rexafs 0.2.13

Rust-powered X-ray absorption spectroscopy analysis and EXAFS fitting
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231

use super::{require, RmcError};
use crate::structure::{Element, Lattice, Structure, Xyz};
use serde::{Deserialize, Serialize};

/// An explicit atom with fixed chemical identity; its vector position is its ID.
#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
#[serde(deny_unknown_fields)]
pub struct Atom {
    /// Atomic number, validated against the rexafs element table.
    pub atomic_number: u8,
    /// Cartesian coordinates in Å. Refinement preserves unwrapped positions.
    pub position: [f64; 3],
}

/// Finite atomic cluster or explicit periodic cell. The cell is fixed throughout
/// refinement; moving an atom moves all its periodic images together.
#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
#[serde(deny_unknown_fields)]
pub struct Configuration {
    /// Nonempty atoms in stable order, with no implicit occupancy or symmetry.
    pub atoms: Vec<Atom>,
    /// Optional Cartesian lattice row vectors a, b, c in Å. None means a finite
    /// cluster with no periodic images. General nonsingular triclinic cells work.
    pub cell: Option<[[f64; 3]; 3]>,
}

impl Configuration {
    /// Copy a parsed XYZ cluster, retaining atom order and Cartesian coordinates.
    /// Validates atomic numbers, symbol consistency and finite coordinates.
    pub fn from_xyz(xyz: &Xyz) -> Result<Self, RmcError> {
        for atom in &xyz.atoms {
            require(
                Element::from_symbol(&atom.symbol).is_some_and(|e| e.z == atom.z),
                "XYZ symbol and atomic number disagree",
            )?;
        }
        let configuration = Self {
            cell: None,
            atoms: xyz
                .atoms
                .iter()
                .map(|a| Atom {
                    atomic_number: a.z,
                    position: a.cart,
                })
                .collect(),
        };
        configuration.validate()?;
        Ok(configuration)
    }

    /// Expand the already symmetry-expanded `structure.sites` into an explicit
    /// periodic supercell. Repetitions along a,b,c must be positive; at most 10,000
    /// atoms are allowed by this reference implementation. Order is a-image,
    /// b-image, c-image, then input site. Coordinates are wrapped into the input
    /// cell first. Mixed or partially occupied sites require a user-created
    /// explicit realization and are rejected instead of selecting a majority.
    pub fn from_structure(structure: &Structure, repeats: [usize; 3]) -> Result<Self, RmcError> {
        require(
            repeats.iter().all(|&n| n > 0),
            "supercell repetitions must be positive",
        )?;
        let count = repeats
            .iter()
            .try_fold(structure.sites.len(), |n, r| n.checked_mul(*r));
        require(
            count.is_some_and(|n| n > 0 && n <= 10_000),
            "supercell must contain 1..=10000 atoms",
        )?;
        let lattice = checked_lattice(structure.lattice.matrix)?;
        let mut species = Vec::new();
        for site in &structure.sites {
            require(
                site.species.len() == 1 && (site.species[0].occupancy - 1.0).abs() <= 1e-12,
                "RMC requires explicit fully occupied single-species sites",
            )?;
            require(
                site.frac.iter().all(|x| x.is_finite()),
                "site coordinates must be finite",
            )?;
            let element = site.species[0].element().ok_or_else(|| {
                RmcError::Invalid(format!("unknown element at site {}", site.label))
            })?;
            species.push(element.z);
        }
        let mut atoms = Vec::with_capacity(count.unwrap());
        for a in 0..repeats[0] {
            for b in 0..repeats[1] {
                for c in 0..repeats[2] {
                    for (site, &atomic_number) in structure.sites.iter().zip(&species) {
                        let frac = std::array::from_fn(|i| {
                            site.frac[i].rem_euclid(1.0) + [a, b, c][i] as f64
                        });
                        atoms.push(Atom {
                            atomic_number,
                            position: lattice.to_cart(frac),
                        });
                    }
                }
            }
        }
        let cell = std::array::from_fn(|i| lattice.matrix[i].map(|v| v * repeats[i] as f64));
        let configuration = Self {
            atoms,
            cell: Some(cell),
        };
        configuration.validate()?;
        Ok(configuration)
    }

