workflow_ET.py 文件源码

def write_overlap_densities(
        path_hdf5: str, paths_fragment_overlaps: List, swaps: Matrix, dt: int=1):
    """
    Write the diagonal of the overlap matrices
    """
    logger.info("writing densities in human readable format")

    # Track the crossing between MOs
    for paths_overlaps in paths_fragment_overlaps:
        overlaps = np.stack(retrieve_hdf5_data(path_hdf5, paths_overlaps))
        for k, mtx in enumerate(np.rollaxis(overlaps, 0)):
            overlaps[k] = mtx[:, swaps[k]][swaps[k]]

    # Print to file the densities for each fragment on a given MO
    for ifrag, paths_overlaps in enumerate(paths_fragment_overlaps):
        # time frame
        frames = overlaps.shape[0]
        ts = np.arange(1, frames + 1).reshape(frames, 1) * dt
        # Diagonal of the 3D-tensor
        densities = np.diagonal(overlaps, axis1=1, axis2=2)
        data = np.hstack((ts, densities))
        # Save data in human readable format
        file_name = 'densities_fragment_{}.txt'.format(ifrag)
        np.savetxt(file_name, data, fmt='{:^3}'.format('%e'))