the connection and downloaded libraries. Keep the computer awake and internet available while a calculation is active; the website may be closed.
Stopping the local engine or putting the computer to sleep can interrupt a calculation. Restore connectivity and inspect the job state before sending a duplicate. Completed local work files are cleaned up after three days.
| Action | Location |
| --- | --- |
| Open or restart Phynite Compute | Open the downloaded launcher again |
| Check connection | Your computer in the account menu |
| View technical messages | Advanced manual setup → Show service logs |
| Cancel a calculation | Use Cancel in the execution log and wait for its final state |
### Update, disconnect, or move computers
1. Finish or cancel active calculations before an update, replacement, or disconnection.
2. For an update, download and open the current launcher. It asks before replacing a changed runtime and preserves the private volume.
3. To move computers, disconnect the old one in Your computer, download Phynite Compute on the new machine, and approve its new code.
> One active personal-computer credential is supported per account. Never copy or share the private runtime volume.
### Troubleshooting
| What you see | What to do |
| --- | --- |
| The local engine is missing | The launcher opens its official installer page. Install it, wait until ready, then reopen Phynite Compute. |
| No code appears | Allow the first runtime download to finish. Reopen the launcher, or use Show service logs under Advanced manual setup. |
| Code expired or was used | Reopen the launcher to request and open the latest code. |
| Approved, but still Offline | First-time library setup can take several minutes. Check service logs and refresh the connection afterward. |
| Job stays queued | Check Connected status, Your computer destination, and completed dependencies. Do not submit a duplicate. |
| OOMKilled / exit 137 | The calculation exceeded available memory. Reduce system size or bands only where scientifically appropriate. |
- [Contact support](/contact)
- [Calculation diagnostics](/guide#diagnostics)
### Advanced manual diagnostics
Normal setup does not require Terminal or PowerShell. Support may ask you to run the pinned command or read recent service logs. These commands use the same read-only, non-root Docker runtime as the launcher.
```text
docker run -d --name phynite-compute --restart unless-stopped --init --read-only --cap-drop ALL --security-opt no-new-privileges --pids-limit 512 --cpus 4 --memory 8g --tmpfs /tmp:rw,size=512m -v phynite-compute:/state public.ecr.aws/p8i3a1t8/phynite/personal-compute@sha256:2e478dd301384eaa9ea754fcf6630de7fe7ad1ccb114fb5f5c5d8dba3d49a185
docker logs --tail 30 phynite-compute
```
> Do not change the image reference, share the private volume, or paste connection codes into support messages.
### Access, data, and scientific checks
The isolated service receives only calculations belonging to the account that approved its code. Disconnecting revokes access. No incoming port, Docker socket, or host home folder is shared.
The runtime uses a read-only image, dedicated storage volume, non-root user, and CPU, memory, and process limits. It requires outgoing internet access for Phynite and verified library downloads.
Local machine owners can modify their own software. Account binding protects access to other accounts; it does not certify a scientific result. Check convergence, numerical settings, solver versions, and pseudopotentials before publication.
- [Convergence studies](/guide#convergence)
- [Prepare publication figures](/guide#publication)
### Related topics
- [Autosave, storage, and multiple devices](/guide#saving)
- [Profile, usage, and subscriptions](/guide#account)
- [Manage plans, billing, and resource usage](/guide#billing)
## Language, region, and accessibility
The studio supports English and Bahasa Indonesia. Choose a language explicitly, or let the device language preference determine the interface.
### Choose a language
1. On the homepage, use the globe menu in the header. Inside Workspace, use the flagged language buttons in the footer, or open Account / Preferences. DFT Lab and Figure Lab keep the canvas free of a footer; use their avatar menu to open Preferences.
2. Choose English or Bahasa Indonesia to override automatic detection.
3. Open another page. The preference is retained on this browser and remains available after a reload.
### How automatic selection works
A saved explicit choice takes priority. In automatic mode, Phynite reads supported languages in the order requested by your browser or device. Indonesian selects Bahasa Indonesia; English selects English.