    /// Validate finite coordinates, elements, atom count and cell geometry.
    /// Pair-distance constraints are checked by `refine`, not by this operation.
    pub fn validate(&self) -> Result<(), RmcError> {
        require(
            !self.atoms.is_empty() && self.atoms.len() <= 10_000,
            "configuration needs 1..=10000 atoms",
        )?;
        for atom in &self.atoms {
            require(
                Element::from_z(atom.atomic_number).is_some(),
                "unknown atomic number",
            )?;
            require(
                atom.position
                    .iter()
                    .all(|x| x.is_finite() && x.abs() <= 1e8),
                "Cartesian coordinates must be finite and within ±1e8 Å",
            )?;
        }
        self.lattice()?;
        Ok(())
    }

    pub(crate) fn lattice(&self) -> Result<Option<Lattice>, RmcError> {
        self.cell.map(checked_lattice).transpose()
    }

    /// Export one frame in plain XYZ, retaining unwrapped coordinates and order.
    /// Periodic cell information is not represented; retain the JSON result too.
    pub fn to_xyz(&self) -> Result<String, RmcError> {
        self.validate()?;
        let mut out = format!(
            "{}\nrexafs RMC; Cartesian Å; cell retained in JSON only\n",
            self.atoms.len()
        );
        for atom in &self.atoms {
            let [x, y, z] = atom.position;
            out.push_str(&format!(
                "{} {x:.12} {y:.12} {z:.12}\n",
                Element::from_z(atom.atomic_number).unwrap().symbol
            ));
        }
        Ok(out)
    }
}

fn checked_lattice(matrix: [[f64; 3]; 3]) -> Result<Lattice, RmcError> {
    require(
        matrix
            .iter()
            .flatten()
            .all(|x| x.is_finite() && x.abs() <= 1e8),
        "invalid cell vectors",
    )?;
    let lattice = Lattice::from_matrix(matrix).map_err(|e| RmcError::Invalid(e.to_string()))?;
    require(
        (0..3).all(|i| {
            let h = lattice.interplanar_spacing(i);
            h.is_finite() && h > 1e-6
        }),
        "cell plane spacings must be finite and greater than 1e-6 Å",
    )?;
    Ok(lattice)
}

pub(crate) fn distance(a: [f64; 3], b: [f64; 3]) -> f64 {
    (a[0] - b[0]).hypot(a[1] - b[1]).hypot(a[2] - b[2])
}

// Enumerating images avoids the incorrect fractional-rounding minimum-image
// shortcut for skew cells. If |r|<R then each fractional component is <R/h_i,
// where h_i is the corresponding interplanar spacing.
pub(crate) fn image_bounds(lattice: &Lattice, radius: f64) -> Result<[i32; 3], RmcError> {
    let bounds: [f64; 3] =
        std::array::from_fn(|i| (radius / lattice.interplanar_spacing(i) + 1.0).ceil());
    require(
        bounds.iter().all(|n| n.is_finite() && *n <= 100.0)
            && bounds.iter().map(|n| 2.0 * n + 1.0).product::<f64>() <= 100_000.0,
        "cell needs too many periodic images; use a larger or better-conditioned cell",
    )?;
    Ok(bounds.map(|n| n as i32))
}

pub(crate) fn distances_allowed(
    configuration: &Configuration,
    lattice: Option<&Lattice>,
    minimum: f64,
    moved: Option<usize>,
) -> Result<bool, RmcError> {
    let bounds = lattice.map(|l| image_bounds(l, minimum)).transpose()?;
    let centers: Vec<_> =
        moved.map_or_else(|| (0..configuration.atoms.len()).collect(), |i| vec![i]);
    for i in centers {
        let first = if moved.is_some() { 0 } else { i };
        for j in first..configuration.atoms.len() {
            let a = configuration.atoms[i].position;
            let b = configuration.atoms[j].position;
            if let (Some(lattice), Some(bounds)) = (lattice, bounds) {
                let delta = std::array::from_fn(|axis| a[axis] - b[axis]);
                let frac = lattice.to_frac(delta).map(|v| v - v.round());
                for x in -bounds[0]..=bounds[0] {
                    for y in -bounds[1]..=bounds[1] {
                        for z in -bounds[2]..=bounds[2] {
                            if i == j && [x, y, z] == [0, 0, 0] {
                                continue;
                            }
                            let image =
                                [frac[0] + x as f64, frac[1] + y as f64, frac[2] + z as f64];
                            if distance(lattice.to_cart(image), [0.0; 3]) < minimum {
                                return Ok(false);
                            }
                        }
                    }
                }
            } else if i != j && distance(a, b) < minimum {
                return Ok(false);
            }
        }
    }
    Ok(true)
}