xtalforge

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Commands and document ​

xtalforge-commands is the only mutation path. A Command returns the new Structure from apply; CommandStack owns the undo/redo history, the clean flag and a bounded log. Document owns the structure, the stack, the selection, the atom groups and the origin of each edit.

rust
use xtalforge::commands::{CommandStack, Origin, atoms::MoveSites};

let mut stack = CommandStack::new();
let mut edited = structure.clone();
stack.push(
    &mut edited,
    Box::new(MoveSites::new(vec![(0, [0.1, 0.0, 0.0])])),
    Origin::User,
)?;

Stack ​

CommandStack::push(&mut structure, command, origin) applies, records and writes the new structure back; an invalid command leaves both untouched; undo(&mut structure) and redo(&mut structure) move through the history. can_undo, can_redo, undo_depth, redo_depth, is_dirty, mark_clean, max_depth/set_max_depth (default 200) and log() expose the state. MacroCommand groups commands; ReplaceStructure, SnapshotEdit and StructureOperation cover whole-structure and function-based edits.

Document ​

Document::new(structure) starts clean. apply(command, origin), undo, redo, dirty, mark_clean, structure(), selection() and the atom-group methods are the public state. Origin is User, Script or Agent.

Catalogue ​

  • atoms: AddSites, DeleteSites, SetElement, MoveSites, SetOccupancy.
  • bonds: AddBond, RemoveBond, SetBondRules.
  • cell: SetLattice (KeepFractional/KeepCartesian), Supercell, ShiftOrigin, WrapIntoCell.
  • symmetry: ReduceToP1, FindSymmetry, SetSpaceGroup, Standardize.
  • groups: AtomGroup, AddAtomGroup, RemoveAtomGroup, SetGroupColor, SetGroupHidden.
  • clipboard: Fragment, copy_selection, PasteFragment.
  • later: SetCharges, Interpenetrate, MarkConnectionPoints (Phase 4-6 wrappers, undoable like every other command).

CommandRecord is one logged edit, PositionPolicy selects KeepFractional/KeepCartesian when the lattice changes, and GroupStore owns the atom groups for Document.

Every command is tested for apply and undo; invalid indices and values return Error::InvalidInput.