xtb-model 0.0.6

Rust wrapper for the extended tight binding program package
Documentation 
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// [[file:../xtb.note::0eb1a5c9][0eb1a5c9]]
use anyhow::*;
use approx::assert_relative_eq;

#[test]
fn test_xtb_3d() -> Result<()> {
    use xtb_model::libxtb::*;
    use xtb_model::{XtbModel, XtbParameters};

    let numbers = [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7];
    let coord = [
         9.77104501e-01,  1.24925555e-01,  8.22139769e+00,
         8.37995371e-01,  8.23489051e+00,  3.74893761e+00,
         4.62693404e+00, -2.45721089e+00,  8.22052352e+00,
         4.62532610e+00,  1.41051267e+00,  5.97940016e+00,
         9.71618351e-01,  1.17570237e-01,  3.75065164e+00,
        -2.80917006e+00,  6.94865315e+00,  5.99166085e+00,
         4.06610161e+00,  4.51252077e+00,  6.46827038e-01,
         2.76223056e-01, -8.50055887e-01,  2.06420987e+00,
         2.84806942e-01,  2.07039689e+00,  8.22836360e+00,
         2.90284064e+00,  8.22939158e+00,  3.73820878e+00,
         6.69188274e+00, -2.46191735e+00,  8.22593771e+00,
         6.69035555e+00,  1.41863696e+00,  5.97712614e+00,
         7.73011343e+00,  1.91963880e+00,  6.45533278e-01,
         3.94842571e+00,  3.36121142e+00,  5.97668593e+00,
        -3.49960564e+00,  5.97197638e+00,  7.67502785e+00,
         2.79250975e-01,  2.06298102e+00,  3.73907675e+00,
        -3.50586965e+00,  5.96534053e+00,  4.31491171e+00,
         1.56432603e-01,  7.25773353e+00,  2.06229892e+00,
        -4.98732693e-02,  6.88619344e+00,  5.98746725e+00,
        -4.50657119e-03, -1.16906911e+00,  5.98934273e+00,
         3.73678498e+00,  1.55157272e-01,  8.27155126e+00,
         3.73119434e+00,  1.47879860e-01,  3.69345547e+00,
    ];
    let lattice = [
         1.13437228e+01, -1.84405404e-03,  1.33836685e-05,
        -3.78300868e+00,  1.06992286e+01, -1.04202175e-03,
        -3.78025723e+00, -5.34955718e+00,  9.26593601e+00,
        ];

    let periodic = [true; 3];
    let env = XtbEnvironment::new();
    env.set_output_verbose();
    let mol = XtbMolecule::create(&env, &numbers, &coord, 0.0, 0, &lattice, &periodic)?;
    let calc = XtbCalculator::new();
    calc.load_parametrization(&mol, &env, XtbMethod::GFN2xTB)?;
    // GFN2-xTB does not support periodic boundary conditions.
    // It should fail for periodic input: Multipoles not available with PBC
    let res = calc.single_point(&mol, &env);
    assert!(res.is_err());

    calc.load_parametrization(&mol, &env, XtbMethod::GFN1xTB)?;
    let res = calc.single_point(&mol, &env)?;
    let energy = res.get_energy(&env)?;
    assert_relative_eq!(energy, -31.906084801853034, epsilon=1e-9);
    let mut gradient = coord.clone();
    res.get_gradient(&env, &mut gradient)?;
    assert_relative_eq!(gradient[0], 5.46952312e-03, epsilon=1e-9);

    let mut params = XtbParameters::default();
    params.output_muted().method("GFN1-xTB").lattice(lattice);
    let mut xtb = XtbModel::create(&numbers, &coord, params)?;
    let mut gradient = coord.clone();
    let energy = xtb.calculate_energy_and_gradient(&mut gradient)?;
    assert_relative_eq!(energy, -31.906084801853034, epsilon=1e-9);
    assert_relative_eq!(gradient[0], 5.46952312e-03, epsilon=1e-9);
    assert_relative_eq!(gradient[39], 0.00134273926, epsilon=1e-9);
    assert_relative_eq!(gradient[58], -0.000601295157, epsilon=1e-9);

    // test update
    let mut coord = coord.clone();
    coord[0] = 0.477104501;
    xtb.update_structure(&coord, None)?;
    let energy = xtb.calculate_energy_and_gradient(&mut gradient)?;
    assert_relative_eq!(energy, -31.872139660919, epsilon=1e-9);

    Ok(())
}
// 0eb1a5c9 ends here