On the initial server response, the browser language header is used. If no supported language is present, an available country hint from the hosting edge can select Indonesian for Indonesia; otherwise English is used.
Phynite does not request GPS access or call a separate IP-location service for language selection. When the detected country suggests another supported language, a small prompt offers to switch. Dismissing it is remembered for that country. Travel does not override an explicit language choice. Preferences are per browser, so another device can use a different language.
### Scientific text and data
Product names such as DFT Lab and Figure Lab, solver keywords, chemical symbols, and shortcut keys remain recognizable across languages. Scientific code, numerical source files, and publication text are not translated automatically.
Dates and usage durations follow the selected interface language where shown. A decimal value in executed QE input retains solver syntax.
Both documentation languages use the same topic links, so changing language keeps you on the same subject. Download the selected language for an offline reference.
### Keyboard and readable layouts
- Use Tab to move through links, buttons, and fields; a visible focus ring identifies the active control.
- Use Enter or Space to activate a focused control, and Escape to dismiss menus or the project dialog.
- In documentation, Primary+K or / focuses search when you are outside editable controls.
- Use the mobile contents control to browse topics without covering the article permanently.
- Reduced-motion device preferences are respected by studio transitions and the landing animation.
### Related topics
- [Autosave, storage, and multiple devices](/guide#saving)
- [Profile, usage, and subscriptions](/guide#account)
- [Connect your computer with Phynite Compute](/guide#local-compute)
## Keyboard and pointer shortcuts
Primary means Command on macOS and Control on Windows/Linux. Shortcuts are scoped to the active editor. Text fields keep their own editing behavior unless an action is explicitly listed.
### DFT Lab
| Shortcut | Action | Context |
| --- | --- | --- |
| Primary + K | Open command menu | DFT Lab workspace |
| Space | Open command menu | Builder, outside editable controls |
| Primary + Z | Undo | Builder editing history |
| Primary + Shift + Z / Primary + Y | Redo | Builder editing history |
| V | Select tool | Viewport editing |
| G | Move tool | Viewport editing |
| A | Add atom | Viewport editing |
| M | Measure tool | Viewport editing |
| F | Focus selection | A selected atom |
| Delete / Backspace | Delete selection | Viewport; not a text input |
| X / Y / Z | Constrain move to an axis | Move mode |
| Shift + X / Y / Z | Constrain move to YZ / XZ / XY plane | Move mode |
| Enter | Apply move | Move mode |
| Escape | Cancel move or close the active tool/dialog | Depends on current interaction |
| Arrow Left / Right | Resize sidebar by 16 px | Focused resize separator |
### Figure Lab
| Shortcut | Action | Context |
| --- | --- | --- |
| Primary + Z | Undo figure change | Outside editable controls |
| Primary + Shift + Z / Primary + Y | Redo figure change | Outside editable controls |
| Primary + S | Keep an explicit checkpoint | Commits a focused number draft first; automatic saving already runs |
| Primary + Shift + E | Export in the selected format | Ready figure outside editable controls |
| + or = | Zoom in | Canvas view |
| - | Zoom out | Canvas view |
| 0 | Fit figure | Canvas view |
| ? | Toggle shortcut help | Figure Lab |
| Space + drag / Alt + drag / middle drag | Pan the page | Figure Lab canvas |
| Primary + mouse wheel | Zoom the page | Figure Lab canvas |
| Escape | Close help or a drawer | Figure Lab |
### Fields and custom menus
| Shortcut | Action |
| --- | --- |
| Tab / Shift + Tab | Move forward/backward through interactive controls. |
| Enter / Space | Activate a focused button or select a highlighted menu option. |
| Arrow Up / Down | Open or move through a custom select; navigate a command menu. |
| Home / End | Move to the first/last enabled option in a custom select. |
| Type letters | Find an option by label in an open custom select; type a command query in the command menu. |
| Escape | Dismiss the current menu; cancel an uncommitted numeric draft. |
| Enter / leave the field | Commit a numeric draft, including decimals or scientific notation where allowed. |
| Primary + Z in text | Undo text editing rather than changing the figure or crystal. |
### Pointer and mobile interaction
Use the viewport camera controls to rotate, pan, and zoom the crystal. Atom tools operate on the selected atom; choose the appropriate tool before dragging.
