MD workflows: Simple, Advanced, and trajectory analysis
LAMMPS simulation changes the physical system; trajectory inspection and analysis measure retained frames. The current simulation editor labels Guided mode “Simple” and the manual/block editor “Advanced”. Keep the source, potential, units, and evidence explicit in both modes.
Install MD/analysis in Settings → Compute and verify the required LAMMPS/analysis capabilities and native isolation. MD uses Your computer in the current workflow.
Use a structure or trajectory with a valid simulation cell, known coordinates, particle identities, and masses. A type-only dump is not enough to infer chemical elements or masses.
Map every particle type before choosing a force field. Check that uploaded potential assets support all elements, the selected atom style, and the expected unit system.
Pause trajectory playback and finish frame analysis before submitting a simulation. Retain the original trajectory and model citation; a successful integrity/runtime check does not establish physical accuracy.
Build a Simple simulation stage
Simple is the guided workflow in the current interface.
Add an MD simulation module to the project and connect its structure, or open Simulation in MD Lab. Add stage chooses a recipe; keep the initial exercise short.
Open the stage configuration and select Simple. Review the recipe, potential, periodic boundary condition, ensemble, timestep, total steps, temperatures, pressure controls where relevant, and random seed.
Inspect Output & Trajectory. Thermo interval and Trajectory interval are step counts, so choose intervals that produce useful data within the planned duration without excessive disk use.
Choose Inspect in.lammps. Verify the complete generated input, source and potential mapping, fixed timestep, stage order, and output commands. Save to library stores a reusable setup; it does not execute the solver.
Choose Run step for one stage, or review Run selected/Run all for the intended ordered chain. Review the compute allocation and submit once.
UI quantity
Displayed unit
Interpretation
Timestep
fs
The generated metal-unit input converts this to ps. Retain the fixed timestep and stage durations.
Temperature / damping
K / ps
Temperature and thermostat relaxation time are different controls.
Pressure / damping
bar / ps
Check the ensemble and periodic directions before pressure coupling.
LJ epsilon / sigma / cutoff
eV / Å / Å
Model parameters must match the intended species and physical study.
Strain rate / safety limit
s⁻¹ / ratio
A rate and total duration imply a planned strain; the safety limit is not a target unit conversion.
Advanced: Blocks and Expert input
Advanced retains managed input validation and isolation requirements.
Advanced is a managed LAMMPS workflow, not an unrestricted shell or a full standalone input file. Phynite owns source loading, units, boundary, masses, force field, clock, and output paths. External execution, include/jump, arbitrary file paths, nested commands, and unmanaged output are rejected. Keep fixed timesteps per stage; adaptive timestep commands are not supported by the retained physical-time contract.
Switch to Advanced. Blocks opens a Command library and an ordered Simulation commands rack. Add a supported block, edit its values, and review its command preview.
Use the block On/Off control, arrows or drag handle to establish the execution order. Disabled blocks remain stored but are omitted from generated input.
Open Expert to inspect the compiled commands. Editing the raw text creates an override that controls that stage even if the block rack is later changed. Regenerate from Blocks removes that override explicitly.
Read browser validation before submission, then inspect in.lammps again. Manual commands must contain run or minimize and pass the native runtime validation and isolation probe.
Analyze retained frames
Review source frames and analysis parameters before running.
Open the completed simulation’s Execution result and choose Inspect trajectory when a retained trajectory is available. Alternatively, import a known trajectory and preserve its original file.
In a project workflow, connect a trajectory to an MD analysis module. Choose Analysis: Radial distribution function, Common neighbor analysis, Polyhedral template matching, or Coordination number.
Set the cutoff in Å where applicable and choose Start frame and Frame stride. Review run includes the actual source and analysis settings. MD Lab also offers a modifier pipeline; preserve modifier order when comparing results.
Inspect the output table, distribution, structural classification, or retained analysis artifacts. Source time remains unknown if it was not declared; frame number alone is not elapsed physical time.
Export the original numerical data and configuration along with any figure. Keep units, frame selection, cutoff, and potential identity in the method notes.