Struct bader::voxel_map::VoxelMap

pub struct VoxelMap {
    pub assigned_atom: Vec<usize>,
    pub minimum_distance: Vec<f64>,
    pub bader_volume: Vec<f64>,
    pub surface_distance: Vec<f64>,
    pub bader_charge: Vec<Vec<f64>>,
    pub bader_maxima: Vec<isize>,
    // some fields omitted
}

A structure for building and processing the map between voxel and maxima. Bader maxima are stored in the voxel_map whilst the contributing weights are stored in the weight_map. The weight_map is only written to once by each point and so once a value has been written it is safe to read by any thread. To check it has been written to weight_get monitors the state of corresponding voxel_map value. Writing to the map is acheived by acquiring the lock, noting the length of the weight_map, pushing the weight vector for voxel p to the weight_map, droping the write lock and then storing the index of the inserted vector using weight_store.

Examples

use bader::voxel_map::VoxelMap;

for p in 0..1isize {
    let voxel_map = VoxelMap::new(10);
    let i = {
        let mut weight = voxel_map.lock();
        (*weight).push(Vec::with_capacity(0));
        weight.len() - 1
    };
    voxel_map.weight_store(p, i)
}

Fields

assigned_atom: Vec<usize>

minimum_distance: Vec<f64>

bader_volume: Vec<f64>

surface_distance: Vec<f64>

bader_charge: Vec<Vec<f64>>

bader_maxima: Vec<isize>

Implementations

impl VoxelMap

pub fn new(size: usize) -> Self

Initialises a VoxelMap of dimensions, size.

pub fn weight_get(&self, p: isize) -> Voxel<'_>

Retrieves the state of the voxel, p. This will lock until p has been stored in the VoxelMap and then return either a Voxel::Maxima or Voxel::Weight. Calling this on a voxel, p, that is below the vacuum_tolerance will deadlock as a voxel is considered stored once voxel_map[p] > -1.

pub fn maxima_get(&self, p: isize) -> isize

Atomic loading of voxel, p, from voxel_map blocks if maxima == -1

pub fn maxima_non_block_get(&self, p: isize) -> isize

Atomic loading of voxel, p, from voxel_map

pub fn voxel_get(&self, p: isize) -> Voxel<'_>

A none locking retrieval of the state of voxel, p. This should only be used once the VoxelMap has been fully populated.

pub fn maxima_list(&self) -> Vec<isize>

Finds the unique values contained in voxel_map and returns them sorted by value.

pub fn maxima_store(&self, p: isize, maxima: isize)

Stores the maxima of voxel, p, in the voxel_map.

pub fn weight_store(&self, p: isize, i: usize)

Stores the index of p's weight contributions in weight_map into the weight_index and unlocks the structure.

pub fn lock(&self) -> Lock<'_>

Locks the structure for write access.

pub fn assign_atoms(&mut self, atoms: &Atoms, density: &Density<'_>)

Assigns each Bader maxima to an atom.

pub fn charge_sum(
    &mut self,
    densities: &[Vec<f64>],
    atoms: &Atoms,
    density: &Density<'_>
)

Sums the densities for each bader volume.

Trait Implementations

impl Sync for VoxelMap