On a small screen, open Results or Inspector from the Figure Lab toolbar, then close the drawer with its backdrop or Escape. The page remains scrollable when zoomed.
Dragging a sidebar separator adjusts its width on desktop. Keyboard users can focus the separator and use the horizontal arrow keys.
> Browser and operating-system shortcuts may intercept a key before the web page receives it. Buttons and menus provide the same primary actions.
### Related topics
- [Troubleshooting and recovery](/guide#troubleshooting)
- [Availability and planned workflows](/guide#roadmap)
- [Units, terms, and scientific references](/guide#reference)
## Reference: calculation fields and units
Use the labels and units shown by the active calculation panel. These entries explain common QE inputs; the exact set of exposed controls depends on the workflow and whether generated or expert input is selected.
### Geometry and electronic setup
| Field or QE keyword | Unit / form | Interpretation |
| --- | --- | --- |
| CELL_PARAMETERS | Three lattice vectors; read the card unit | Defines the simulated cell, including vacuum. |
| ATOMIC_POSITIONS | crystal or a stated length unit | crystal means fractional coordinates in the supplied lattice basis. |
| ecutwfc | Ry | Maximum plane-wave kinetic energy for the wavefunctions. |
| ecutrho | Ry | Charge-density and potential cutoff; converge with the chosen potential. |
| K_POINTS automatic | N1 N2 N3 s1 s2 s3 | Mesh counts and offsets for reciprocal integration; offsets are not fractional atom shifts. |
| K_POINTS crystal_b | Reciprocal path vertices and weights | A line-mode path for band sampling; it is not the SCF integration mesh. |
| nbnd | Integer | Number of electronic states calculated at each k point. |
| tot_charge | Electron-charge convention used by QE | Positive values remove electrons; review periodic-charge treatment. |
| nspin / noncolin / lspinorb | Discrete settings | Spin model and spin-orbit coupling; compatible pseudopotentials are required. |
### Convergence and relaxation
| Keyword | Meaning | Interpretation |
| --- | --- | --- |
| conv_thr | SCF threshold in Ry | Controls the estimated electronic energy error; not a force threshold. |
| electron_maxstep | Maximum electronic iterations | A limit; reaching it does not establish convergence. |
| mixing_beta | Density-mixing parameter | Can affect convergence stability; no single value fits all systems. |
| degauss | Smearing width in Ry | An integration/occupation choice, not automatically a physical lattice temperature. |
| forc_conv_thr | Force threshold in Ry/bohr | Used with ionic relaxation; electronic convergence must be sufficiently tight. |
| press | Target pressure in kbar | Relevant to cell relaxation; distinguish applied pressure from residual stress. |
| cell_dofree | Allowed cell degrees of freedom | Defines which metric components can relax; inspect suitability for a slab or constrained strain. |
### Numerical entry and units
Numeric fields accept intermediate drafts while you type. Enter or leaving the field commits a valid value; Escape cancels a draft in supported controls. An empty axis bound means automatic, while a zero is an explicit physical bound.
Do not convert all scientific values to display-region formatting. QE inputs, CSV source files, and code use the syntax required by their parser. The interface language does not rewrite a solver input or change a numerical dataset.
> Refer to the installed QE version and its official INPUT_PW documentation for precise keyword semantics. This reference does not promise support for every QE module in the Phynite form.
