c4c62503da100cbf491a761998c04d5e0db42413,qcengine/programs/nwchem/harvester.py,,harvest_hessian,#Any#,663

Before Change

    Hess file name has to be "nwchem.hess". (default)

    
    raise NotImplementedError()


def extract_formatted_properties(psivars: PreservingDict) -> AtomicResultProperties:
    Get named properties out of the general variables extracted out of the result file

After Change

    

    // Change the "D[+-]" notation of Fortran output to "E[+-]" used by Python
    hess_conv = hess.replace("D", "E")

    // Parse all of the float values
    hess_triu = [float(x) for x in hess_conv.strip().splitlines()]

    // The value in the Hessian matrix is the upper triangle
    //  We first convert it to a 2D array
    n = int(np.sqrt(8 * len(hess_triu) + 1) - 1) // 2  // Size of the 2D matrix
    hess_arr = np.zeros((n, n))
    hess_arr[np.triu_indices(n)] = hess_triu

    // Symmetrize it
    return hess_arr.T + hess_arr - np.diag(np.diag(hess_arr))


def extract_formatted_properties(psivars: PreservingDict) -> AtomicResultProperties:
    Get named properties out of the general variables extracted out of the result file

Instances