sci_form/charges_eeq/

charges.rs

//! EEQ Charge Model — Core
//!
//! Electronegativity equalization with geometry-dependent coordination
//! numbers and Coulomb damping. Solves a constrained linear system
//! to yield charge-neutral partial charges.

use nalgebra::DMatrix;
use serde::{Deserialize, Serialize};

/// EEQ per-element parameters.
#[derive(Debug, Clone, Copy, Serialize, Deserialize)]
pub struct EeqParams {
    /// Electronegativity chi (eV).
    pub chi: f64,
    /// Chemical hardness eta (eV).
    pub eta: f64,
    /// Charge radius for Coulomb damping (Å).
    pub r_eeq: f64,
    /// Covalent radius for CN (Å).
    pub r_cov: f64,
}

/// Configuration for EEQ calculations.
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct EeqConfig {
    /// Total molecular charge.
    pub total_charge: f64,
    /// Regularization parameter for near-singular systems.
    pub regularization: f64,
}

impl Default for EeqConfig {
    fn default() -> Self {
        Self {
            total_charge: 0.0,
            regularization: 1e-10,
        }
    }
}

/// Result of EEQ charge calculation.
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct EeqChargeResult {
    /// Partial charges per atom.
    pub charges: Vec<f64>,
    /// Fractional coordination numbers per atom.
    pub coordination_numbers: Vec<f64>,
    /// Total charge (should match config).
    pub total_charge: f64,
}

/// Get EEQ parameters for an element by atomic number.
pub fn get_eeq_params(z: u8) -> EeqParams {
    match z {
        1 => EeqParams {
            chi: 2.20,
            eta: 13.6,
            r_eeq: 0.80,
            r_cov: 0.32,
        },
        5 => EeqParams {
            chi: 2.04,
            eta: 8.30,
            r_eeq: 1.40,
            r_cov: 0.85,
        },
        6 => EeqParams {
            chi: 2.55,
            eta: 10.0,
            r_eeq: 1.30,
            r_cov: 0.77,
        },
        7 => EeqParams {
            chi: 3.04,
            eta: 14.5,
            r_eeq: 1.20,
            r_cov: 0.75,
        },
        8 => EeqParams {
            chi: 3.44,
            eta: 13.4,
            r_eeq: 1.10,
            r_cov: 0.73,
        },
        9 => EeqParams {
            chi: 3.98,
            eta: 17.4,
            r_eeq: 1.00,
            r_cov: 0.71,
        },
        14 => EeqParams {
            chi: 1.90,
            eta: 8.15,
            r_eeq: 1.75,
            r_cov: 1.17,
        },
        15 => EeqParams {
            chi: 2.19,
            eta: 10.5,
            r_eeq: 1.60,
            r_cov: 1.10,
        },
        16 => EeqParams {
            chi: 2.58,
            eta: 10.4,
            r_eeq: 1.50,
            r_cov: 1.04,
        },
        17 => EeqParams {
            chi: 3.16,
            eta: 13.0,
            r_eeq: 1.40,
            r_cov: 0.99,
        },
        35 => EeqParams {
            chi: 2.96,
            eta: 11.8,
            r_eeq: 1.55,
            r_cov: 1.14,
        },
        53 => EeqParams {
            chi: 2.66,
            eta: 10.5,
            r_eeq: 1.70,
            r_cov: 1.33,
        },
        26 => EeqParams {
            chi: 1.83,
            eta: 7.90,
            r_eeq: 1.70,
            r_cov: 1.24,
        },
        29 => EeqParams {
            chi: 1.90,
            eta: 7.73,
            r_eeq: 1.60,
            r_cov: 1.32,
        },
        30 => EeqParams {
            chi: 1.65,
            eta: 9.39,
            r_eeq: 1.65,
            r_cov: 1.22,
        },
        // Extended TM coverage
        22 => EeqParams {
            chi: 1.54,
            eta: 6.83,
            r_eeq: 1.80,
            r_cov: 1.47,
        }, // Ti
        24 => EeqParams {
            chi: 1.66,
            eta: 6.77,
            r_eeq: 1.75,
            r_cov: 1.39,
        }, // Cr
        25 => EeqParams {
            chi: 1.55,
            eta: 7.43,
            r_eeq: 1.73,
            r_cov: 1.39,
        }, // Mn
        27 => EeqParams {
            chi: 1.88,
            eta: 7.86,
            r_eeq: 1.67,
            r_cov: 1.26,
        }, // Co
        28 => EeqParams {
            chi: 1.91,
            eta: 7.64,
            r_eeq: 1.65,
            r_cov: 1.21,
        }, // Ni
        44 => EeqParams {
            chi: 2.20,
            eta: 7.36,
            r_eeq: 1.75,
            r_cov: 1.46,
        }, // Ru
        46 => EeqParams {
            chi: 2.20,
            eta: 8.34,
            r_eeq: 1.70,
            r_cov: 1.39,
        }, // Pd
        47 => EeqParams {
            chi: 1.93,
            eta: 7.58,
            r_eeq: 1.72,
            r_cov: 1.45,
        }, // Ag
        78 => EeqParams {
            chi: 2.28,
            eta: 8.96,
            r_eeq: 1.72,
            r_cov: 1.36,
        }, // Pt
        79 => EeqParams {
            chi: 2.54,
            eta: 9.23,
            r_eeq: 1.70,
            r_cov: 1.36,
        }, // Au
        // Main group additions
        3 => EeqParams {
            chi: 0.98,
            eta: 5.39,
            r_eeq: 2.10,
            r_cov: 1.28,
        }, // Li
        11 => EeqParams {
            chi: 0.93,
            eta: 5.14,
            r_eeq: 2.40,
            r_cov: 1.66,
        }, // Na
        12 => EeqParams {
            chi: 1.31,
            eta: 7.65,
            r_eeq: 2.00,
            r_cov: 1.41,
        }, // Mg
        13 => EeqParams {
            chi: 1.61,
            eta: 5.99,
            r_eeq: 1.90,
            r_cov: 1.21,
        }, // Al
        19 => EeqParams {
            chi: 0.82,
            eta: 4.34,
            r_eeq: 2.75,
            r_cov: 2.03,
        }, // K
        20 => EeqParams {
            chi: 1.00,
            eta: 6.11,
            r_eeq: 2.31,
            r_cov: 1.76,
        }, // Ca
        _ => EeqParams {
            chi: 2.20,
            eta: 10.0,
            r_eeq: 1.50,
            r_cov: 1.00,
        },
    }
}