### Related topics
- [Keyboard and pointer shortcuts](/guide#shortcuts)
- [Troubleshooting and recovery](/guide#troubleshooting)
- [Availability and planned workflows](/guide#roadmap)
## Troubleshooting and recovery
Start with the exact state and the most recent message. Repeatedly rerunning a failing input often wastes time without fixing its cause.
### Common problems
| Problem | What to do |
| --- | --- |
| Figure opens empty | Check that the project has completed plottable data. Open a specific run, retry source loading, or import an original numerical file. |
| Band + DOS is not verified | Check geometry/electronic source identity and energy metadata. Do not force unrelated calculations into a verified pair. |
| Lines or labels appear too dense | Set final dimensions, reduce unnecessary layers, use a grid, and inspect bounds and legend placement. |
| Cloud save stays pending | Check network, sign-in, document limits, and account allowance. Keep the local browser copy and export a Source package. |
| Cloud revision conflict | Open History and compare local and remote versions. Resolve deliberately before further automatic synchronization. |
| Outdated data after switching accounts | Wait for the current account workspace to load. If needed, reload and check the signed-in identity. |
| SCF does not converge | Inspect geometry, occupations, spin, pseudopotentials, mixing, cutoffs, and solver logs before adjusting iteration limits. |
| Resource check rejects a k mesh | Use a physically justified mesh within the deployment limits; set nonperiodic directions to one. Larger jobs need appropriate capacity. |
| Export fails | Check data validity, output size, font availability, and network; try again after the preview completes. |
| Old raw download expired | Open retained numerical data if available, import your original file, or run again. A preview image cannot recover missing numerical samples. |
### What to include in a support request
- The page, action, and exact visible error.
- Project and calculation names or IDs that you are comfortable sharing.
- Whether the failure happens before submission, in queue, during execution, during upload, or in Figure Lab.
- Relevant solver-log excerpts and the expected behavior.
- Never include passwords, browser cookies, access tokens, or the private computer configuration.
### Related topics
- [Keyboard and pointer shortcuts](/guide#shortcuts)
- [Availability and planned workflows](/guide#roadmap)
- [Units, terms, and scientific references](/guide#reference)
## Troubleshooting: locate a failed workflow stage
Identify the first stage that did not complete. Retrying a downstream action cannot repair an earlier missing structure, disconnected worker, or incompatible numerical source.
### Decision table
| What you see | Likely stage | Next check |
| --- | --- | --- |
| New project is unavailable | Account workspace initialization | Allow the workspace to load. On a cloud error, reload; do not clear browser data containing unsynchronized edits. |
| Structure will not import | Parsing or geometry | Check format, encoding, lattice, coordinates, and occupancies. Keep the source file for diagnosis. |
| Run is rejected immediately | Submission validation | Inspect the field error, resource limits, authentication, and method compatibility. |
| Run remains Queued | Worker or dependency | Check destination, private worker heartbeat, shared availability, and predecessors. |
| Worker starts but QE exits | Runtime or scientific input | Read the first solver error. Check pseudopotential files, species names, syntax, memory, and disk. |
| SCF cycles do not settle | Electronic self-consistency | Inspect geometry, occupations, magnetism, mixing, thresholds, and near-degenerate states. |
| Solver finished but result unavailable | Upload or completion | Keep the worker running; inspect network, credential validity, and final upload state. |
| Open in Figure Lab fails | Numerical source retrieval | Retry the source. Older runs may need their original numerical file when retained datasets are absent. |
| Overlay or pair warns about context | Scientific comparison | Read geometry, energy-reference, and path identity. Use independent panels when comparability is not established. |
| Export fails | Rendering or font resources | Reconnect, reduce an oversized raster, and retry. Keep the figure document and source package. |
### Collect useful evidence
1. Record the page and exact action, time, project, and run identifier.
2. Copy the visible error and relevant solver-log lines around the first failure.
3. Note the destination, allocation, operating system, worker image, and whether the problem repeats.
4. For a plot issue, retain the numerical dataset, figure Source package, and expected axis convention.
5. Contact support with the smallest reproducible example. Remove private credentials, cookies, passwords, and unrelated project data.
