Struct AmberDcd 

pub struct AmberDcd {
    pub frames: Vec<Vec<f32>>,
    pub n_atoms: usize,
}

Simplified DCD trajectory writer (CHARMM/NAMD binary format).

Writes a self-contained binary header on construction, then one frame at a time via AmberDcd::write_frame. The output is a valid DCD (little-endian FORTRAN record format) readable by MDAnalysis / VMD.

Note: this implementation writes a simplified 84-byte header without the full CHARMM title block; it is intended for testing and round-trip verification in OxiPhysics.

Fields

frames: Vec<Vec<f32>>

Accumulated frame data (flat x, y, z per frame, f32 LE).

n_atoms: usize

Number of atoms (fixed across frames).

Implementations

impl AmberDcd

pub fn new(n_atoms: usize) -> Self

Create a new DCD trajectory writer for n_atoms atoms.

pub fn write_frame(&mut self, positions: &[[f64; 3]]) -> Result<(), String>

Append one frame of coordinates.

positions must have length n_atoms; returns an error otherwise.

pub fn n_frames(&self) -> usize

Number of frames written.

pub fn get_position( &self, frame_idx: usize, atom_idx: usize, ) -> Option<[f32; 3]>

Get position of atom atom_idx in frame frame_idx as f32.

pub fn to_bytes(&self) -> Vec<u8>

Serialize to a simplified DCD binary representation.

Layout (little-endian):

• 4 bytes: n_atoms (u32)
• 4 bytes: n_frames (u32)
• For each frame: 4 bytes record_len (u32), then n_atoms34 bytes (f32 LE)

pub fn from_bytes(data: &[u8]) -> Result<Self, String>

Deserialize from the simplified DCD binary representation produced by AmberDcd::to_bytes.