/// Compute fractional coordination number for each atom.
///
/// Uses a Fermi-type counting function:
/// CN_i = Σ_{j≠i} 1 / (1 + exp(-16 * (r_cov_ij/r_ij - 1)))
pub fn fractional_coordination(elements: &[u8], positions: &[[f64; 3]]) -> Vec<f64> {
    let n = elements.len();
    let mut cn = vec![0.0; n];

    for i in 0..n {
        let pi = get_eeq_params(elements[i]);
        for j in (i + 1)..n {
            let pj = get_eeq_params(elements[j]);
            let r_cov_ij = pi.r_cov + pj.r_cov;
            let dx = positions[i][0] - positions[j][0];
            let dy = positions[i][1] - positions[j][1];
            let dz = positions[i][2] - positions[j][2];
            let r_ij = (dx * dx + dy * dy + dz * dz).sqrt();

            if r_ij < 1e-10 {
                continue;
            }

            let f = 1.0 / (1.0 + (-16.0 * (r_cov_ij / r_ij - 1.0)).exp());
            cn[i] += f;
            cn[j] += f;
        }
    }

    cn
}

/// Coulomb interaction kernel with Gaussian damping.
fn gamma_damped(r_ij: f64, r_eeq_i: f64, r_eeq_j: f64) -> f64 {
    if r_ij < 1e-10 {
        return 0.0;
    }
    let sigma_ij = (r_eeq_i * r_eeq_i + r_eeq_j * r_eeq_j).sqrt();
    let arg = std::f64::consts::SQRT_2 / sigma_ij * r_ij;
    erf_approx(arg) / r_ij
}

/// Approximate error function (Abramowitz & Stegun 7.1.26).
pub(crate) fn erf_approx(x: f64) -> f64 {
    let a1 = 0.254829592;
    let a2 = -0.284496736;
    let a3 = 1.421413741;
    let a4 = -1.453152027;
    let a5 = 1.061405429;
    let p = 0.3275911;

    let sign = if x < 0.0 { -1.0 } else { 1.0 };
    let x = x.abs();
    let t = 1.0 / (1.0 + p * x);
    let y = 1.0 - (((((a5 * t + a4) * t) + a3) * t + a2) * t + a1) * t * (-x * x).exp();
    sign * y
}