### Protect recoverable work
Keep the current browser session open when it contains an unsynchronized figure or project. Export source files before clearing site storage.
A retry creates or repeats work according to the active action. Inspect existing queued and running calculations before submitting duplicates.
Replacing a personal credential invalidates the old worker. Finish or cancel active work before rotating it so a completed solver can still upload its result.
### Related topics
- [Keyboard and pointer shortcuts](/guide#shortcuts)
- [Troubleshooting and recovery](/guide#troubleshooting)
- [Availability and planned workflows](/guide#roadmap)
## Availability and planned workflows
The workspace distinguishes available tools from promoted future features. A coming-soon card is informational and does not submit a job.
### Molecular dynamics
The Workspace card previews a future workflow for atomic trajectories, finite-temperature dynamics, and time-dependent analysis. MD is currently Coming soon.
It is intentionally absent from the executable calculation menu. There is no working MD submission or trajectory-analysis promise behind the promotional card.
### Managed plans
Free includes DFT Lab and Figure Lab, imports, templates, exports, and DFT and MD runs on one connected personal computer per account. There is no Phynite activation or hourly local compute fee. Cloud compute uses Quanta: 1 Quanta = US$1, billed by usage.
Paid Cloud access requires confirmed server-side activation. Requesting Cloud does not grant access or take payment. Optional storage offers are 10 GB for US$0.50/month, 50 GB for US$1.50/month, and 100 GB for US$3/month; requests and transfer are quoted separately. Existing account limits remain until activation. See /pricing for estimates and terms.
### Related topics
- [Keyboard and pointer shortcuts](/guide#shortcuts)
- [Troubleshooting and recovery](/guide#troubleshooting)
- [Units, terms, and scientific references](/guide#reference)
## Units, terms, and scientific references
The interface exposes a connected workflow, but the scientific meaning still comes from the selected model, solver method, and numerical data.
### Units and terms
| Term | Meaning |
| --- | --- |
| Å / angstrom | Length unit for atomic-scale geometry; 1 Å = 10^-10 m. |
| Bohr | Atomic unit of length; approximately 0.529177 Å. |
| eV / Ry | Energy units; 1 Ry is approximately 13.605693 eV. Verify which unit each input field expects. |
| Fractional coordinates | Coefficients of the real-space cell vectors. |
| Reciprocal coordinates | Coordinates in the reciprocal lattice basis; interpretation depends on the declared convention. |
| Γ | The Brillouin-zone center, k = 0. |
| SCF / NSCF | Self-consistent / non-self-consistent electronic calculation. |
| DOS / PDOS | Density of states / projected density of states. |
| DFPT | Density-functional perturbation theory. |
| vCPU / core allocation | Requested execution parallelism; not measured utilization. |
| GiB / MB | GiB uses 1024^3 bytes; this guide labels decimal storage totals in MB and RAM allocations in GiB. |
| Provenance | Source identity, method, metadata, and processing history that explain where a result came from. |
### Read alongside the guide
Use the official Quantum ESPRESSO documentation for the exact semantics of pw.x, bands.x, dos.x, projwfc.x, ph.x, q2r.x, and matdyn.x options.
Use Materials Project documentation to understand database structure provenance and conventions; SeeK-path documentation for standardized paths; and BoltzTraP2 documentation for interpolation and transport assumptions.
This guide describes the implemented Phynite interface and its current behavior. It is not a substitute for a method-specific convergence study or validation against the scientific literature.
### Related topics
- [Keyboard and pointer shortcuts](/guide#shortcuts)
- [Troubleshooting and recovery](/guide#troubleshooting)
- [Availability and planned workflows](/guide#roadmap)
## Scientific references
- https://www.quantum-espresso.org/documentation/
- https://docs.materialsproject.org/
- https://seekpath.readthedocs.io/
- https://www.boltztrap.org/