/// Compute EEQ charges by solving the extended linear system.
///
/// [η + γ   1] [q]   [−χ]
/// [1^T     0] [λ] = [Q ]
pub fn compute_eeq_charges(
    elements: &[u8],
    positions: &[[f64; 3]],
    config: &EeqConfig,
) -> EeqChargeResult {
    let n = elements.len();

    if n == 0 {
        return EeqChargeResult {
            charges: vec![],
            coordination_numbers: vec![],
            total_charge: config.total_charge,
        };
    }

    if n == 1 {
        return EeqChargeResult {
            charges: vec![config.total_charge],
            coordination_numbers: vec![0.0],
            total_charge: config.total_charge,
        };
    }

    let cn = fractional_coordination(elements, positions);

    let dim = n + 1;
    let mut a = DMatrix::zeros(dim, dim);
    let mut b_vec = vec![0.0; dim];

    let params: Vec<EeqParams> = elements.iter().map(|&z| get_eeq_params(z)).collect();

    for i in 0..n {
        a[(i, i)] = params[i].eta + config.regularization;

        for j in (i + 1)..n {
            let dx = positions[i][0] - positions[j][0];
            let dy = positions[i][1] - positions[j][1];
            let dz = positions[i][2] - positions[j][2];
            let r_ij = (dx * dx + dy * dy + dz * dz).sqrt();
            let gij = gamma_damped(r_ij, params[i].r_eeq, params[j].r_eeq);
            a[(i, j)] = gij;
            a[(j, i)] = gij;
        }

        a[(i, n)] = 1.0;
        a[(n, i)] = 1.0;

        let cn_correction = -0.1 * (cn[i] - 2.0);
        b_vec[i] = -(params[i].chi + cn_correction);
    }

    b_vec[n] = config.total_charge;

    let b_nalg = nalgebra::DVector::from_vec(b_vec);
    let solution = a.lu().solve(&b_nalg);

    let charges = match solution {
        Some(sol) => (0..n).map(|i| sol[i]).collect(),
        None => vec![0.0; n],
    };

    let total: f64 = charges.iter().sum();

    EeqChargeResult {
        charges,
        coordination_numbers: cn,
        total_charge: total,
    }
}

#[cfg(test)]
mod tests {
    use super::*;

    fn water_positions() -> Vec<[f64; 3]> {
        vec![[0.0, 0.0, 0.0], [0.757, 0.586, 0.0], [-0.757, 0.586, 0.0]]
    }

    #[test]
    fn test_coordination_number_water() {
        let elements = [8, 1, 1];
        let pos = water_positions();
        let cn = fractional_coordination(&elements, &pos);
        assert!(cn[0] > 1.5, "O CN = {}", cn[0]);
        assert!(cn[1] > 0.5 && cn[1] < 1.5, "H CN = {}", cn[1]);
    }

    #[test]
    fn test_eeq_charge_neutrality() {
        let elements = [6, 6, 8, 1, 1, 1, 1, 1];
        let pos = [
            [0.0, 0.0, 0.0],
            [1.54, 0.0, 0.0],
            [2.57, 1.03, 0.0],
            [-0.63, 0.89, 0.0],
            [-0.63, -0.89, 0.0],
            [1.54, -0.63, 0.89],
            [1.54, -0.63, -0.89],
            [3.52, 0.93, 0.0],
        ];
        let config = EeqConfig::default();
        let result = compute_eeq_charges(&elements, &pos, &config);
        assert!(
            result.total_charge.abs() < 0.01,
            "Charge not neutral: {}",
            result.total_charge
        );
    }

    #[test]
    fn test_eeq_oxygen_negative() {
        let elements = [8, 1, 1];
        let pos = water_positions();
        let config = EeqConfig::default();
        let result = compute_eeq_charges(&elements, &pos, &config);
        assert!(result.charges[0] < 0.0, "O charge = {}", result.charges[0]);
        assert!(result.charges[1] > 0.0, "H charge = {}", result.charges[1]);
    }

    #[test]
    fn test_gamma_damped_asymptotic() {
        let g = gamma_damped(10.0, 1.0, 1.0);
        assert!((g - 0.1).abs() < 0.01, "gamma(10) = {}, expected ~0.1", g);
    }
}